Use of engineered bacterial compositions for the treatment of infectious diseases

Abstract

Provided herein are bacterial compositions useful for treating and / or preventing diseases or disorders associated with chronic liver disease, neutropenia, and / or solid organ transplantation. In some embodiments, treating and / or preventing includes treating infectious complications resulting from chronic liver disease, neutropenia, and / or solid organ transplantation. The bacterial compositions disclosed herein are designed to exhibit one or more functional characteristics useful for treating such diseases and disorders.

Description

[Technical Field]

[0001] CROSS-REFERENCE TO RELATED APPLICATIONS This PCT application claims the benefit of priority to U.S. Provisional Patent Application No. 63 / 482,293, filed January 30, 2023, which is incorporated herein by reference in its entirety.

[0002] Reference to an electronically submitted sequence listing The contents of the electronically submitted Sequence Listing (4268_096PC01_Seqlisting_ST26, size: 421,080 bytes, and created date: January 30, 2024) submitted with this application are hereby incorporated by reference in their entirety.

[0003] The present disclosure relates to bacterial compositions useful for treating infectious complications resulting from a wide range of diseases or disorders (e.g., chronic liver disease, cancer neutropenia, and solid organ transplants) in a subject (e.g., a human subject). More specifically, the bacterial compositions provided herein are designed to exhibit certain properties useful for reducing or preventing the risk of infection from certain microbial pathogens in a subject. As further described herein, by treating such pathogens, the bacterial compositions provided herein may be useful for treating a wide range of diseases or disorders described herein. [Background technology]

[0004] Chronic liver disease (CLD) is a frequent and leading cause of death, especially in developing countries. In the United States, according to the Centers for Disease Control and Prevention's 2017 Vital Statistics Report, approximately 4.5 million adults, representing 1.8% of the adult population, had chronic liver disease and cirrhosis. Chronic liver disease and cirrhosis resulted in 41,473 deaths (12.8 deaths per 100,000 population). Due to impaired liver function, many CLD patients are highly susceptible to bacterial infections, and many CLD-related deaths are directly related to such infections. The most common infections in patients with cirrhosis, spontaneous bacterial peritonitis (SBP), and bloodstream infections (BSIs) are generally caused by commensal gastrointestinal microorganisms. The presence of potentially pathogenic gastrointestinal microorganisms, combined with increased intestinal permeability, can lead to the translocation of these potential pathogens, resulting in SBP and BSIs. This same phenomenon can cause bacterial infections in subjects with other diseases and disorders associated with immune dysfunction and / or febrile neutropenia (e.g., solid organ transplants, chemotherapy for solid and hematologic malignancies), as well as other conditions requiring acute or long-term care in intensive care unit settings (see, e.g., Ford et al., Lancet 2(10):e438-44 (Oct. 2015), and Freedberg DE et al., Intensive Care Med 44(8):1203-1211 (Aug. 2018)).

[0005] Thus, there remains a need for new and alternative approaches to prevent and / or treat bacterial infections in subjects suffering from chronic liver disease, neutropenia, and / or diseases or disorders associated with immune dysfunction and / or gastrointestinal barrier dysfunction. Summary of the Invention

[0006] Provided herein are methods of treating diseases and disorders as described herein, e.g., chronic liver disease, a disease or disorder associated with solid organ transplantation, or neutropenia. Also provided are bacterial compositions.

[0007] In some aspects, a method of treating chronic liver disease in a subject in need thereof comprises administering to the subject a composition comprising a plurality of bacteria, wherein the plurality of bacteria comprises a first bacterial species and a second bacterial species, wherein the first species and the second species are not the same, and wherein the first species and the second species are selected from the group consisting of Anaerotruncus colihominis, Blautia coccoides, Blautia hominis, Blautia obeum, Blautia wexlerae, Butyricicoccus sp2, Clostridium aldenense, Clostridium bolteae, Clostridium innocuum, Clostridium scindens, Clostridium symbiosum, Dorea longicatena, Eisenbergiella tayi, Emergencia timonensis, Erysipelatoclostridium ramosum, Eubacterium callanderi, Faecalicatena cortorta, Faecalicatena orotica, Flavonifractor plautii, Hungatella effluvii, Intestinimonas butyriciproducens, Intestinimonas massiliensis, Lactonifactor longoviformis, Lawsonibacter_sp7, Massilimaliae timonensis, Murimonas intestini, Niameybacter sp1, Ruminococcaceae NG13 sp6, or Turicibacter sanguinis.

[0008] In some embodiments, treating chronic liver disease includes (i) reducing or preventing the occurrence of an infection in the subject, (ii) reducing or preventing symptoms of chronic liver disease in the subject, or (iii) both (i) and (ii).

[0009] In some embodiments, the chronic liver disease is caused by and / or associated with toxins (e.g., chronic alcohol and / or drug abuse), infections, metabolic disorders, autoimmune diseases, genetic abnormalities, or a combination thereof. In some embodiments, the chronic liver disease is idiopathic. In some embodiments, the chronic liver disease includes cirrhosis, liver fibrosis, alcoholic liver disease, nonalcoholic fatty liver disease (NAFLD), nonalcoholic steatohepatitis (NASH), hepatitis (including viral and alcoholic hepatitis), primary biliary cirrhosis (PBC), primary sclerosing cholangitis (PSC), alpha-1 antitrypsin deficiency, hereditary hemochromatosis, Wilson's disease, autoimmune hepatitis (AIH), Budd-Chiari syndrome, and combinations thereof. In some embodiments, chronic liver disease includes abdominal fluid accumulation (ascites), vomiting, gallstones, itching, jaundice, kidney failure, muscle loss, loss of appetite, bruising, spider veins in the skin, fatigue, weight loss, confusion, swelling of the legs (e.g., ankles), portal hypertension, hepatic encephalopathy, and combinations thereof. In some embodiments, chronic liver disease includes hepatic encephalopathy.

[0010] In some aspects, provided herein are methods of treating neutropenia in a subject in need thereof, the method comprising administering to the subject a composition comprising a plurality of bacteria, wherein the plurality of bacteria comprises a first bacterial species and a second bacterial species, wherein the first species and the second species are not the same, and wherein the first species and the second species are selected from the group consisting of Anaerotruncus colihominis, Blautia coccoides, Blautia hominis, Blautia obeum, Blautia wexlerae, Butyricicoccus sp2, Clostridium aldenense, Clostridium bolteae, Clostridium innocuum, Clostridium scindens, Clostridium symbiosum, Dorea longicatena, Eisenbergiella tayi, Emergencia timonensis, Erysipelatoclostridium ramosum, Eubacterium callanderi, Faecalicatena cortorta, Faecalicatena orotica, Flavonifractor plautii, Hungatella effluvii, Intestinimonas butyriciproducens, Intestinimonas massiliensis, Lactonifactor longoviformis, Lawsonibacter_sp7, Massilimaliae timonensis, Murimonas intestini, Niameybacter sp1, Ruminococcaceae NG13 sp6, or Turicibacter selected independently from sanguinis.

[0011] In some embodiments, treating neutropenia includes (i) reducing or preventing the occurrence of an infection in the subject, (ii) reducing or preventing the symptoms of neutropenia in the subject, or (iii) both (i) and (ii). In some embodiments, neutropenia includes cancer neutropenia.

[0012] In some aspects, provided herein are methods of treating a disease or disorder associated with solid organ transplantation in a subject in need thereof, the method comprising administering to the subject a composition comprising a plurality of bacteria, wherein the plurality of bacteria comprises a first bacterial species and a second bacterial species, wherein the first and second species are not the same, and wherein the first and second species are selected from the group consisting of Anaerotruncus colihominis, Blautia coccoides, Blautia hominis, Blautia obeum, Blautia wexlerae, Butyricicoccus sp2, Clostridium aldenense, Clostridium bolteae, Clostridium innocuum, Clostridium scindens, Clostridium symbiosum, Dorea longicatena, Eisenbergiella tayi, Emergencia timonensis, Erysipelatoclostridium ramosum, Eubacterium callanderi, Faecalicatena cortorta, Faecalicatena orotica, Flavonifractor plautii, Hungatella effluvii, Intestinimonas butyriciproducens, Intestinimonas massiliensis, Lactonifactor longoviformis, Lawsonibacter_sp7, Massilimaliae timonensis, Murimonas intestini, Niameybacter sp1, Ruminococcaceae NG13 sp6, or Turicibacter selected independently from sanguinis.

[0013] In some embodiments, treating a disease or disorder associated with solid organ transplantation comprises (i) reducing or preventing the occurrence of an infection in the subject, (ii) reducing or preventing symptoms of a disease or disorder associated with solid organ transplantation in the subject, or (iii) both (i) and (ii). In some embodiments, the solid organ transplant comprises a liver transplant.

[0014] For any of the methods provided herein, in some embodiments, the first species and / or second species is selected from Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi. In some embodiments, the plurality of bacteria includes each of Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.

[0015] In some embodiments, the plurality of bacteria further comprises Emergencia timonensis. In some embodiments, the plurality of bacteria further comprises Intestinimonas butyriciproducens. In some embodiments, the plurality of bacteria further comprises Clostridium symbiosum. In some embodiments, the plurality of bacteria further comprises Clostridium scindens. In some embodiments, the plurality of bacteria further comprises Faecalicatena cortorta. In some embodiments, the plurality of bacteria further comprises Lactonifactor longoviformis. In some embodiments, the plurality of bacteria further comprises Massilimaliae timonensis. In some embodiments, the plurality of bacteria further comprises Hungatella effluvii. In some embodiments, the plurality of bacteria further comprises Butyricicoccus sp2. In some embodiments, the plurality of bacteria further comprises Intestinimonas massiliensis. In some embodiments, the plurality of bacteria further comprises Niameybacter sp1. In some embodiments, the plurality of bacteria further comprises Turicibacter sanguinis. In some embodiments, the plurality of bacteria further comprises Ruminococcaceae NG13 sp6. In some embodiments, the plurality of bacteria further comprises Dorea longicatena. In some embodiments, the plurality of bacteria further comprises Blautia obeum. In some embodiments, the plurality of bacteria further comprises Lawsonibacter_sp7. In some embodiments, the plurality of bacteria further comprises Blautia hominis. In some embodiments, the plurality of bacteria further comprises Blautia wexlerae. In some embodiments, the plurality of bacteria further comprises Eubacterium callanderi.

[0016] In some embodiments, the plurality of bacteria comprises, consists essentially of, or consists of the following bacterial species: (a) (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Emergencia timonensis, (10) Clostridium aldenense, (11) Intestinimonas butyriciproducens, (12) Eisenbergiella tayi, (13) Clostridium symbiosum, and (14) Clostridium scindens; (b) (1) Clostridium innocuum, (2) Clostridium bolteae, (3)Flavonifractor plautii, (4)Blautia coccoides, (5)Anaerotruncus colihominis, (6)Murimonas intestini, (7)Erysipelatoclostridium ramosum, (8)Faecalicatena orotica, (9)Clostridium aldenense, (10)Intestinimonas butyriciproducens, (11)Eisenbergiella tayi, (12)Clostridium symbiosum, (13)Clostridium scindens, and (14)Emergencia timonensis, (c)(1)Clostridium innocuum, (2)Clostridium bolteae, (3)Flavonifractor plautii, (4)Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatenaorotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergencia timonensis, (15) Faecalicatena cortorta, (16) Lactonifactor longoviformis, and (17) Ruminococcaceae NG13 sp6, (d)(1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergencia timonensis, (15) Faecalicatena cortorta, (16) Lactonifactor longoviformis, (17) Massilimaliae timonensis, (18) Hungatella effluvii, and (19) Butyricicoccus sp2, (e)(1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridiumaldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergencia timonensis, (15) Faecalicatena cortorta, (16) Lactonifactor longoviformis, (17) Massilimaliae timonensis, (18) Hungatella effluvii, (19) Butyricicoccus sp2, (20) Intestinimonas massiliensis, (21) Niameybacter sp1, and (22) Turicibacter sanguinis, (f)(1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Emergencia timonensis, (10) Clostridium aldenense, (11) Eisenbergiella tayi, (12) Dorea longicatena, and (13) Blautia obeum, (g)(1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridiumsymbiosum, (13) Clostridium scindens, (14) Emergencia timonensis, (15) Blautia obeum, and (16) Lawsonibacter_sp7, (h)(1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergencia timonensis, (15) Faecalicatena cortorta, (16) Lactonifactor longoviformis, (17) Ruminococcaceae NG13 sp6, (18) Blautia obeum, and (19) Lawsonibacter_sp7, (i)(1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, and (13) Emergencia timonensis, (j)(1) Clostridium innocuum, (2) Clostridiumbolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergencia timonensis, (15) Faecalicatena cortorta, (16) Lactonifactor longoviformis, (17) Intestinimonas massiliensis, (18) Niameybacter sp1, and (19) Turicibacter sanguinis, or (k)(1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia hominis, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Emergencia timonensis, (10) Clostridium aldenense, (11) Eisenbergiella tayi, (12) Clostridium scindens, (13) Dorea longicatena, (14) Blautia obeum, (15) Blautia wexlerae, and (16) Eubacterium callanderi.

[0017] In some embodiments, (a) Anaerotruncus colihominis comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, or SEQ ID NO:81; (b) Blautia coccoides comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, or SEQ ID NO:78; or (c) Blautia (d) Blautia obeum comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:26, SEQ ID NO:158, SEQ ID NO:159, SEQ ID NO:160, SEQ ID NO:161, SEQ ID NO:162, or SEQ ID NO:163; or (e) Blautia wexlerae comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:30, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41, SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO:166, SEQ ID NO:167, SEQ ID NO:168, SEQ ID NO:169, SEQ ID NO:170, SEQ ID NO:171, or SEQ ID NO:172; (f) Butyricicoccus sp2 comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:20 or SEQ ID NO:132; or (g) Clostridiumaldenense comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:10, SEQ ID NO:100, SEQ ID NO:101, SEQ ID NO:102, SEQ ID NO:103, or SEQ ID NO:104; (h) Clostridium bolteae comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:2, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:69, or SEQ ID NO:70; or (i) Clostridium (j) Clostridium scindens comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:1, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, or SEQ ID NO:65; (k) Clostridium symbiosum comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:13 or SEQ ID NO:110; (l) Dorea longicatena comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:25, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, SEQ ID NO:54, SEQ ID NO:55, SEQ ID NO:56, SEQ ID NO:57, SEQ ID NO:58, SEQ ID NO:59, SEQ ID NO:60, SEQ ID NO:152, SEQ ID NO:153, SEQ ID NO:154, SEQ ID NO:155, SEQ ID NO:156, or SEQ ID NO:157; or (m) Eisenbergiella(n) Emergencia timonensis comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109; (n) Emergencia timonensis comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 9, SEQ ID NO: 97, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 15, SEQ ID NO: 115, or SEQ ID NO: 116; or (o) Erysipelatoclostridium (p) Eubacterium callanderi comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:7, SEQ ID NO:87, SEQ ID NO:88, SEQ ID NO:89, SEQ ID NO:90, or SEQ ID NO:91; (p) Eubacterium callanderi comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:31, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:173, SEQ ID NO:174, SEQ ID NO:175, SEQ ID NO:176, or SEQ ID NO:177; or (q) Faecalicatena cortorta comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:16, SEQ ID NO:117, SEQ ID NO:118, SEQ ID NO:119, or SEQ ID NO:120; (r) Faecalicatena orotica comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:8, SEQ ID NO:92, SEQ ID NO:93, SEQ ID NO:94, SEQ ID NO:95, or SEQ ID NO:96; or (s) Flavonifractorplautii comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:3, SEQ ID NO:71, SEQ ID NO:72, or SEQ ID NO:73; (t) Hungatella effluvia comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:19, SEQ ID NO:126, SEQ ID NO:127, SEQ ID NO:128, SEQ ID NO:129, SEQ ID NO:130, or SEQ ID NO:131; (u) Intestinimonas butyriciproducens comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:11 or SEQ ID NO:105; (v) Intestinimonas massiliensis comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:21 or SEQ ID NO:133; (w) Lactonifactor longoviformis comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:17, SEQ ID NO:121, SEQ ID NO:122, SEQ ID NO:123, SEQ ID NO:124, SEQ ID NO:28, or SEQ ID NO:165; (x) Lawsonibacter_sp7 comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:27 or SEQ ID NO:164; or (y) Massilimaliae timonensis has a 16S sequence that has at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity with the sequence set forth in SEQ ID NO: 18 or SEQ ID NO: 125.(z) Murimonas intestini comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:6, SEQ ID NO:82, SEQ ID NO:83, SEQ ID NO:84, SEQ ID NO:85, SEQ ID NO:86; (aa) Niameybacter sp1 comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:22 or SEQ ID NO:134; (bb) Ruminococcaceae NG13 sp6 comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:24, SEQ ID NO:149, SEQ ID NO:150, or SEQ ID NO:151. or (cc) Turicibacter sanguinis comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:23, SEQ ID NO:135, SEQ ID NO:136, SEQ ID NO:137, SEQ ID NO:138, SEQ ID NO:139, SEQ ID NO:140, SEQ ID NO:141, SEQ ID NO:142, SEQ ID NO:143, SEQ ID NO:144, SEQ ID NO:145, SEQ ID NO:146, SEQ ID NO:147, or SEQ ID NO:148.

[0018] In some embodiments, (a) Anaerotruncus colihominis comprises the 16S rDNA sequence set forth in SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, or SEQ ID NO:81; (b) Blautia coccoides comprises the 16S rDNA sequence set forth in SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, or SEQ ID NO:78; (c) Blautia hominis comprises the 16S rDNA sequence set forth in SEQ ID NO:29, SEQ ID NO:32, SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, or SEQ ID NO:37; (d) Blautia obeum comprises the 16S rDNA sequence set forth in SEQ ID NO:26, SEQ ID NO:158, SEQ ID NO:159, SEQ ID NO:160, SEQ ID NO:161, SEQ ID NO:162, or SEQ ID NO:163; or (e) Blautia wexlerae comprises the 16S rDNA sequence set forth in SEQ ID NO:30, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41, SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO:166, SEQ ID NO:167, SEQ ID NO:168, SEQ ID NO:169, SEQ ID NO:170, SEQ ID NO:171, or SEQ ID NO:172; (f) Butyricicoccus sp2 comprises the 16S rDNA sequence set forth in SEQ ID NO:20 or SEQ ID NO:132; (g) Clostridium aldenense comprises the 16S rDNA sequence set forth in SEQ ID NO:10, SEQ ID NO:100, SEQ ID NO:101, SEQ ID NO:102, SEQ ID NO:103, or SEQ ID NO:104; (h) Clostridium bolteae comprises the 16S rDNA sequence set forth in SEQ ID NO:22 or SEQ ID NO:134; (i) Clostridium (j) Clostridium scindens comprises the 16S rDNA sequence set forth in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65; (k) Clostridium symbiosum comprises the 16S rDNA sequence set forth in SEQ ID NO: 13 or SEQ ID NO: 110; (l) Dorealongicatena comprises the 16S rDNA sequence set forth in SEQ ID NO:25, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, SEQ ID NO:54, SEQ ID NO:55, SEQ ID NO:56, SEQ ID NO:57, SEQ ID NO:58, SEQ ID NO:59, SEQ ID NO:60, SEQ ID NO:152, SEQ ID NO:153, SEQ ID NO:154, SEQ ID NO:155, SEQ ID NO:156, or SEQ ID NO:157; (m) Eisenbergiella tayi comprises the 16S rDNA sequence set forth in SEQ ID NO:12, SEQ ID NO:106, SEQ ID NO:107, SEQ ID NO:108, or SEQ ID NO:109; (n) Emergencia timonensis comprises the 16S rDNA sequence set forth in SEQ ID NO:9, SEQ ID NO:97, SEQ ID NO:98, SEQ ID NO:99, SEQ ID NO:15, SEQ ID NO:115, or SEQ ID NO:116; or (o) Erysipelatoclostridium (p) Eubacterium callanderi comprises the 16S rDNA sequence set forth in SEQ ID NO:31, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:173, SEQ ID NO:174, SEQ ID NO:175, SEQ ID NO:176, or SEQ ID NO:177; (q) Faecalicatena cortorta comprises the 16S rDNA sequence set forth in SEQ ID NO:16, SEQ ID NO:117, SEQ ID NO:118, SEQ ID NO:119, or SEQ ID NO:120; (r) Faecalicatena orotica comprises the 16S rDNA sequence set forth in SEQ ID NO:8, SEQ ID NO:92, SEQ ID NO:93, SEQ ID NO:94, SEQ ID NO:95, or SEQ ID NO:96; (s) Flavonifractor plautii comprises the 16S rDNA sequence set forth in SEQ ID NO:3, SEQ ID NO:71, SEQ ID NO:72, or SEQ ID NO:73; (t) Hungatella effluvia comprises the 16S rDNA sequence set forth in SEQ ID NO:19, SEQ ID NO:126, SEQ ID NO:127, SEQ ID NO:128, SEQ ID NO:129, SEQ ID NO:130, or SEQ ID NO:131; (u) Intestinimonas(v) Intestinimonas massiliensis comprises the 16S rDNA sequence set forth in SEQ ID NO: 21 or SEQ ID NO: 133; (w) Lactonifactor longoviformis comprises the 16S rDNA sequence set forth in SEQ ID NO: 17, SEQ ID NO: 121, SEQ ID NO: 122, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 28, or SEQ ID NO: 165; (x) Lawsonibacter_sp7 comprises the 16S rDNA sequence set forth in SEQ ID NO: 27 or SEQ ID NO: 164; (y) Massilimaliae timonensis comprises the 16S rDNA sequence set forth in SEQ ID NO: 18 or SEQ ID NO: 125; (z) Murimonas intestini comprises the 16S rDNA sequence set forth in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86. rDNA sequence as set forth in SEQ ID NO:23, SEQ ID NO:135, SEQ ID NO:136, SEQ ID NO:137, SEQ ID NO:138, SEQ ID NO:139, SEQ ID NO:140, SEQ ID NO:141, SEQ ID NO:142, SEQ ID NO:143, SEQ ID NO:144, SEQ ID NO:145, SEQ ID NO:146, SEQ ID NO:147, or SEQ ID NO:148.

[0019]

[0010] In some aspects, provided herein are methods of treating chronic liver disease in a subject in need thereof, the methods comprising administering to the subject a composition comprising a first bacterial species and a second bacterial species, wherein the first and second species are not the same, and the first and second species are independently selected from the group consisting of SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, SEQ ID NO:81, SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, SEQ ID NO:78, SEQ ID NO:26, SEQ ID NO:158, SEQ ID NO:159, SEQ ID NO:160, SEQ ID NO:161, SEQ ID NO:162, SEQ ID NO:163, SEQ ID NO:20, SEQ ID NO:132, SEQ ID NO:10, SEQ ID NO:100, SEQ ID NO:101, SEQ ID NO:10266, SEQ ID NO:10367, SEQ ID NO:10468, SEQ ID NO:69, SEQ ID NO:70, SEQ ID NO:1, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, SEQ ID NO:65, SEQ ID NO:14, SEQ ID NO:111, SEQ ID NO:112, SEQ ID NO:113, SEQ ID NO:114, SEQ ID NO:13, SEQ ID NO:110, SEQ ID NO:25, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, SEQ ID NO:54, SEQ ID NO:55, SEQ ID NO:56, SEQ ID NO:57, SEQ ID NO:58, SEQ ID NO:59, SEQ ID NO: No. 60, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO: 155, SEQ ID NO: 156, SEQ ID NO: 157, SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 9, SEQ ID NO: 97, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 15, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, SEQ ID NO: 91, SEQ ID NO: 16, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 119, SEQ ID NO: 120, SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO:95, SEQ ID NO:96, SEQ ID NO:3, SEQ ID NO:71, SEQ ID NO:72, SEQ ID NO:73, SEQ ID NO:19, SEQ ID NO:126, SEQ ID NO:127, SEQ ID NO:128, SEQ ID NO:129, SEQ ID NO:130, SEQ ID NO:131, SEQ ID NO:11, SEQ ID NO:105, SEQ ID NO:21, SEQ ID NO:133, SEQ ID NO:17, SEQ ID NO:121, SEQ ID NO:122, SEQ ID NO:123, SEQ ID NO:124, SEQ ID NO:28, SEQ ID NO:27, SEQ ID NO:164, SEQ ID NO:18, SEQ ID NO:125, SEQ ID NO:6, SEQ ID NO:82, SEQ ID NO:83, SEQ ID NO:84, SEQ ID NO:85, SEQ ID NO:86, SEQ ID NO:22,SEQ ID NO:134, SEQ ID NO:24, SEQ ID NO:149, SEQ ID NO:150, SEQ ID NO:151, SEQ ID NO:23, SEQ ID NO:135, SEQ ID NO:136, SEQ ID NO:137, SEQ ID NO:138, SEQ ID NO:139, SEQ ID NO:140, SEQ ID NO:141, SEQ ID NO:142, SEQ ID NO:143, SEQ ID NO:144, SEQ ID NO:145, SEQ ID NO:146, SEQ ID NO:147, SEQ ID NO:148, SEQ ID NO:29, SEQ ID NO:32, SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, or SEQ ID NO:37, SEQ ID NO:30, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41 1, SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO:166, SEQ ID NO:167, SEQ ID NO:168, SEQ ID NO:169, SEQ ID NO:170, SEQ ID NO:171, SEQ ID NO:172, SEQ ID NO:31, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:173, SEQ ID NO:174, SEQ ID NO:175, SEQ ID NO:176, or SEQ ID NO:177.

[0020] In some aspects, provided herein are methods of treating chronic liver disease in a subject in need of treatment for neutropenia, the method comprising administering to the subject a composition comprising a first bacterial species and a second bacterial species, wherein the first species and the second species are not the same, and the first species and the second species are independently selected from the group consisting of SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, SEQ ID NO:81, SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, SEQ ID NO:78, SEQ ID NO:26, SEQ ID NO:158, SEQ ID NO:159, SEQ ID NO:160, SEQ ID NO:161, SEQ ID NO:162, SEQ ID NO:163, SEQ ID NO:20 , SEQ ID NO:132, SEQ ID NO:10, SEQ ID NO:100, SEQ ID NO:101, SEQ ID NO:10266, SEQ ID NO:10367, SEQ ID NO:10468, SEQ ID NO:69, SEQ ID NO:70, SEQ ID NO:1, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, SEQ ID NO:65, SEQ ID NO:14, SEQ ID NO:111, SEQ ID NO:112, SEQ ID NO:113, SEQ ID NO:114, SEQ ID NO:13, SEQ ID NO:110, SEQ ID NO:25, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, SEQ ID NO:54, SEQ ID NO:55, SEQ ID NO:56, SEQ ID NO:57, SEQ ID NO:58, SEQ ID NO:59, SEQ ID NO: No. 60, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO: 155, SEQ ID NO: 156, SEQ ID NO: 157, SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 9, SEQ ID NO: 97, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 15, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, SEQ ID NO: 91, SEQ ID NO: 16, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 119, SEQ ID NO: 120, SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94 Column number 95, SEQ ID NO:96, SEQ ID NO:3, SEQ ID NO:71, SEQ ID NO:72, SEQ ID NO:73, SEQ ID NO:19, SEQ ID NO:126, SEQ ID NO:127, SEQ ID NO:128, SEQ ID NO:129, SEQ ID NO:130, SEQ ID NO:131, SEQ ID NO:11, SEQ ID NO:105, SEQ ID NO:21, SEQ ID NO:133, SEQ ID NO:17, SEQ ID NO:121, SEQ ID NO:122, SEQ ID NO:123, SEQ ID NO:124, SEQ ID NO:28, SEQ ID NO:165, SEQ ID NO:27, SEQ ID NO:164, SEQ ID NO:18, SEQ ID NO:125, SEQ ID NO:6, SEQ ID NO:82, SEQ ID NO:83, SEQ ID NO:84, SEQ ID NO:85, SEQ ID NO:86SEQ ID NO:22, SEQ ID NO:134, SEQ ID NO:24, SEQ ID NO:149, SEQ ID NO:150, SEQ ID NO:151, SEQ ID NO:23, SEQ ID NO:135, SEQ ID NO:136, SEQ ID NO:137, SEQ ID NO:138, SEQ ID NO:139, SEQ ID NO:140, SEQ ID NO:141, SEQ ID NO:142, SEQ ID NO:143, SEQ ID NO:144, SEQ ID NO:145, SEQ ID NO:146, SEQ ID NO:147, SEQ ID NO:148, SEQ ID NO:29, SEQ ID NO:32, SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, or SEQ ID NO:37, SEQ ID NO:30, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 166, SEQ ID NO: 167, SEQ ID NO: 168, SEQ ID NO: 169, SEQ ID NO: 170, SEQ ID NO: 171, SEQ ID NO: 172, SEQ ID NO: 31, SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 173, SEQ ID NO: 174, SEQ ID NO: 175, SEQ ID NO: 176, or SEQ ID NO: 177.

[0021]

[0013] In some aspects, provided herein are methods of treating a disease or disorder associated with solid organ transplantation in a subject in need thereof, the method comprising administering to the subject a composition comprising a first bacterial species and a second bacterial species, wherein the first and second species are not the same, and the first and second species are independently selected from the group consisting of SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, SEQ ID NO:81, SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, SEQ ID NO:78, SEQ ID NO:26, SEQ ID NO:158, SEQ ID NO:159, SEQ ID NO:160, SEQ ID NO:161, SEQ ID NO:162. , SEQ ID NO: 163, SEQ ID NO: 20, SEQ ID NO: 132, SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 10266, SEQ ID NO: 10367, SEQ ID NO: 10468, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 14, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, SEQ ID NO: 114, SEQ ID NO: 13, SEQ ID NO: 110, SEQ ID NO: 25, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56, SEQ ID NO: 57, Column number 58, SEQ ID NO:59, SEQ ID NO:60, SEQ ID NO:152, SEQ ID NO:153, SEQ ID NO:154, SEQ ID NO:155, SEQ ID NO:156, SEQ ID NO:157, SEQ ID NO:12, SEQ ID NO:106, SEQ ID NO:107, SEQ ID NO:108, SEQ ID NO:109, SEQ ID NO:9, SEQ ID NO:97, SEQ ID NO:98, SEQ ID NO:99, SEQ ID NO:15, SEQ ID NO:115, SEQ ID NO:116, SEQ ID NO:7, SEQ ID NO:87, SEQ ID NO:88, SEQ ID NO:89, SEQ ID NO:90, SEQ ID NO:91, SEQ ID NO:16, SEQ ID NO:117, SEQ ID NO:118, SEQ ID NO:119, SEQ ID NO:120, SEQ ID NO:92, SEQ ID NO:93, SEQ ID NO:94, SEQ ID NO:95, SEQ ID NO:96, SEQ ID NO:3, SEQ ID NO:71, SEQ ID NO:72, SEQ ID NO:73, SEQ ID NO:19, SEQ ID NO:126, SEQ ID NO:127, SEQ ID NO:128, SEQ ID NO:129, SEQ ID NO:130, SEQ ID NO:131, SEQ ID NO:11, SEQ ID NO:105, SEQ ID NO:21, SEQ ID NO:133, SEQ ID NO:17, SEQ ID NO:121, SEQ ID NO:122, SEQ ID NO:123, SEQ ID NO:124, SEQ ID NO:28, SEQ ID NO:165, SEQ ID NO:27, SEQ ID NO:164, SEQ ID NO:18, SEQ ID NO:125, SEQ ID NO:6, SEQ ID NO:82, SEQ ID NO:83, SEQ ID NO:84,SEQ ID NO:85, SEQ ID NO:86, SEQ ID NO:22, SEQ ID NO:134, SEQ ID NO:24, SEQ ID NO:149, SEQ ID NO:150, SEQ ID NO:151, SEQ ID NO:23, SEQ ID NO:135, SEQ ID NO:136, SEQ ID NO:137, SEQ ID NO:138, SEQ ID NO:139, SEQ ID NO:140, SEQ ID NO:141, SEQ ID NO:142, SEQ ID NO:143, SEQ ID NO:144, SEQ ID NO:145, SEQ ID NO:146, SEQ ID NO:147, SEQ ID NO:148, SEQ ID NO:29, SEQ ID NO:32, SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, or SEQ ID NO:37, SEQ ID NO:30, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 166, SEQ ID NO: 167, SEQ ID NO: 168, SEQ ID NO: 169, SEQ ID NO: 170, SEQ ID NO: 171, SEQ ID NO: 172, SEQ ID NO: 31, SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 173, SEQ ID NO: 174, SEQ ID NO: 175, SEQ ID NO: 176, or SEQ ID NO: 177.

[0022]

[0013] In some aspects, provided herein are methods of treating a disease or disorder associated with solid organ transplantation in a subject in need thereof, the method comprising administering to the subject a composition comprising a first bacterial species and a second bacterial species, wherein the first and second species are not the same, and the first and second species are independently selected from the group consisting of SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, SEQ ID NO:81, SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, SEQ ID NO:78, SEQ ID NO:26, SEQ ID NO:158, SEQ ID NO:159, SEQ ID NO:160, SEQ ID NO:161, SEQ ID NO:162. , SEQ ID NO: 163, SEQ ID NO: 20, SEQ ID NO: 132, SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 10266, SEQ ID NO: 10367, SEQ ID NO: 10468, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 14, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, SEQ ID NO: 114, SEQ ID NO: 13, SEQ ID NO: 110, SEQ ID NO: 25, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56, SEQ ID NO: 57, Column number 58, SEQ ID NO:59, SEQ ID NO:60, SEQ ID NO:152, SEQ ID NO:153, SEQ ID NO:154, SEQ ID NO:155, SEQ ID NO:156, SEQ ID NO:157, SEQ ID NO:12, SEQ ID NO:106, SEQ ID NO:107, SEQ ID NO:108, SEQ ID NO:109, SEQ ID NO:9, SEQ ID NO:97, SEQ ID NO:98, SEQ ID NO:99, SEQ ID NO:15, SEQ ID NO:115, SEQ ID NO:116, SEQ ID NO:7, SEQ ID NO:87, SEQ ID NO:88, SEQ ID NO:89, SEQ ID NO:90, SEQ ID NO:91, SEQ ID NO:16, SEQ ID NO:117, SEQ ID NO:118, SEQ ID NO:119, SEQ ID NO:120, SEQ ID NO:92, SEQ ID NO:93, SEQ ID NO:94, SEQ ID NO:95, SEQ ID NO:96, SEQ ID NO:3, SEQ ID NO:71, SEQ ID NO:72, SEQ ID NO:73, SEQ ID NO:19, SEQ ID NO:126, SEQ ID NO:127, SEQ ID NO:128, SEQ ID NO:129, SEQ ID NO:130, SEQ ID NO:131, SEQ ID NO:11, SEQ ID NO:105, SEQ ID NO:21, SEQ ID NO:133, SEQ ID NO:17, SEQ ID NO:121, SEQ ID NO:122, SEQ ID NO:123, SEQ ID NO:124, SEQ ID NO:28, SEQ ID NO:165, SEQ ID NO:27, SEQ ID NO:164, SEQ ID NO:18, SEQ ID NO:125, SEQ ID NO:6, SEQ ID NO:82, SEQ ID NO:83, SEQ ID NO:84,SEQ ID NO:85, SEQ ID NO:86, SEQ ID NO:22, SEQ ID NO:134, SEQ ID NO:24, SEQ ID NO:149, SEQ ID NO:150, SEQ ID NO:151, SEQ ID NO:23, SEQ ID NO:135, SEQ ID NO:136, SEQ ID NO:137, SEQ ID NO:138, SEQ ID NO:139, SEQ ID NO:140, SEQ ID NO:141, SEQ ID NO:142, SEQ ID NO:143, SEQ ID NO:144, SEQ ID NO:145, SEQ ID NO:146, SEQ ID NO:147, SEQ ID NO:148, SEQ ID NO:29, SEQ ID NO:32, SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, or SEQ ID NO:37, SEQ ID NO:30, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 166, SEQ ID NO: 167, SEQ ID NO: 168, SEQ ID NO: 169, SEQ ID NO: 170, SEQ ID NO: 171, SEQ ID NO: 172, SEQ ID NO: 31, SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 173, SEQ ID NO: 174, SEQ ID NO: 175, SEQ ID NO: 176, or SEQ ID NO: 177.

[0023] For any of the methods provided herein, in some embodiments, the first species and / or second species is selected from the group consisting of SEQ ID NO:1, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, SEQ ID NO:65, SEQ ID NO:2, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:69, SEQ ID NO:70, SEQ ID NO:3, SEQ ID NO:71, SEQ ID NO:72, SEQ ID NO:73, SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, SEQ ID NO:78, SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, SEQ ID NO:81, SEQ ID NO:6, SEQ ID NO:82, SEQ ID NO:83, SEQ ID NO:84, SEQ ID NO:85, The present invention relates to a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to any one of SEQ ID NO:86, SEQ ID NO:7, SEQ ID NO:87, SEQ ID NO:88, SEQ ID NO:89, SEQ ID NO:90, SEQ ID NO:91, SEQ ID NO:8, SEQ ID NO:92, SEQ ID NO:93, SEQ ID NO:94, SEQ ID NO:95, SEQ ID NO:96, SEQ ID NO:10, SEQ ID NO:100, SEQ ID NO:101, SEQ ID NO:102, SEQ ID NO:103, SEQ ID NO:104, SEQ ID NO:12, SEQ ID NO:106, SEQ ID NO:107, SEQ ID NO:108, or SEQ ID NO:109. In some embodiments, the plurality of bacteria comprises each of the following: (a) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:1, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, or SEQ ID NO:65; (b) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:2, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:69, or SEQ ID NO:70; (c) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:3, SEQ ID NO:71, SEQ ID NO:72, or SEQ ID NO:73.(d) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, or SEQ ID NO:78; (e) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, or SEQ ID NO:81; (f) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:6, SEQ ID NO:82, SEQ ID NO:83, SEQ ID NO:84, SEQ ID NO:85, or SEQ ID NO:86. (g) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:7, SEQ ID NO:87, SEQ ID NO:88, SEQ ID NO:89, SEQ ID NO:90, or SEQ ID NO:91; (h) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:8, SEQ ID NO:92, SEQ ID NO:93, SEQ ID NO:94, SEQ ID NO:95, or SEQ ID NO:96; (i) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:10, SEQ ID NO:100, SEQ ID NO:101, SEQ ID NO:102, SEQ ID NO:103, or SEQ ID NO:104. rDNA sequences, and (j) 16S rDNA sequences having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequences set forth in SEQ ID NO:12, SEQ ID NO:106, SEQ ID NO:107, SEQ ID NO:108, or SEQ ID NO:109.

[0024] For any of the methods provided herein, in some embodiments, the plurality of bacteria further comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:9, SEQ ID NO:97, SEQ ID NO:98, or SEQ ID NO:99. In some embodiments, the plurality of bacteria further comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:15, SEQ ID NO:115, or SEQ ID NO:116. In some embodiments, the plurality of bacteria further comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:11 or SEQ ID NO:105. In some embodiments, the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 13 or SEQ ID NO: 110. In some embodiments, the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 14, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, or SEQ ID NO: 114. In some embodiments, the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 16, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 119, or SEQ ID NO: 120. In some embodiments, the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:17.In some embodiments, the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 28. In some embodiments, the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 18 or SEQ ID NO: 125. In some embodiments, the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 19, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 128, SEQ ID NO: 129, SEQ ID NO: 130, or SEQ ID NO: 131. In some embodiments, the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:20 or SEQ ID NO: 132. In some embodiments, the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:21 or SEQ ID NO: 133. In some embodiments, the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:22 or SEQ ID NO:134. In some embodiments, the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:23, SEQ ID NO:135, SEQ ID NO:136, SEQ ID NO:137, SEQ ID NO:138, SEQ ID NO:139, SEQ ID NO:140, SEQ ID NO:141, SEQ ID NO:142, SEQ ID NO:143, SEQ ID NO:144, SEQ ID NO:145, SEQ ID NO:146, SEQ ID NO:147, or SEQ ID NO:148.In some embodiments, the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:24, SEQ ID NO:149, SEQ ID NO:150, or SEQ ID NO: 151. For any of the methods provided herein, in some embodiments, the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:25, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, SEQ ID NO:54, SEQ ID NO:55, SEQ ID NO:56, SEQ ID NO:57, SEQ ID NO:58, SEQ ID NO:59, SEQ ID NO:60, SEQ ID NO:152, SEQ ID NO:153, SEQ ID NO:154, SEQ ID NO:155, SEQ ID NO:156, or SEQ ID NO:157. In some embodiments, the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:26, SEQ ID NO:158, SEQ ID NO:159, SEQ ID NO:160, SEQ ID NO:161, SEQ ID NO:162, or SEQ ID NO:163. In some embodiments, the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:27 or SEQ ID NO:164. In some embodiments, the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:29, SEQ ID NO:32, SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, or SEQ ID NO:37.In some embodiments, the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:30, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41, SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO:166, SEQ ID NO:167, SEQ ID NO:168, SEQ ID NO:169, SEQ ID NO:170, SEQ ID NO:171, or SEQ ID NO: 172. In some embodiments, the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:31, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:173, SEQ ID NO:174, SEQ ID NO:175, SEQ ID NO:176, or SEQ ID NO:177.

[0025] For any of the methods provided herein, in some embodiments, the plurality of bacteria comprises, consists essentially of, or consists of: (a) (1) a 16S rDNA sequence set forth in SEQ ID NO:1, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, or SEQ ID NO:65; (2) a 16S rDNA sequence set forth in SEQ ID NO:2, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:69, or SEQ ID NO:70; (3) a 16S rDNA sequence set forth in SEQ ID NO:3, SEQ ID NO:71, SEQ ID NO:72, or SEQ ID NO:73; (4) a 16S rDNA sequence set forth in SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, or SEQ ID NO:78; (5) a 16S rDNA sequence set forth in SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, or SEQ ID NO:81; (6) a 16S rDNA sequence set forth in SEQ ID NO:6, SEQ ID NO:82, SEQ ID NO:83, SEQ ID NO:84, SEQ ID NO:85, SEQ ID NO:86. rDNA sequence, (7) a 16S rDNA sequence shown in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91; (8) a 16S rDNA sequence shown in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96; (9) a 16S rDNA sequence shown in SEQ ID NO: 9, SEQ ID NO: 97, SEQ ID NO: 98, or SEQ ID NO: 99; (10) a 16S rDNA sequence shown in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104; (11) a 16S rDNA sequence shown in SEQ ID NO: 11 or SEQ ID NO: 105; (12) a 16S rDNA sequence shown in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109; (13) a 16S rDNA sequence shown in SEQ ID NO: 13 or SEQ ID NO: 110 rDNA sequence, (14) the 16S rDNA sequence shown in SEQ ID NO: 14, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, or SEQ ID NO: 114, and (15) the 16S rDNA sequence shown in SEQ ID NO: 15, SEQ ID NO: 115, or SEQ ID NO: 116, (b)(1) the 16S rDNA sequence shown in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65rDNA sequence, (2) SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70 ... (3) SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73, (4) SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78, (5) SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81, (6) SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86, (7) SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91, rDNA sequence, (8) a 16S rDNA sequence shown in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96, (9) a 16S rDNA sequence shown in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104, (10) a 16S rDNA sequence shown in SEQ ID NO: 11 or SEQ ID NO: 105, (11) a 16S rDNA sequence shown in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109, (12) a 16S rDNA sequence shown in SEQ ID NO: 13 or SEQ ID NO: 110, (13) a 16S rDNA sequence shown in SEQ ID NO: 14, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, or SEQ ID NO: 114, and (14) a 16S rDNA sequence shown in SEQ ID NO: 15, SEQ ID NO: 115, or SEQ ID NO: 116. rDNA sequence, (c) (1) a 16S rDNA sequence set forth in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65, (2) a 16S rDNA sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70, (3) a 16S rDNA sequence set forth in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73rDNA sequence, (4) a 16S rDNA sequence shown in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78, (5) a 16S rDNA sequence shown in SEQ ID NO: 5, (6) a 16S rDNA sequence shown in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86, (7) a 16S rDNA sequence shown in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91, (8) a 16S rDNA sequence shown in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96, (9) a 16S rDNA sequence shown in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104, (10) a 16S rDNA sequence shown in SEQ ID NO: 11 or SEQ ID NO: 105 rDNA sequence, (11) the 16S rDNA sequence shown in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109, (12) the 16S rDNA sequence shown in SEQ ID NO: 13 or SEQ ID NO: 110, (13) the 16S rDNA sequence shown in SEQ ID NO: 14, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, or SEQ ID NO: 114, (14) the 16S rDNA sequence shown in SEQ ID NO: 15, SEQ ID NO: 115, or SEQ ID NO: 116, (15) the 16S rDNA sequence shown in SEQ ID NO: 16, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 119, or SEQ ID NO: 120, (16) the 16S rDNA sequence shown in SEQ ID NO: 28 or SEQ ID NO: 165, and (17) the 16S rDNA sequence shown in SEQ ID NO: 24, SEQ ID NO: 149, SEQ ID NO: 150, or SEQ ID NO: 151. rDNA sequence, (d) (1) a 16S rDNA sequence set forth in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65; (2) a 16S rDNA sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70; (3) a 16S rDNA sequence set forth in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73; (4) a 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78rDNA sequence, (5) a 16S rDNA sequence shown in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81, (6) a 16S rDNA sequence shown in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86, (7) a 16S rDNA sequence shown in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91, (8) a 16S rDNA sequence shown in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96, (9) a 16S rDNA sequence shown in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104, (10) a 16S rDNA sequence shown in SEQ ID NO: 11 or SEQ ID NO: 105, (11) a 16S rDNA sequence shown in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109 rDNA sequence, (12) the 16S rDNA sequence shown in SEQ ID NO: 13 or SEQ ID NO: 110, (13) the 16S rDNA sequence shown in SEQ ID NO: 14, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, or SEQ ID NO: 114, (14) the 16S rDNA sequence shown in SEQ ID NO: 15, SEQ ID NO: 115, or SEQ ID NO: 116, (15) the 16S rDNA sequence shown in SEQ ID NO: 16, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 119, or SEQ ID NO: 120, (16) the 16S rDNA sequence shown in SEQ ID NO: 17, SEQ ID NO: 121, SEQ ID NO: 122, SEQ ID NO: 123, or SEQ ID NO: 124, and (17) the 16S rDNA sequence shown in SEQ ID NO: 24, SEQ ID NO: 149, SEQ ID NO: 150, or SEQ ID NO: 151, (e)(1) the 16S rDNA sequence shown in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65 rDNA sequence, (2) a 16S rDNA sequence shown in SEQ ID NO:2, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:69, or SEQ ID NO:70, (3) a 16S rDNA sequence shown in SEQ ID NO:3, SEQ ID NO:71, SEQ ID NO:72, or SEQ ID NO:73, (4) a 16S rDNA sequence shown in SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, or SEQ ID NO:78rDNA sequence, (5) a 16S rDNA sequence shown in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81, (6) a 16S rDNA sequence shown in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86, (7) a 16S rDNA sequence shown in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91, (8) a 16S rDNA sequence shown in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96, (9) a 16S rDNA sequence shown in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104, (10) a 16S rDNA sequence shown in SEQ ID NO: 11 or SEQ ID NO: 105, (11) a 16S rDNA sequence shown in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109 rDNA sequence, (12) the 16S rDNA sequence shown in SEQ ID NO: 13 or SEQ ID NO: 110, (13) the 16S rDNA sequence shown in SEQ ID NO: 14, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, or SEQ ID NO: 114, (14) the 16S rDNA sequence shown in SEQ ID NO: 15, SEQ ID NO: 115, or SEQ ID NO: 116, (15) the 16S rDNA sequence shown in SEQ ID NO: 16, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 119, or SEQ ID NO: 120, (16) the 16S rDNA sequence shown in SEQ ID NO: 17, SEQ ID NO: 121, SEQ ID NO: 122, SEQ ID NO: 123, or SEQ ID NO: 124, and (17) the 16S rDNA sequence shown in SEQ ID NO: 24, SEQ ID NO: 149, SEQ ID NO: 150, or SEQ ID NO: 151, (f)(1) the 16S rDNA sequence shown in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65 rDNA sequence, (2) a 16S rDNA sequence shown in SEQ ID NO:2, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:69, or SEQ ID NO:70, (3) a 16S rDNA sequence shown in SEQ ID NO:3, SEQ ID NO:71, SEQ ID NO:72, or SEQ ID NO:73, (4) a 16S rDNA sequence shown in SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, or SEQ ID NO:78rDNA sequence, (5) a 16S rDNA sequence shown in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81, (6) a 16S rDNA sequence shown in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86, (7) a 16S rDNA sequence shown in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91, (8) a 16S rDNA sequence shown in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96, (9) a 16S rDNA sequence shown in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 10 2, the 16S rDNA sequence shown in SEQ ID NO: 103 or SEQ ID NO: 104, (10) the 16S rDNA sequence shown in SEQ ID NO: 11 or SEQ ID NO: 105, (11) the 16S rDNA sequence shown in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109, (12) the 16S rDNA sequence shown in SEQ ID NO: 13 or SEQ ID NO: 110, (13) the 16S rDNA sequence shown in SEQ ID NO: 14, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, or SEQ ID NO: 114, (14) the 16S rDNA sequence shown in SEQ ID NO: 15, SEQ ID NO: 115, or SEQ ID NO: 116, (15) the 16S rDNA sequence shown in SEQ ID NO: 16, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 119, or SEQ ID NO: 120, (16) the 16S rDNA sequence shown in SEQ ID NO: 17, SEQ ID NO: 121, SEQ ID NO: 122, SEQ ID NO: 123, or SEQ ID NO: 124 rDNA sequence, (17) the 16S rDNA sequence shown in SEQ ID NO: 18 or SEQ ID NO: 125, (18) the 16S rDNA sequence shown in SEQ ID NO: 19, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 128, SEQ ID NO: 129, SEQ ID NO: 130, or SEQ ID NO: 131, and (19) the 16S rDNA sequence shown in SEQ ID NO: 20 or SEQ ID NO: 132, (g) (1) the 16S rDNA sequence shown in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65, (2) the 16S rDNA sequence shown in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70, (3) the 16S rDNA sequence shown in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73, (4) the 16S rDNA sequence shown in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78 rDNA sequence, (5) a 16S rDNA sequence shown in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81, (6) a 16S rDNA sequence shown in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86, (7) a 16S rDNA sequence shown in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91rDNA sequence, (8) a 16S rDNA sequence shown in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96, (9) a 16S rDNA sequence shown in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104, (10) a 16S rDNA sequence shown in SEQ ID NO: 11 or SEQ ID NO: 105, (11) a 16S rDNA sequence shown in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109, (12) a 16S rDNA sequence shown in SEQ ID NO: 13 or SEQ ID NO: 110, (13) a 16S rDNA sequence shown in SEQ ID NO: 14, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, or SEQ ID NO: 114, (14) a 16S rDNA sequence shown in SEQ ID NO: 15, SEQ ID NO: 115, or SEQ ID NO: 116 rDNA sequence, (15) the 16S rDNA sequence shown in SEQ ID NO: 16, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 119, or SEQ ID NO: 120, (16) the 16S rDNA sequence shown in SEQ ID NO: 17, SEQ ID NO: 121, SEQ ID NO: 122, SEQ ID NO: 123, or SEQ ID NO: 124, (17) the 16S rDNA sequence shown in SEQ ID NO: 18 or SEQ ID NO: 125, (18) the 16S rDNA sequence shown in SEQ ID NO: 19, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 128, SEQ ID NO: 129, SEQ ID NO: 130, or SEQ ID NO: 131, (19) the 16S rDNA sequence shown in SEQ ID NO: 20 or SEQ ID NO: 132, (20) the 16S rDNA sequence shown in SEQ ID NO: 21 or SEQ ID NO: 133, (21) the 16S rDNA sequence shown in SEQ ID NO: 22 or SEQ ID NO: 134 rDNA sequence, and (22) the 16S rDNA sequence shown in SEQ ID NO:23, SEQ ID NO:135, SEQ ID NO:136, SEQ ID NO:137, SEQ ID NO:138, SEQ ID NO:139, SEQ ID NO:140, SEQ ID NO:141, SEQ ID NO:142, SEQ ID NO:143, SEQ ID NO:144, SEQ ID NO:145, SEQ ID NO:146, SEQ ID NO:147, or SEQ ID NO:148; (h) (1) the 16S rDNA sequence shown in SEQ ID NO:1, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, or SEQ ID NO:65; (2) the 16S rDNA sequence shown in SEQ ID NO:2, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:69, or SEQ ID NO:70;rDNA sequence, (3) a 16S rDNA sequence shown in SEQ ID NO:3, SEQ ID NO:71, SEQ ID NO:72, or SEQ ID NO:73, (4) a 16S rDNA sequence shown in SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, or SEQ ID NO:78, (5) a 16S rDNA sequence shown in SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, or SEQ ID NO:81, (6) a 16S rDNA sequence shown in SEQ ID NO:6, SEQ ID NO:82, SEQ ID NO:83, SEQ ID NO:84, SEQ ID NO:85, or SEQ ID NO:86, (7) a 16S rDNA sequence shown in SEQ ID NO:7, SEQ ID NO:88, SEQ ID NO:89, SEQ ID NO:90, or SEQ ID NO:91, (8) a 16S rDNA sequence shown in SEQ ID NO:8, SEQ ID NO:92, SEQ ID NO:93, SEQ ID NO:94, SEQ ID NO:95, or SEQ ID NO:96, (9) a 16S rDNA sequence shown in SEQ ID NO:9, SEQ ID NO:97, SEQ ID NO:98, or SEQ ID NO:99 rDNA sequence, (10) a 16S rDNA sequence shown in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104, (11) a 16S rDNA sequence shown in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109, (12) a 16S rDNA sequence shown in SEQ ID NO: 25, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56, SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO: 155, SEQ ID NO: 156, or SEQ ID NO: 157, and (13) a 16S rDNA sequence shown in SEQ ID NO: 26, SEQ ID NO: 158, SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 161, SEQ ID NO: 162, or SEQ ID NO: 163. rDNA sequences, (i) (1) a 16S rDNA sequence set forth in SEQ ID NO:1, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, or SEQ ID NO:65, (2) a 16S rDNA sequence set forth in SEQ ID NO:2, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:69, or SEQ ID NO:70, (3) a 16S rDNA sequence set forth in SEQ ID NO:3, SEQ ID NO:71, SEQ ID NO:72, or SEQ ID NO:73rDNA sequence, (4) a 16S rDNA sequence shown in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78, (5) a 16S rDNA sequence shown in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81, (6) a 16S rDNA sequence shown in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86, (7) a 16S rDNA sequence shown in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91, (8) a 16S rDNA sequence shown in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96, (9) a 16S rDNA sequence shown in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104, (10) a 16S rDNA sequence shown in SEQ ID NO: 11 or SEQ ID NO: 105 rDNA sequence, (11) a 16S rDNA sequence shown in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109, (12) a 16S rDNA sequence shown in SEQ ID NO: 13 or SEQ ID NO: 110, (13) a 16S rDNA sequence shown in SEQ ID NO: 14, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, or SEQ ID NO: 114, (14) a 16S rDNA sequence shown in SEQ ID NO: 15, SEQ ID NO: 115, or SEQ ID NO: 116, (15) a 16S rDNA sequence shown in SEQ ID NO: 26, SEQ ID NO: 158, SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 161, SEQ ID NO: 162, or SEQ ID NO: 163, and (16) a 16S rDNA sequence shown in SEQ ID NO: 27 or SEQ ID NO: 164, (j)(1) a 16S rDNA sequence shown in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65 rDNA sequence, (2) a 16S rDNA sequence shown in SEQ ID NO:2, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:69, or SEQ ID NO:70, (3) a 16S rDNA sequence shown in SEQ ID NO:3, SEQ ID NO:71, SEQ ID NO:72, or SEQ ID NO:73, (4) a 16S rDNA sequence shown in SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, or SEQ ID NO:78rDNA sequence, (5) a 16S rDNA sequence shown in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81, (6) a 16S rDNA sequence shown in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86, (7) a 16S rDNA sequence shown in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91, (8) a 16S rDNA sequence shown in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96, (9) a 16S rDNA sequence shown in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104, (10) a 16S rDNA sequence shown in SEQ ID NO: 11 or SEQ ID NO: 105, (11) a 16S rDNA sequence shown in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109 rDNA sequence, (12) the 16S rDNA sequence shown in SEQ ID NO: 13 or SEQ ID NO: 110, (13) the 16S rDNA sequence shown in SEQ ID NO: 14, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, or SEQ ID NO: 114, (14) the 16S rDNA sequence shown in SEQ ID NO: 15, SEQ ID NO: 115, or SEQ ID NO: 116, (15) the 16S rDNA sequence shown in SEQ ID NO: 16, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 119, or SEQ ID NO: 120, (16) the 16S rDNA sequence shown in SEQ ID NO: 28 or SEQ ID NO: 165, (17) the 16S rDNA sequence shown in SEQ ID NO: 24, SEQ ID NO: 149, SEQ ID NO: 150, or SEQ ID NO: 151, (18) the 16S rDNA sequence shown in SEQ ID NO: 26, SEQ ID NO: 158, SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 161, SEQ ID NO: 162, or SEQ ID NO: 163 rDNA sequence, and (19) the 16S rDNA sequence shown in SEQ ID NO: 27 or SEQ ID NO: 164, (k) (1) the 16S rDNA sequence shown in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65, (2) the 16S rDNA sequence shown in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70, (3) the 16S rDNA sequence shown in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73rDNA sequence, (4) a 16S rDNA sequence shown in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78, (5) a 16S rDNA sequence shown in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81, (6) a 16S rDNA sequence shown in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86, (7) a 16S rDNA sequence shown in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91 (8) a 16S rDNA sequence shown in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96; (9) a 16S rDNA sequence shown in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104; (10) a 16S rDNA sequence shown in SEQ ID NO: 11 or SEQ ID NO: 105; (11) a 16S rDNA sequence shown in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109; (12) a 16S rDNA sequence shown in SEQ ID NO: 13 or SEQ ID NO: 110; and (13) a 16S rDNA sequence shown in SEQ ID NO: 15, SEQ ID NO: 115, or SEQ ID NO: 116; (1) (1) a 16S rDNA sequence shown in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65. rDNA sequence, (2) a 16S rDNA sequence shown in SEQ ID NO:2, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:69, or SEQ ID NO:70, (3) a 16S rDNA sequence shown in SEQ ID NO:3, SEQ ID NO:71, SEQ ID NO:72, or SEQ ID NO:73, (4) a 16S rDNA sequence shown in SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, or SEQ ID NO:78, (5) a 16S rDNA sequence shown in SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, or SEQ ID NO:81, (6) a 16S rDNA sequence shown in SEQ ID NO:6, SEQ ID NO:82, SEQ ID NO:83, SEQ ID NO:84, SEQ ID NO:85, or SEQ ID NO:86, (7) a 16S rDNA sequence shown in SEQ ID NO:7, SEQ ID NO:87, SEQ ID NO:88, SEQ ID NO:89, SEQ ID NO:90, or SEQ ID NO:91, (8) a 16S rDNA sequence shown in SEQ ID NO:8, SEQ ID NO:92, SEQ ID NO:93, SEQ ID NO:94, SEQ ID NO:95, or SEQ ID NO:96 rDNA sequence, (9) a 16S rDNA sequence shown in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104, (10) a 16S rDNA sequence shown in SEQ ID NO: 11 or SEQ ID NO: 105, (11) a 16S rDNA sequence shown in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109, (12) a 16S rDNA sequence shown in SEQ ID NO: 13 or SEQ ID NO: 110rDNA sequence, (13) the 16S rDNA sequence shown in SEQ ID NO: 14, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, or SEQ ID NO: 114, (14) the 16S rDNA sequence shown in SEQ ID NO: 15, SEQ ID NO: 115, or SEQ ID NO: 116, (15) the 16S rDNA sequence shown in SEQ ID NO: 16, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 119, or SEQ ID NO: 120, (16) the 16S rDNA sequence shown in SEQ ID NO: 17, SEQ ID NO: 121, SEQ ID NO: 122, SEQ ID NO: 123, or SEQ ID NO: 124, (17) the 16S rDNA sequence shown in SEQ ID NO: 21 or SEQ ID NO: 133, (18) the 16S rDNA sequence shown in SEQ ID NO: 22 or SEQ ID NO: 134 rDNA sequence, and (19) a 16S rDNA sequence set forth in SEQ ID NO:23, SEQ ID NO:135, SEQ ID NO:136, SEQ ID NO:137, SEQ ID NO:138, SEQ ID NO:139, SEQ ID NO:140, SEQ ID NO:141, SEQ ID NO:142, SEQ ID NO:143, SEQ ID NO:144, SEQ ID NO:145, SEQ ID NO:146, SEQ ID NO:147, or SEQ ID NO:148, or (m) (1) a 16S rDNA sequence set forth in SEQ ID NO:1, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, or SEQ ID NO:65, (2) a 16S rDNA sequence set forth in SEQ ID NO:2, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:69, or SEQ ID NO:70, (3) a 16S rDNA sequence set forth in SEQ ID NO:3, SEQ ID NO:71, SEQ ID NO:72, or SEQ ID NO:73, (4) a 16S rDNA sequence set forth in SEQ ID NO:29, SEQ ID NO:32, SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, or SEQ ID NO:37. rDNA sequence, (5) a 16S rDNA sequence shown in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81, (6) a 16S rDNA sequence shown in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86, (7) a 16S rDNA sequence shown in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91, (8) a 16S rDNA sequence shown in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96, (9) a 16S rDNA sequence shown in SEQ ID NO: 9, SEQ ID NO: 97, SEQ ID NO: 98, or SEQ ID NO: 99rDNA sequence, (10) a 16S rDNA sequence shown in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104, (11) a 16S rDNA sequence shown in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109, (12) a 16S rDNA sequence shown in SEQ ID NO: 14, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, or SEQ ID NO: 114, (13) a 16S rDNA sequence shown in SEQ ID NO: 25, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56, SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO: 155, SEQ ID NO: 156, or SEQ ID NO: 157 rDNA sequence, (14) the 16S rDNA sequence shown in SEQ ID NO:26, SEQ ID NO:158, SEQ ID NO:159, SEQ ID NO:160, SEQ ID NO:161, SEQ ID NO:162, or SEQ ID NO:163, (15) the 16S rDNA sequence shown in SEQ ID NO:30, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41, SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO:166, SEQ ID NO:167, SEQ ID NO:168, SEQ ID NO:169, SEQ ID NO:170, SEQ ID NO:171, or SEQ ID NO:172, and (16) the 16S rDNA sequence shown in SEQ ID NO:31, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:173, SEQ ID NO:174, SEQ ID NO:175, SEQ ID NO:176, or SEQ ID NO:177.

[0026] For any of the methods provided herein, in some embodiments, following administration, colonization of the subject's gastrointestinal tract by pathogenic microorganisms is reduced or prevented. In some embodiments, following administration, the abundance of pathogenic microorganisms in the subject's gastrointestinal tract is reduced. In some embodiments, the pathogenic microorganisms include Enterococcus faecium (e.g., vancomycin-resistant), Enterococcus species, Klebsiella pneumonia (e.g., carbapenem-resistant), E. coli, Staphylococcus aureus, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter species, Enterococcus faecalis, Klebsiella oxytoca, Klebsiella aerogenes, Streptococcus species, or combinations thereof.

[0027] For any of the methods provided herein, in some embodiments, the plurality of bacteria further comprises additional bacterial species having one or more characteristics selected from the following: (1) capable of colonization (long-term and / or transient) when administered to a subject; (2) capable of anti-inflammatory activity (e.g., inhibiting TNF-α-induced IL-8 secretion in epithelial cells in vitro, ability to downregulate expression of inflammatory genes (e.g., CXCL1, CXCL2, CXCL3, CXCL11, ICAM1)); (3) inability to induce pro-inflammatory activity; (4) inability to induce pro-inflammatory activity; ) capable of producing secondary bile acids (e.g., 7α-dehydroxylase and bile salt hydrolase activity); (5) capable of producing tryptophan metabolites (e.g., indole, 3-methylindole, indolepropionic acid); (6) capable of restoring and / or maintaining epithelial integrity (e.g., as determined by a primary epithelial cell monolayer barrier integrity assay); (7) capable of producing short-chain fatty acids (e.g., butyrate, propionate); (8) capable of inhibiting HDAC activity; (9) capable of producing medium-chain fatty acids (e.g., valerate, hexanoate). (10) capable of expressing catalase activity; (11) capable of possessing alpha-fucosidase activity; (12) capable of producing vitamin B (e.g., thiamine (B1) and / or pyridoxamine (B6)); (13) capable of reducing fecal calprotectin levels; (14) inability to activate the toll-like receptor pathway (e.g., TLR4 or TLR5); (15) capable of activating the toll-like receptor pathway (e.g., TLR2); (16) capable of restoring colonization resistance; (17) capable of utilizing a wide range of carbon sources; (18) capable of reducing carriage of VRE pathogens. (19) can reduce CRE pathogen carriage, (20) can reduce E. coli pathogen carriage, (21) can reduce claudin-2 expression, (22) can associate with healthy human gut microbiota, (23) cannot associate with toxin and hemolysin genes associated with clostridial pathogens and does not produce significant cytopathic effects in vitro, (24) is sensitive to multiple clinically relevant antibiotics, (25) cannot associate with genes likely involved in both observed antibiotic resistance and transmissibility, and (26) can inhibit epithelial cell apoptosis.(27) One or more genes induced in IFN-γ-treated colon organoids (e.g., inflammatory chemokine signaling, NF-κB signaling, TNF family signaling, type I interferon signaling, type II interferon signaling, TLR signaling, lymphocyte trafficking, Th17 cell differentiation, Th1 differentiation, Th2 differentiation, apoptosis, inflammasome, autophagy, oxidative stress, MHC class I and II antigen presentation, complement, mTor, nod-like receptor signaling, PI3K signaling, or a combination thereof) (28) can decrease the expression of one or more inhibitory receptors (e.g., TIGIT, TIM-3, or LAG-3) on CD8+ T cells; (29) can increase the expression of one or more genes / proteins associated with CD8+ T cell activation and / or function (e.g., CD45RO, CD69, IL-24, TNF-α, perforin, or IFN-γ); (30) can enhance and / or ameliorate chemotherapeutic drug resistance; (31) can enhance the efficacy of immune checkpoint inhibitor therapy; (32) can inhibit CD8+ T cell proliferation and proliferation against tumors. (33) can induce an IL-10 / IL-6 cytokine ratio in macrophages favoring anti-inflammatory IL-10; (34) can induce a similar pathogen defense response in macrophages with less inflammatory response than donor-derived spore-based compositions (i.e., spore-based compositions); (35) can increase the amount of anti-inflammatory mediators (e.g., IL-1 receptor antagonist (IL-1RA), IL-4, IL-10, IL-11, IL-13, TGF-β); (36) can reduce colonic inflammation; (37) can prevent gastrointestinal dysbiosis; (38) can increase the diversity of the gastrointestinal microbiome in a subject; (39) can improve the integrity of the mucosa and / or epithelial barrier in a subject compared to a reference control (e.g., an untreated patient or a subject prior to treatment); (40) can promote mucosal healing; (41) can reduce the incidence of infection; (42) can reduce the need for antibiotics in a subject; (43) can reduce the amount of infectious disease biomarkers in the stool of a subject; (44) can increase the amount of biomarkers of the administered species in the stool of a subject.(45) Targeted delivery (e.g., by encapsulation or coating one or more dosage components with an enteric polymer) of many (e.g., 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9% of the administered species to the intestine of a subject, compared to the number of colony-forming units administered; (46) A composition or pharmaceutical composition described herein to a subject. (47) capable of being co-administered with an additional agent described herein without substantially reducing the therapeutic efficacy of the administered species; (48) capable of being co-administered with a carrier or excipient described herein without substantially reducing the therapeutic efficacy of the administered species; (49) capable of utilizing lactulose; (50) comprising a lantibiotic operon; (51) capable of being associated with reduced abundance in patients with liver disease (e.g., cirrhosis); or (52) any combination thereof.

[0028] In some embodiments, each of the plurality of bacteria is capable of forming spores. In some embodiments, each of the plurality of bacteria is in a spore form. In some embodiments, each of the plurality of bacteria is not a vegetative cell. In some embodiments, the composition further comprises a pharmaceutically acceptable excipient. In some embodiments, the composition is orally administered to the subject. In some embodiments, the method further comprises administering an additional agent to the subject. In some embodiments, the additional agent is administered simultaneously with the composition or sequentially. In some embodiments, the additional agent comprises a standard of care. In some embodiments, the standard of care comprises lactulose, rifaximin, or both.

[0029] Some aspects of the present disclosure relate to compositions comprising a plurality of bacteria, the plurality of bacteria comprising a first bacterial species and a second bacterial species, wherein the first species and the second species are not the same, and the first species and the second species are selected from the group consisting of Anaerotruncus colihominis, Blautia coccoides, Blautia hominis, Blautia obeum, Blautia wexlerae, Butyricicoccus sp2, Clostridium aldenense, Clostridium bolteae, Clostridium innocuum, Clostridium scindens, Clostridium symbiosum, Dorea longicatena, Eisenbergiella tayi, Emergencia timonensis, Erysipelatoclostridium ramosum, Eubacterium callanderi, Faecalicatena cortorta, Faecalicatena orotica, Flavonifractor plautii, Hungatella effluvii, Intestinimonas butyriciproducens, Intestinimonas massiliensis, Lactonifactor longoviformis, Lawsonibacter_sp7, Massilimaliae timonensis, Murimonas intestini, Niameybacter sp1, Ruminococcaceae NG13 sp6, or Turicibacter sanguinis.

[0030] Some aspects of the present disclosure relate to compositions comprising a plurality of bacteria, wherein the plurality of bacteria comprises a first bacterial species and a second bacterial species, wherein the first and second species are not the same, wherein the first and second species are not the same, and wherein the first and second species are independently selected from Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi.

[0031] In some embodiments, the plurality of bacteria further comprises Emergencia timonensis. In some embodiments, the plurality of bacteria further comprises Intestinimonas butyriciproducens, Clostridium symbiosum, Clostridium scindens, and / or Emergencia timonensis. In some embodiments, the plurality of bacteria further comprises Faecalicatena cortorta and / or Lactonifactor longoviformis. In some embodiments, the plurality of bacteria further comprises Massilimaliae timonensis, Hungatella effluvii, and / or Butyricicoccus sp2. In some embodiments, the plurality of bacteria further comprises Intestinimonas massiliensis, Niameybacter sp1, and / or Turicibacter sanguinis. In some embodiments, the plurality of bacteria further comprises Ruminococcaceae NG13 sp6. In some embodiments, the plurality of bacteria further comprises Dorea longicatena. In some embodiments, the plurality of bacteria further comprises Blautia obeum. In some embodiments, the plurality of bacteria further comprises Lawsonibacter_sp7. In some embodiments, the plurality of bacteria further comprises Blautia hominis. In some embodiments, the plurality of bacteria further comprises Blautia wexlerae. In some embodiments, the plurality of bacteria further comprises Eubacterium callanderi.

[0032] Some aspects of the present disclosure relate to compositions comprising a plurality of bacteria, wherein the plurality of bacteria comprises a first bacterial species and a second bacterial species, wherein the first and second species are not the same, and wherein the first and second species are independently selected from the group consisting of SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, or SEQ ID NO:81, SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, SEQ ID NO:78, SEQ ID NO:26, SEQ ID NO:158, SEQ ID NO:159, SEQ ID NO:160, SEQ ID NO:161, SEQ ID NO:162, SEQ ID NO:163, SEQ ID NO:20, SEQ ID NO:132, SEQ ID NO:10, SEQ ID NO:1 00, SEQ ID NO:101, SEQ ID NO:10266, SEQ ID NO:10367, SEQ ID NO:10468, SEQ ID NO:69, SEQ ID NO:70, SEQ ID NO:1, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, SEQ ID NO:65, SEQ ID NO:14, SEQ ID NO:111, SEQ ID NO:112, SEQ ID NO:113, SEQ ID NO:114, SEQ ID NO:13, SEQ ID NO:110, SEQ ID NO:25, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, SEQ ID NO:54, SEQ ID NO:55, SEQ ID NO:56, SEQ ID NO:57, SEQ ID NO:58, SEQ ID NO:59, SEQ ID NO:60, SEQ ID NO:152, SEQ ID NO:153, SEQ ID NO:154, SEQ ID NO:155, SEQ ID NO:156, SEQ ID NO:157, SEQ ID NO:12, SEQ ID NO:106, SEQ ID NO:107, SEQ ID NO:108, SEQ ID NO:109, SEQ ID NO:9, SEQ ID NO:97, SEQ ID NO:98, SEQ ID NO:99, SEQ ID NO:15, SEQ ID NO:115, SEQ ID NO:116, SEQ ID NO:7, SEQ ID NO:87, SEQ ID NO:88, SEQ ID NO:89, SEQ ID NO:90, SEQ ID NO:91, SEQ ID NO:16, SEQ ID NO:117, SEQ ID NO:118, SEQ ID NO:119, SEQ ID NO:120, SEQ ID NO:8, SEQ ID NO:92, SEQ ID NO:93, SEQ ID NO:94, SEQ ID NO:95, or SEQ ID NO:96, SEQ ID NO:3 , SEQ ID NO:71, SEQ ID NO:72, or SEQ ID NO:73, SEQ ID NO:19, SEQ ID NO:126, SEQ ID NO:127, SEQ ID NO:128, SEQ ID NO:129, SEQ ID NO:130, SEQ ID NO:131, SEQ ID NO:11, SEQ ID NO:105, SEQ ID NO:21, SEQ ID NO:133, SEQ ID NO:17, SEQ ID NO:121, SEQ ID NO:122, SEQ ID NO:123, SEQ ID NO:124, SEQ ID NO:28, SEQ ID NO:165, SEQ ID NO:27, SEQ ID NO:164, SEQ ID NO:18, SEQ ID NO:125, SEQ ID NO:6, SEQ ID NO:82, SEQ ID NO:83, SEQ ID NO:84, SEQ ID NO:85, SEQ ID NO:86, SEQ ID NO:22, SEQ ID NO:134,SEQ ID NO:24, SEQ ID NO:149, SEQ ID NO:150, SEQ ID NO:151, SEQ ID NO:23, SEQ ID NO:135, SEQ ID NO:136, SEQ ID NO:137, SEQ ID NO:138, SEQ ID NO:139, SEQ ID NO:140, SEQ ID NO:141, SEQ ID NO:142, SEQ ID NO:143, SEQ ID NO:144, SEQ ID NO:145, SEQ ID NO:146, SEQ ID NO:147, SEQ ID NO:148, SEQ ID NO:29, SEQ ID NO:32, SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, or SEQ ID NO:37, SEQ ID NO:30, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41, SEQ ID NO: No. 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 166, SEQ ID NO: 167, SEQ ID NO: 168, SEQ ID NO: 169, SEQ ID NO: 170, SEQ ID NO: 171, SEQ ID NO: 172, SEQ ID NO: 31, SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 173, SEQ ID NO: 174, SEQ ID NO: 175, SEQ ID NO: 176, or SEQ ID NO: 177.

[0033] Some aspects of the present disclosure relate to compositions comprising a plurality of bacteria, wherein the plurality of bacteria comprises a first bacterial species and a second bacterial species, wherein the first and second species are not the same, and wherein the first and second species are not the same, and wherein the first and / or second species are selected from the group consisting of SEQ ID NO:1, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, SEQ ID NO:65, SEQ ID NO:2, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:69, SEQ ID NO:70, SEQ ID NO:3, SEQ ID NO:71, SEQ ID NO:72, SEQ ID NO:73, SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, SEQ ID NO:78, SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, SEQ ID NO:81, SEQ ID NO: No. 6, SEQ ID NO:82, SEQ ID NO:83, SEQ ID NO:84, SEQ ID NO:85, SEQ ID NO:86, SEQ ID NO:7, SEQ ID NO:87, SEQ ID NO:88, SEQ ID NO:89, SEQ ID NO:90, SEQ ID NO:91, SEQ ID NO:8, SEQ ID NO:92, SEQ ID NO:10093, SEQ ID NO:10194, SEQ ID NO:102, SEQ ID NO:103, SEQ ID NO:10495, SEQ ID NO:96, SEQ ID NO:10, or a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to any one of the sequences set forth in SEQ ID NO:12, SEQ ID NO:106, SEQ ID NO:107, SEQ ID NO:108, or SEQ ID NO:109.

[0034] In some embodiments, the plurality of bacteria further comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:9, SEQ ID NO:97, SEQ ID NO:98, or SEQ ID NO:99. In some embodiments, the plurality of bacteria further comprises: (a) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:11 or SEQ ID NO:105; (b) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:13 or SEQ ID NO:110; (c) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:14, SEQ ID NO:111, SEQ ID NO:112, SEQ ID NO:113, or SEQ ID NO:114. rDNA sequence, and / or (d) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:15, SEQ ID NO:115, or SEQ ID NO:116.

[0035] In some embodiments, the plurality of bacteria further comprises: (a) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:16, SEQ ID NO:117, SEQ ID NO:118, SEQ ID NO:119, or SEQ ID NO:120, and / or (b) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:17, SEQ ID NO:121, SEQ ID NO:122, SEQ ID NO:123, SEQ ID NO:124, SEQ ID NO:28, or SEQ ID NO:165. In some embodiments, the plurality of bacteria further comprises: (a) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:18 or SEQ ID NO:125; (b) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:19, SEQ ID NO:126, SEQ ID NO:127, SEQ ID NO:128, SEQ ID NO:129, SEQ ID NO:130, or SEQ ID NO:131; and / or (c) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:20 or SEQ ID NO:132.In some embodiments, the plurality of bacteria further comprises: (a) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:21 or SEQ ID NO:133; (b) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:22 or SEQ ID NO:134. rDNA sequence, and / or (c) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:23, SEQ ID NO:135, SEQ ID NO:136, SEQ ID NO:137, SEQ ID NO:138, SEQ ID NO:139, SEQ ID NO:140, SEQ ID NO:141, SEQ ID NO:142, SEQ ID NO:143, SEQ ID NO:144, SEQ ID NO:145, SEQ ID NO:146, SEQ ID NO:147, or SEQ ID NO: 148. In some embodiments, the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:24, SEQ ID NO:149, SEQ ID NO:150, or SEQ ID NO:151. In some embodiments, the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:25, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, SEQ ID NO:54, SEQ ID NO:55, SEQ ID NO:56, SEQ ID NO:57, SEQ ID NO:58, SEQ ID NO:59, SEQ ID NO:60, SEQ ID NO:152, SEQ ID NO:153, SEQ ID NO:154, SEQ ID NO:155, SEQ ID NO:156, or SEQ ID NO:157.In some embodiments, the plurality of bacteria further comprises: (a) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:18 or SEQ ID NO:125; (b) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:19, SEQ ID NO:126, SEQ ID NO:127, SEQ ID NO:128, SEQ ID NO:129, SEQ ID NO:130, or SEQ ID NO:131; and / or (c) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:20 or SEQ ID NO:132. In some embodiments, the plurality of bacteria further comprises: (a) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:21 or SEQ ID NO:133; (b) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:22 or SEQ ID NO:134. rDNA sequence, and / or (c) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:23, SEQ ID NO:135, SEQ ID NO:136, SEQ ID NO:137, SEQ ID NO:138, SEQ ID NO:139, SEQ ID NO:140, SEQ ID NO:141, SEQ ID NO:142, SEQ ID NO:143, SEQ ID NO:144, SEQ ID NO:145, SEQ ID NO:146, SEQ ID NO:147, or SEQ ID NO: 148. In some embodiments, the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:24, SEQ ID NO:149, SEQ ID NO:150, or SEQ ID NO:151.In some embodiments, the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:25, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, SEQ ID NO:54, SEQ ID NO:55, SEQ ID NO:56, SEQ ID NO:57, SEQ ID NO:58, SEQ ID NO:59, SEQ ID NO:60, SEQ ID NO:152, SEQ ID NO:153, SEQ ID NO:154, SEQ ID NO:155, SEQ ID NO:156, or SEQ ID NO: 157. In some embodiments, the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:26, SEQ ID NO:158, SEQ ID NO:159, SEQ ID NO:160, SEQ ID NO:161, SEQ ID NO:162, or SEQ ID NO:163. In some embodiments, the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:27 or SEQ ID NO:164.In some embodiments, the plurality of bacteria further comprises: (a) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in any one of SEQ ID NO:29, SEQ ID NO:32, SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, or SEQ ID NO:37; (b) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in any one of SEQ ID NO:30, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41, SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO:166, SEQ ID NO:167, SEQ ID NO:168, SEQ ID NO:169, SEQ ID NO:170, SEQ ID NO:171, or SEQ ID NO:172. rDNA sequence, and / or (c) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to any one of SEQ ID NO:31, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:173, SEQ ID NO:174, SEQ ID NO:175, SEQ ID NO:176, or SEQ ID NO:177.

[0036] For any of the compositions provided herein, in some embodiments, the plurality of bacteria further comprises additional bacterial species having one or more characteristics selected from the following: (1) capable of colonization (long-term and / or transient) when administered to a subject; (2) capable of anti-inflammatory activity (e.g., inhibiting TNF-α-induced IL-8 secretion in epithelial cells in vitro, ability to downregulate expression of inflammatory genes (e.g., CXCL1, CXCL2, CXCL3, CXCL11, ICAM1)); (3) incapable of inducing pro-inflammatory activity; (4) capable of producing secondary bile acids (e.g., 7α-dehydroxylase and bile salt hydrolase activity); (5) capable of producing tryptophan metabolites (e.g., indole, 3-methylindole, indolepropionic acid); (6) capable of restoring and / or maintaining epithelial integrity (e.g., as determined by a primary epithelial cell monolayer barrier integrity assay); (7) capable of producing short-chain fatty acids (e.g., butyrate, propionate); (8) capable of inhibiting HDAC activity; (9) capable of producing medium-chain fatty acids (e.g., valerate, hexanoate). (10) capable of expressing catalase activity; (11) capable of possessing alpha-fucosidase activity; (12) capable of producing vitamin B (e.g., thiamine (B1) and / or pyridoxamine (B6)); (13) capable of reducing fecal calprotectin levels; (14) inability to activate the toll-like receptor pathway (e.g., TLR4 or TLR5); (15) capable of activating the toll-like receptor pathway (e.g., TLR2); (16) capable of restoring colonization resistance; (17) capable of utilizing a wide range of carbon sources; (18) capable of reducing carriage of VRE pathogens. (19) can reduce CRE pathogen carriage, (20) can reduce E. coli pathogen carriage, (21) can reduce claudin-2 expression, (22) can associate with healthy human gut microbiota, (23) cannot associate with toxin and hemolysin genes associated with clostridial pathogens and do not produce significant cytopathic effects in vitro, (24) are sensitive to multiple clinically relevant antibiotics, (25) cannot associate with genes likely involved in both the observed antibiotic resistance and transmissibility, and (26) can inhibit epithelial cell apoptosis.(27) One or more genes induced in IFN-γ-treated colon organoids (e.g., inflammatory chemokine signaling, NF-κB signaling, TNF family signaling, type I interferon signaling, type II interferon signaling, TLR signaling, lymphocyte trafficking, Th17 cell differentiation, Th1 differentiation, Th2 differentiation, apoptosis, inflammasome, autophagy, oxidative stress, MHC class I and II antigen presentation, complement, mTor, nod-like receptor signaling, PI3K signaling, or a combination thereof) (28) can decrease the expression of one or more inhibitory receptors (e.g., TIGIT, TIM-3, or LAG-3) on CD8+ T cells; (29) can increase the expression of one or more genes / proteins associated with CD8+ T cell activation and / or function (e.g., CD45RO, CD69, IL-24, TNF-α, perforin, or IFN-γ); (30) can enhance and / or ameliorate chemotherapeutic drug resistance; (31) can enhance the efficacy of immune checkpoint inhibitor therapy; (32) can inhibit CD8+ T cell proliferation and proliferation against tumors. (33) can induce an IL-10 / IL-6 cytokine ratio in macrophages favoring anti-inflammatory IL-10; (34) can induce a similar pathogen defense response in macrophages with less inflammatory response than donor-derived spore-based compositions (i.e., spore-based compositions); (35) can increase the amount of anti-inflammatory mediators (e.g., IL-1 receptor antagonist (IL-1RA), IL-4, IL-10, IL-11, IL-13, TGF-β); (36) can reduce colonic inflammation; (37) can prevent gastrointestinal dysbiosis; (38) can increase the diversity of the gastrointestinal microbiome in a subject; (39) can improve the integrity of the mucosa and / or epithelial barrier in a subject compared to a reference control (e.g., an untreated patient or a subject prior to treatment); (40) can promote mucosal healing; (41) can reduce the incidence of infection; (42) can reduce the need for antibiotics in a subject; (43) can reduce the amount of infectious disease biomarkers in the stool of a subject; (44) can increase the amount of biomarkers of the administered species in the stool of a subject.(45) Targeted delivery (e.g., by encapsulation or coating one or more dosage components with an enteric polymer) of many (e.g., 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9% of the administered species to the intestine of a subject, compared to the number of colony-forming units administered; (46) A composition or pharmaceutical composition described herein to a subject. (47) capable of being co-administered with an additional agent described herein without substantially reducing the therapeutic efficacy of the administered species; (48) capable of being co-administered with a carrier or excipient described herein without substantially reducing the therapeutic efficacy of the administered species; (49) capable of utilizing lactulose; (50) comprising a lantibiotic operon; (51) capable of being associated with reduced abundance in patients with liver disease (e.g., cirrhosis); or (52) any combination thereof.

[0037] In some embodiments, each of the plurality of bacteria is capable of forming spores. In some embodiments, each of the plurality of bacteria is in a spore form. In some embodiments, the composition further comprises a pharmaceutically acceptable excipient. [Brief explanation of the drawings]

[0038] [Figure 1] A table listing exemplary designed bacterial compositions described herein is provided. The SEQ ID NOs of the 16S sequences of bacterial species present in different designed bacterial compositions are provided. "0" indicates that a bacterial species is not included, and "1" indicates that a bacterial species is included in a given bacterial composition. Bacterial species that are part of the phylogenetic core and R group are also shown. [Figure 2-1]Figure 1 shows the ability of different bacterial compositions to eradicate or reduce the abundance of vancomycin-resistant Enterococcus (VRE) and carbapenem-resistant Enterobacteriaceae (CRE) in a mouse model. A provides a schematic of the experimental design. Animals were infected with either VRE or CRE, as indicated, and then treated with one of the following: (1) PBS, (2) DE1, (3) DE2, (4) DE3, (5) DE4, (6) DE5.1, (7) DE6, and (8) fecal microbial transplant (FMT). Naive animals (i.e., no pathogen infection and no treatment) served as controls. [Figure 2-2] Figure 1 shows the ability of different bacterial compositions to eradicate or reduce the abundance of vancomycin-resistant Enterococcus (VRE) and carbapenem-resistant Enterobacteriaceae (CRE) in a mouse model. Figure 2B provides a comparison of VRE titers over 21 days after VRE exposure. Figure 3C provides a comparison of CRE titers over 21 days after CRE exposure. In Figures 2B and 2C, VRE and CRE titers are shown as colony-forming units (CFU) / g feces. "LOD" refers to limit of detection. [Figure 2-3] Figure 1 shows the ability of different bacterial compositions to eradicate or reduce the abundance of vancomycin-resistant Enterococcus (VRE) and carbapenem-resistant Enterobacteriaceae (CRE) in a mouse model. Figure 2 shows colonization of different bacterial species present in DE2 after administration to mice infected with CRE. [Figure 2-4] Figure 1 shows the ability of different bacterial compositions to eradicate or reduce the abundance of vancomycin-resistant Enterococcus (VRE) and carbapenem-resistant Enterobacteriaceae (CRE) in a mouse model. E shows colonization of different bacterial species present in DE3 after administration to mice infected with CRE. [Figure 2-5]Figure 1 shows the ability of different bacterial compositions to eradicate or reduce the abundance of vancomycin-resistant Enterococcus (VRE) and carbapenem-resistant Enterobacteriaceae (CRE) in a mouse model. F shows colonization of different bacterial species present in DE5.1 after administration to mice infected with CRE. [Figure 2-6] Figure 1 shows the ability of different bacterial compositions to eradicate or reduce the abundance of vancomycin-resistant Enterococcus (VRE) and carbapenem-resistant Enterobacteriaceae (CRE) in a mouse model. G shows colonization of different bacterial species present in DE2 after administration to mice infected with VRE. [Figure 2-7] Figure 1 shows the ability of different bacterial compositions to eradicate or reduce the abundance of vancomycin-resistant Enterococcus (VRE) and carbapenem-resistant Enterobacteriaceae (CRE) in a mouse model. H shows colonization of different bacterial species present in DE3 after administration to mice infected with VRE. [Figure 2-8] Figure 1 shows the ability of different bacterial compositions to eradicate or reduce the abundance of vancomycin-resistant Enterococcus (VRE) and carbapenem-resistant Enterobacteriaceae (CRE) in a mouse model. I shows colonization of different bacterial species present in DE5.1 after administration to mice infected with VRE. [Figure 3]This study demonstrates the ability of different bacterial compositions to eradicate or reduce the abundance of three pathogens (i.e., carbapenem-resistant Klebsiella pneumoniae, extended-spectrum beta-lactamase+ Escherichia coli, and vancomycin-resistant Enterococcus) in a mouse model. After pathogen challenge (days 4-9), mice were treated with one of the following: (1) PBS, (2) DE3, (3) DE7, (4) DE10, (5) DE9, or (6) DE8. A provides a comparison of CRE titers over 21 days after CRE challenge. B provides a comparison of ESBL+ E. coli (EC) titers over 21 days after EC challenge. C provides a comparison of VRE titers over 21 days after VRE challenge. Pathogen titers are shown as colony-forming units (CFU) / g. [Figure 4] We demonstrate the ability of different bacterial compositions to eradicate or reduce the abundance of three pathogens (i.e., carbapenem-resistant Klebsiella pneumoniae, vancomycin-resistant Enterococcus, and carbapenem-resistant Escherichia coli) in an in vitro gut ecology model (iGEM). Cr-Kpn (A), VRE (B), or Cr-E. coli (C) was added before vancomycin pretreatment (day 4), and Cr-Kpn (A) or VRE (B) was added again during vancomycin pretreatment (day 6). The test bacterial compositions (i.e., DE3, DE5.1, DE7, DE9, DE10, DE2, or FMTFMT) were added over 7 days (days 10–16) starting the day after the end of vancomycin treatment (microbiome intervention). Pathogen load was measured by scoring colony-forming units (CFUs) on pathogen-selective plates. [Figure 5A]We demonstrate the ability of the DE2 bacterial composition to eradicate or reduce the abundance of three pathogens (i.e., carbapenem-resistant Klebsiella pneumoniae, vancomycin-resistant Enterococcus, and carbapenem-resistant Escherichia coli) in an in vitro gut ecology model (iGEM). Cr-Kpn was added before vancomycin pretreatment (day 4). Bacterial composition DE2 was added over a 5-day period (days 10–14) starting the day after the end of vancomycin treatment. [Figure 5B] We demonstrate the ability of the DE2 bacterial composition to eradicate or reduce the abundance of three pathogens (i.e., carbapenem-resistant Klebsiella pneumoniae, vancomycin-resistant Enterococcus, and carbapenem-resistant Escherichia coli) in an in vitro gut ecology model (iGEM). VRE was added before vancomycin pretreatment (day 4), and VRE was added again during vancomycin pretreatment (day 6). Bacterial composition DE2 was added over a 5-day period (days 10–14), starting the day after the end of vancomycin treatment. [Figure 5C] We demonstrate the ability of the DE2 bacterial composition to eradicate or reduce the abundance of three pathogens (i.e., carbapenem-resistant Klebsiella pneumoniae, vancomycin-resistant Enterococcus, and carbapenem-resistant Escherichia coli) in an in vitro gut ecology model (iGEM). Cr-E. coli was added before vancomycin pretreatment (day 4). Bacterial composition DE2 was added over a 5-day period (days 10–14) starting the day after the end of vancomycin treatment. [Figure 5D]We demonstrate the ability of the DE2 bacterial composition to eradicate or reduce the abundance of three pathogens (i.e., carbapenem-resistant Klebsiella pneumoniae, vancomycin-resistant Enterococcus, and carbapenem-resistant Escherichia coli) in an in vitro gut ecology model (iGEM). Pathogen load was measured by scoring colony-forming units (CFUs) on pathogen-selective plates. [Figure 5E] We demonstrate the ability of the DE2 bacterial composition to eradicate or reduce the abundance of three pathogens (i.e., carbapenem-resistant Klebsiella pneumoniae, vancomycin-resistant Enterococcus, and carbapenem-resistant Escherichia coli) in an in vitro gut ecology model (iGEM). Pathogen load was measured by scoring colony-forming units (CFUs) on pathogen-selective plates. [Figure 5F] We demonstrate the ability of the DE2 bacterial composition to eradicate or reduce the abundance of three pathogens (i.e., carbapenem-resistant Klebsiella pneumoniae, vancomycin-resistant Enterococcus, and carbapenem-resistant Escherichia coli) in an in vitro gut ecology model (iGEM). Pathogen load was measured by scoring colony-forming units (CFUs) on pathogen-selective plates. [Figure 5G]We demonstrate the ability of the DE2 bacterial composition to eradicate or reduce the abundance of three pathogens (i.e., carbapenem-resistant Klebsiella pneumoniae, vancomycin-resistant Enterococcus, and carbapenem-resistant Escherichia coli) in an in vitro gut ecology model (iGEM). We also demonstrate the ability of the DE3 and DE5.2 bacterial compositions to reduce the abundance of Cr-E. coli compared to spore preparations and FMT in iGEM. Cr-E. coli was added prior to vancomycin pretreatment (day 4). The bacterial composition, spore preparations, and FMT were added over a 5-day period (days 10–14), starting the day after the end of vancomycin treatment. Pathogen load was measured by scoring colony-forming units (CFUs) on pathogen-selective plates. [Figure 6] Table 1 provides the average concentrations of secondary bile acids produced under culture conditions for DE2, DE3, DE8, DE10, DE9, DE7, and FCMA.BA. Table 2 provides the average concentrations of the following bile acids: 12-ketolithocholic acid, 3-oxocholic acid, cholic acid, deoxycholic acid, glycocholic acid, ketodeoxychlic acid-like, taurocholic acid, and ursocholic acid. Table 3 provides the average concentrations of the following bile acids: 3-oxochenodeoxycholic acid, chenodeoxycholic acid, glycochendeoxycholic acid, isolithocholic acid, lithocholic acid, taurochendeoxycjolic acid, ursodeoxycholic acid, and z-ketolithocholic acid-like 3. [Figure 7]Figure 1A shows the effect of DE5.2 on carbapenem-resistant Klebsiella pneumoniae (Cr-Kpn) eradication in a mouse model. Figure 1B shows the effect of DE11 on carbapenem-resistant Klebsiella pneumoniae (Cr-Kpn) eradication in a mouse model. After pathogen challenge (days 4-9), mice were treated with either PBS (control) or one of the test bacterial compositions (i.e., DE5.2 in A and DE11 in B). The effect on Cr-Kpn eradication is shown as pathogen titer over 21 days after pathogen challenge. Pathogen titer is shown as colony-forming units (CFU) / g feces. [Figure 8] A shows the effect of DE5.2 on vancomycin-resistant Enterococcus (VRE) eradication. B shows the effect of DE11 on vancomycin-resistant Enterococcus (VRE) eradication. After pathogen challenge (days 2-7), mice were treated with either PBS (control) or one of the test bacterial compositions (i.e., DE5.2 in A and DE11 in B). The effect on VRE eradication is shown as VRE titer over 21 days after VRE challenge. VRE titer is shown as colony-forming units (CFU) / g feces. [Figure 9] FIG. 1 shows a schematic diagram of an in vitro IFN-γ-induced epithelial barrier damage assay using the ALTIS REPLIGUT® System. [Figure 10A] The effect of the following bacterial compositions on protecting against IFN-γ-induced barrier damage is shown: DE3, DE5.2, DE9, DE10, and DE2. Relative fluorescence units (RFU) were measured. The effect is shown as the relative fluorescence units (RFU) of Lucifer Yellow fluorescence of IFN-γ alone compared to the DE culture supernatants tested. [Figure 10B] The effect of the following bacterial compositions on protecting against IFN-γ-induced barrier damage is shown: DE3, DE5.2, DE9, DE10, and DE2. Relative fluorescence units (RFU) were measured. The effect is shown as the relative fluorescence units (RFU) of Lucifer Yellow fluorescence of IFN-γ alone compared to the DE culture supernatants tested. [Figure 11A]This paper demonstrates the ability of bacterial spore preparations to eradicate or reduce the abundance of three pathogens (i.e., carbapenem-resistant Klebsiella pneumoniae, extended-spectrum beta-lactamase+ Escherichia coli, and vancomycin-resistant Enterococcus) in a mouse model. After pathogen challenge, mice were treated with one of the following: (1) PBS, (2) bacterial spore preparation. A comparison of CRE titers over a 21-day period following CRE challenge is provided. Pathogen titers are expressed as colony-forming units (CFU) / g feces. [Figure 11B] This study demonstrates the ability of a bacterial spore preparation to eradicate or reduce the abundance of three pathogens (i.e., carbapenem-resistant Klebsiella pneumoniae, extended-spectrum beta-lactamase+ Escherichia coli, and vancomycin-resistant Enterococcus) in a mouse model. After pathogen challenge, mice were treated with one of the following: (1) PBS, (2) bacterial spore preparation. A comparison of ESBL+ E. coli (EC) titers over 21 days after EC challenge is provided. Pathogen titers are expressed as colony-forming units (CFU) / g feces. [Figure 11C] This study demonstrates the ability of a bacterial spore preparation to eradicate or reduce the abundance of three pathogens (i.e., carbapenem-resistant Klebsiella pneumoniae, extended-spectrum beta-lactamase+ Escherichia coli, and vancomycin-resistant Enterococcus) in a mouse model. After pathogen challenge, mice were treated with one of the following: (1) PBS, or (2) the bacterial spore preparation. A comparison of VRE titers over a 21-day period following VRE challenge is provided. Pathogen titers are expressed as colony-forming units (CFU) / g feces. DETAILED DESCRIPTION OF THE INVENTION

[0039] Provided herein are methods of treating a disease or disorder in a subject in need thereof (e.g., treating infectious complications resulting from chronic liver disease, cancer neutropenia, and / or a disease or disorder associated with solid organ transplantation), comprising administering to the subject a bacterial composition specifically designed to contain a plurality of certain commensal bacteria. As further described herein, the plurality of commensal bacteria exhibits certain properties (e.g., those disclosed herein) useful for reducing or preventing colonization (i.e., facilitating eradication) and / or reducing the abundance of certain microbial pathogens in the gastrointestinal tract of the subject. Additional aspects are provided throughout this disclosure.

[0040] To facilitate understanding of the disclosure set forth herein, a number of terms and phrases are defined. Additional definitions are set forth throughout the detailed description.

[0041] I. Definition It should be noted that the term "a" or "an" entity refers to one or more of that entity; for example, "a bacterial composition" is understood to represent one or more bacterial compositions. Thus, the terms "a" (or "an"), "one or more," and "at least one" may be used interchangeably herein.

[0042] Furthermore, "and / or," when used herein, should be construed as a specific disclosure of each of the two specified features or components with or without the other. Thus, the term "and / or" used herein in phrases such as "A and / or B" is intended to include "A and B," "A or B," "A" (alone), and "B" (alone). Similarly, the term "and / or" used in phrases such as "A, B, and / or C" is intended to encompass each of the following embodiments: A, B, and C; A, B, or C; A or C; A or B; B or C; A and C; A and B; B and C; A (alone); B (alone); and C (alone).

[0043] Whenever an embodiment is described herein using the language "comprising," it is understood that other, similar embodiments are also provided that are described using the terms "consisting of" and / or "consisting essentially of." As used herein, "comprising" is synonymous with "including," "containing," or "characterized by" and is inclusive or open-ended and does not exclude additional, unrecited elements or method steps. As used herein, "consisting of" excludes any element, step, or ingredient not specified in the claim element. As used herein, "consisting essentially of" does not exclude materials or steps that do not materially affect the basic and novel characteristics of the claim.

[0044] Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure pertains.

[0045] Units, prefixes, and symbols are shown in their Systeme International de Unites (SI) accepted format. Numerical ranges are inclusive of the numbers defining the range. Unless otherwise indicated, nucleotide sequences are written left to right in 5' to 3' orientation. Amino acid sequences are written left to right in amino to carboxy orientation. The headings provided herein are not intended to limit the various aspects of this disclosure, which may be had by reference to the specification in its entirety. Accordingly, the terms defined immediately below are more fully defined by reference to the specification in its entirety.

[0046] The term "at least" before a number or series of numbers is understood to include the number adjacent to the term "at least" and all subsequent numbers or integers that may be logically included, as is clear from the context. For example, the number of nucleotides in a nucleic acid molecule must be an integer. For example, "at least 18 nucleotides of a 21-nucleotide nucleic acid molecule" means that 18, 19, 20, or 21 nucleotides have the specified property. When "at least" precedes a series of numbers or ranges, it is understood that "at least" can modify each number in the series or range. "At least" is also not limited to integers (e.g., "at least 5%" includes 5.0%, 5.1%, and 5.18%, regardless of the number of significant digits).

[0047] As used herein, the term "approximately" or "about," unless otherwise stated or otherwise clear from the context (except where such number would exceed 100% of possible values), refers to a value that is similar to a stated reference value and within a range of values ​​that is within 25%, 20%, 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12%, 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, or less in either direction (above or below) of the stated reference value. When the term "approximately" or "about" is applied to a particular value herein, the value without the term "approximately" or "about" is also disclosed herein.

[0048] As described herein, any concentration range, percentage range, ratio range, or integer range, unless otherwise indicated, should be understood to include any integer value within the recited range, and, where appropriate, fractions thereof (such as tenths and hundredths of integers).

[0049] The terms "treat," "treating," and "treatment," as used herein, refer to any type of intervention or process performed on a subject, or the administration of an active agent (e.g., any of the bacterial compositions provided herein) to a subject, with the purpose of reversing, alleviating, ameliorating, inhibiting, preventing, or slowing the progression, onset, severity, or recurrence of symptoms, complications, conditions, or biochemical signs associated with a disease or condition described herein (e.g., chronic liver disease, neutropenia, and / or diseases or disorders associated with solid organ transplantation). As used herein, the terms "treat," "treating," and "treatment" refer to the administration of an effective dose or effective dosage. As further described herein, in some aspects, treating a disease or disorder described herein includes reducing or preventing the occurrence of infection in a subject suffering from the disease or disorder.

[0050] The terms "prevent," "preventing," and "prevention," as used herein, refer to partially or completely delaying the onset of a disease or disorder described herein, partially or completely delaying the onset of one or more symptoms, characteristics, or clinical manifestations of a disease or disorder described herein, partially or completely delaying the onset of one or more symptoms, characteristics, or manifestations of a disease or disorder described herein, partially or completely delaying the progression of a disease or disorder described herein, and / or reducing the risk of developing a condition associated with a disease or disorder described herein. In some embodiments, any of the bacterial compositions provided herein may be useful in preventing the development of an infection in a subject suffering from a disease or disorder provided herein. As further described herein, in some embodiments, the bacterial compositions provided herein may be useful in treating a disease or disorder in a subject by preventing the development of an infection.

[0051] The term "microbiota" refers to the biological community of microorganisms occurring (persistently or transiently) in and on an animal subject, typically a mammal such as a human, and includes eukaryotes, archaea, bacteria, and viruses (including bacterial viruses, i.e., phages).

[0052] The term "microbiome" refers to the genetic content of the microbial community living in and on the human body, both persistently and transiently, including eukaryotes, archaea, bacteria, and viruses (including bacterial viruses (i.e., phages)), where "genetic content" includes genomic DNA, RNA such as ribosomal RNA, epigenome, plasmids, and all other types of genetic information.

[0053] The term "ecological niche" or "niche" refers to the ecological region occupied by an organism or group of organisms. A niche describes how an organism or population or organisms responds to the distribution of resources, physical parameters (e.g., host tissue space), and competitors (e.g., by growing when resources are abundant and when predators, parasites, and pathogens are scarce), and how they in turn modify those same factors (e.g., limiting access to resources by other organisms, acting as a food source for predators and a consumer of prey).

[0054] The term "gut dysbiosis" refers to a state of the microbiota in a subject's GI tract or other body region, including mucous membranes or skin surfaces, in which normal diversity and / or function of the ecological network is disrupted. This unhealthy state can result from a decrease in diversity, an overgrowth of one or more pathogens or pathogenic bacteria, symbionts that can cause disease only if certain genetic and / or environmental conditions are present in the subject, or a shift to an ecological microbial network that no longer provides essential functions for the host subject and therefore no longer promotes health. As described herein, in some embodiments, diseases or disorders that can be treated with the present disclosure (e.g., diseases or disorders associated with chronic liver disease, neutropenia, and / or solid organ transplants) can be associated with dysbiosis.

[0055] As used herein, "operational taxonomic unit" or "OTU"(s) refers to the terminal leaves of a phylogenetic tree and is defined by a nucleic acid sequence, e.g., a whole genome, or a specific gene sequence, and all sequences that share sequence identity with this nucleic acid sequence at the species level. In some embodiments, the specific gene sequence can be a 16S rDNA sequence or a portion of a 16S rDNA sequence. In some aspects, the whole genomes of two entities are sequenced and compared. In some aspects, selected regions, such as multilocus sequence tags (MLST), specific genes, or sets of genes, can be genetically compared. In some aspects, OTUs that share 97% or greater average nucleotide identity across the entire 16S or variable regions of 16S rDNA, e.g., the V4 region, are considered the same OTU (see, e.g., Claesson MJ, Wang Q, O'Sullivan O, Greene-Diniz R, Cole JR, Ros RP, and O'Toole P W. 2010). Comparison of two next-generation sequencing technologies for resolving highly complex microbiome composition using tandem variable 16S rRNA gene regions.Nucleic Acids Res 38:e200.Konstantinidis KT, Ramette A, and Tiedje J M.2006.The bacterial species definition in the genomic era.Philos Trans R Soc Lond B Biol Sci 361:1929-1940).When complete genomes are included, MLST, specific genes, or sets of gene OTUs that share 95% or more nucleotide identity are considered the same OTU (see, e.g., Achtman M, and Wagner M. 2008. Microbial diversity and the genetic nature of microbial species. Nat. Rev. Microbiol. 6:431-440. Konstantinidis KT, Ramette A, and Tiedje J M. 2006. The bacterial species definition in the genomic era. Philos Trans R Soc Lond B Biol Sci 361:1929-1940). OTUs are often defined by comparing sequences between organisms. Generally, sequences with less than 95% sequence identity are not considered to be part of the same OTU. In some cases, OTUs are characterized by a combination of nucleotide markers, genes, and / or single nucleotide variants (SNVs). In some embodiments, the referenced genes are highly conserved genes (e.g., "housekeeping" genes). The characteristics that define an OTU can be a combination of the above. Such characterization can be, for example, using WGS data or whole genome sequences. If the OTUs are the same, they will generally share common functional characteristics.

[0056] As used herein, the term "phylogenetic tree" refers to a graphical representation of the evolutionary relationships of one gene sequence to another, generated using a set of defined phylogenetic reconstruction algorithms (e.g., parsimony, maximum likelihood, or Bayesian). Nodes in the tree represent distinct ancestral sequences, and the confidence in any node is provided by bootstrap or Bayesian posterior probabilities, which measure branching uncertainty.

[0057] Identification and references to the bacterial species described herein can be found throughout this disclosure, including in the figures / drawings, tables, and sequence listing. When a taxonomic name is used or referenced for a particular bacterium, it is understood that the bacterium may have previously had a different taxonomic name(s), and one of skill in the art will have resources available to identify and associate previous taxonomic names with those described herein, as used in the art, or both. Such resources include Bergey's Manual of Systematics of Archea and Bacteria (1999); st Ed.), Bergey's Manual of Systematic Bacteriology(2 nd Ed.), online version available at onlinelibrary.wiley.com / doi / book / 10.1002 / 9781118960608, and the National Center for Biotechnology Information (NCBI) database available online at www.ncbi.nlm.nih.gov / taxonomy.

[0058] As used herein, the terms "subject," "individual," and "patient" are used interchangeably and refer to any animal subject, including humans, laboratory animals (e.g., primates, rats, mice), farm animals (e.g., cows, sheep, goats, pigs, turkeys, and chickens), and household pets (e.g., dogs, cats, and rodents).

[0059] "Colonization" of a host organism includes the non-transient settlement of bacteria or other microscopic organisms. In the case of treatment, the host is generally referred to herein as a "subject," typically a human or other mammal. As used herein, "reducing" or "inhibiting" the colonization of the gastrointestinal tract (or any other microbiota niche) of a host subject by pathogenic bacteria includes reducing the residence time of the pathogen in the gastrointestinal tract, as well as reducing the number (or concentration) of pathogens attached to the luminal surface of the gastrointestinal tract or the gastrointestinal tract. Measurement of the reduction in attached pathogens can be demonstrated, for example, by biopsy samples, or the reduction can be measured indirectly, for example, by measuring the amount of pathogen in the stool of a mammalian host.

[0060] As used herein, the term "inhibit" (or grammatical variations thereof) includes both complete and partial inhibition.

[0061] As used herein, the term "multiple bacteria" refers to a combination of two or more bacteria. A "combination" of two or more bacteria includes the physical coexistence of two bacteria in either the same substance or product, or a physically associated product, as well as the temporal co-administration or co-localization of two bacteria.

[0062] In the case of nucleic acids, the term "substantial homology" indicates that two nucleic acids, or designated sequences thereof, when optimally aligned and compared, are identical in at least about 80% of the nucleotides, at least about 90%-95% of the nucleotides, or at least about 98%-99.5%, with appropriate nucleotide insertions or deletions. In some embodiments, two nucleic acids (e.g., 16S rDNA sequences) share substantial homology if they have at least about 95%, at least about 95.5%, at least about 96%, at least about 96.5%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.1%, at least about 99.2%, at least about 99.3%, at least about 99.4%, at least about 99.5%, at least about 99.6%, at least about 99.7%, at least about 99.8%, or at least about 99.9% sequence identity. In some embodiments, bacteria that share substantial homology within their 16S rDNA sequences can be considered to be of the same species. In some embodiments, bacteria that are of the same species share one or more functional characteristics (e.g., as described herein). Alternatively, substantial homology exists when the segments will hybridize under selective hybridization conditions, to the complement of the strand.

[0063] In the context of polypeptides, the term "substantial homology" indicates that two polypeptides, or their designated sequences, when optimally aligned and compared, are identical in at least about 80% of the amino acids, at least about 90%-95%, or at least about 98%-99.5% of the amino acids, with appropriate amino acid insertions or deletions.

[0064] The percent identity between two sequences is a function of the number of identical positions shared by the sequences (i.e., percent homology = number of identical positions / total number of positions x 100), taking into account the number of gaps and the length of each gap that need to be introduced for optimal alignment of the two sequences. The comparison of sequences and determination of percent identity between two sequences can be accomplished using a mathematical algorithm, as described in the non-limiting examples below.

[0065] The percent identity between two nucleotide sequences can be determined using the GAP program in the GCG software package (available at worldwideweb.gcg.com) using the NWSgapdna.CMP matrix and a gap weight of 40, 50, 60, 70, or 80 and a length weight of 1, 2, 3, 4, 5, or 6. The percent identity between two nucleotide or amino acid sequences can also be determined using the algorithm of E. Meyers and W. Miller (CABIOS, 4:11-17 (1989)) as incorporated into the ALIGN program (version 2.0), using a PAM120 weight residue table, a gap length penalty of 12, and a gap penalty of 4. Additionally, percent identity between two amino acid sequences can be determined using the Needleman and Wunsch (J. Mol. Biol. (48):444-453 (1970)) algorithm incorporated into the GAP program of the GCG software package (available at worldwideweb.gcg.com), using either a Blossum 62 matrix or a PAM250 matrix, with a gap weight of 16, 14, 12, 10, 8, 6, or 4 and a length weight of 1, 2, 3, 4, 5, or 6.

[0066] The nucleic acid and protein sequences described herein can also be used as "query sequences" to search public databases, for example, to identify related sequences. Such searches can be performed using the NBLAST and XBLAST programs (version 2.0) of Altschul, et al. (1990) J. Mol. Biol. 215:403-10. BLAST nucleotide searches can be performed with the NBLAST program, score = 100, wordlength = 12, to obtain nucleotide sequences homologous to the nucleic acid molecules described herein. BLAST protein searches can be performed with the XBLAST program, score = 50, wordlength = 3, to obtain amino acid sequences homologous to the protein molecules described herein. To obtain gapped alignments for comparison purposes, Gapped BLAST can be utilized as described in Altschul et al. (1997) Nucleic Acids Res. 25(17):3389-3402. When utilizing BLAST and Gapped BLAST programs, the default parameters of the respective programs (e.g., XBLAST and NBLAST) can be used. See worldwideweb.ncbi.nlm.nih.gov. Other methods to determine identity known in the art can be used.

[0067] As used herein, the terms "ug" and "uM" are used interchangeably with "μg" and "μM", respectively.

[0068] II. Bacterial (Microbiome) Composition Some embodiments of the present disclosure relate to compositions comprising a plurality of bacteria ("bacterial compositions"), which comprise one or more OTUs or bacterial species and are useful for the treatment and / or prevention of a wide range of diseases and disorders (e.g., those described herein). Unless otherwise indicated, the plurality of bacteria may comprise any suitable bacteria useful for the treatment and / or prevention of the diseases and disorders described herein. For example, in some embodiments, the plurality of bacteria comprises bacteria fermented from culture ("cultured bacteria"), including bacteria derived directly from the feces of a healthy human or biologically pure cultures. As used herein, "bacteria derived directly from the feces of a healthy human subject" (or equivalent) refers to bacteria that have not been cultured. Thus, in some embodiments, the bacterial compositions provided herein comprise a plurality of bacteria, each of which is derived directly from the feces of a human (e.g., a healthy human subject). In some embodiments, the bacterial compositions provided herein comprise a plurality of bacteria, each of which is cultured. In some embodiments, the plurality of bacteria comprises a mixture of bacteria derived directly from the feces of a healthy human subject and cultured bacteria. In some embodiments, the plurality of bacteria useful in the present disclosure comprises spores, vegetative cells, or both. Thus, in some embodiments, the bacterial compositions provided herein comprise a plurality of bacteria, wherein one or more of the plurality of bacteria are in the spore form. In some embodiments, the bacterial compositions provided herein comprise a plurality of bacteria, wherein each of the plurality of bacteria is in the spore form. In some embodiments, such bacterial compositions do not comprise any vegetative cells. In some embodiments, the bacterial compositions provided herein comprise a plurality of bacteria, wherein one or more of the plurality of bacteria are in the vegetative form. In some embodiments, the bacterial compositions provided comprise a plurality of bacteria, wherein one or more of the plurality of bacteria are in the spore form and one or more of the plurality of bacteria are in the vegetative form.

[0069] Non-limiting examples of bacteria useful in the present disclosure include those that exhibit one or more of the following characteristics: one or more characteristics selected from the following: (1) capable of colonization (long-term and / or transient) when administered to a subject; (2) capable of anti-inflammatory activity (e.g., inhibiting TNF-α-induced IL-8 secretion in epithelial cells in vitro, ability to down-regulate expression of inflammatory genes (e.g., CXCL1, CXCL2, CXCL3, CXCL11, ICAM1)); (3) inability to induce pro-inflammatory activity; (4) inability to produce secondary bile acids (e.g., 7α-dehydrogenase); (5) capable of producing tryptophan metabolites (e.g., indole, 3-methylindole, indolepropionic acid); (6) capable of restoring and / or maintaining epithelial integrity (e.g., as determined by a primary epithelial cell monolayer barrier integrity assay); (7) capable of producing short-chain fatty acids (e.g., butyrate, propionate); (8) capable of inhibiting HDAC activity; (9) capable of producing medium-chain fatty acids (e.g., valerate, hexanoate); (10) capable of expressing catalase activity; (11) capable of inhibiting HDAC activity; (12) capable of producing vitamin B (e.g., thiamine (B1) and / or pyridoxamine (B6)), (13) capable of reducing fecal calprotectin levels, (14) inability to activate the toll-like receptor pathway (e.g., TLR4 or TLR5), (15) capable of activating the toll-like receptor pathway (e.g., TLR2), (16) capable of restoring colonization resistance, (17) capable of utilizing a wide range of carbon sources, (18) capable of reducing the carriage of VRE pathogens, (19) capable of reducing the carriage of CRE pathogens, (20) capable of preventing E. coli disease. (21) can reduce the carriage of pathogens, (22) can reduce the expression of claudin-2, (23) can associate with healthy human gut microbiota, (24) cannot associate with toxin and hemolysin genes associated with clostridial pathogens and do not produce significant cytopathic effects in vitro, (25) are sensitive to multiple clinically relevant antibiotics, (26) cannot associate with genes likely involved in both the observed antibiotic resistance and transmissibility, (27) can inhibit epithelial cell apoptosis, and (28) can associate with one or more genes (e.g.,(28) downregulating one or more inhibitory receptors (inhibitory receptors) on CD8+ T cells; (29) downregulating genes associated with inflammatory chemokine signaling, NF-κB signaling, TNF family signaling, type I interferon signaling, type II interferon signaling, TLR signaling, lymphocyte trafficking, Th17 cell differentiation, Th1 differentiation, Th2 differentiation, apoptosis, inflammasomes, autophagy, oxidative stress, MHC class I and II antigen presentation, complement, mTor, nod-like receptor signaling, PI3K signaling, or a combination thereof; (29) can increase the expression of one or more genes / proteins associated with CD8+ T cell activation and / or function (e.g., CD45RO, CD69, IL-24, TNF-α, perforin, or IFN-γ); (30) can enhance and / or ameliorate chemotherapeutic drug resistance; (31) can enhance the efficacy of immune checkpoint inhibitor therapy; (32) can promote the recruitment of CD8+ T cells to tumors; (33) can promote the expression of anti-inflammatory IL-10 / IL-11 in macrophages; (34) can induce a similar pathogen defense response in macrophages with less inflammatory response than donor-derived spore-based compositions (i.e., spore-based compositions); (35) can increase the amount of anti-inflammatory mediators (e.g., IL-1 receptor antagonist (IL-1RA), IL-4, IL-10, IL-11, IL-13, TGF-β); (36) can reduce colonic inflammation; (37) can treat and / or prevent diseases or disorders, such as those associated with gastrointestinal dysbiosis; (38) can improve gastrointestinal myelin production in a subject; (39) can increase the diversity of the chromobiome, (40) can improve the integrity of the mucosa and / or epithelial barrier of a subject compared to a reference control (e.g., an untreated patient or a subject before treatment), (41) can promote mucosal healing, (42) can reduce the incidence of infection, (43) can reduce the need for antibiotics in a subject, (44) can increase the amount of infectious disease biomarkers in the stool of a subject, (45) can increase the amount of biomarkers of the administered species in the stool of a subject, (46) can increase the number of administered species in the intestine of a subject (e.g., compared to the number of colony forming units of the administered species), (47) can increase the number of administered species in the intestine of a subject (e.g., compared to the number of administered colony forming units), (48) can increase the number of administered species in the intestine of a subject (e.g., compared to the number of administered colony forming units), (49) can increase the number of administered species in the intestine of a subject (e.g., compared to the number of administered colony forming units), (50) can increase the number of administered species in the intestine of a subject (e.g., compared to the number of administered colony forming units), (60) can increase the number of administered species in the intestine of a subject (e.g., compared to the number of administered colony forming units), (61) can increase the number of administered species in the intestine of a subject (e.g., compared to the number of administered colony forming units), (62) can increase the number of administered species in the intestine of a subject (e.g., compared to the number of administered colony forming units), (63) can increase the number of administered species in the intestine of a subject (e.g., compared to the number of administered colony forming units), (64) can increase the number of administered species in the intestine of a subject (e.g., compared to the number of administered colony forming units), (6(46) capable of targeted delivery of 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9% or all of the administered species (e.g., by encapsulation or by coating one or more dosage components with an enteric polymer); (47) capable of exerting a therapeutic effect following a single administration of a composition or pharmaceutical composition described herein to a subject; (48) capable of co-administration with an additional agent described herein without substantially reducing the therapeutic effect of the administered species; (49) capable of lactulose utilization; (50) comprising a lantibiotic operon; (51) capable of being associated with decreased abundance in patients with liver disease (e.g., cirrhosis); or (52) any combination thereof.

[0070] As will be apparent from the present disclosure, when the plurality of bacteria comprises one or more bacterial species exhibiting one or more of the above-described characteristics, in some embodiments, the plurality of bacteria also exhibits one or more of the above-described characteristics. Thus, in some embodiments, the bacterial compositions provided herein include a plurality of bacteria exhibiting one, two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen ... thirteen, fourteen, fifteen, six, seven, eight, nine, ten, ten, eighteen, nineteen, twenty, twenty-one, twenty-two, twenty-three, twenty-four, twenty-five, twenty-six, twenty-seven, twenty-eight, twenty-nine, thirty, thirty-one, thirty-two, thirty-three, thirty-four, thirty-five, thirty-six, thirty-seven, thirty-eight, thirty-nine, forty-one, fourteen, fourteen, fourteen, fourteen, five, fourteen, six, four-seven, four-eight, four-nine, fifty, five-one, or all of the above-described characteristics. In some embodiments, the plurality of bacteria exhibits one of the characteristics provided above. In some embodiments, the plurality of bacteria exhibit two of the characteristics provided above. In some embodiments, the plurality of bacteria exhibit three of the characteristics provided above. In some embodiments, the plurality of bacteria exhibit three of the characteristics provided above. In some embodiments, the plurality of bacteria exhibit four of the characteristics provided above. In some embodiments, the plurality of bacteria exhibit five of the characteristics provided above. In some embodiments, the plurality of bacteria exhibit six of the characteristics provided above. In some embodiments, the plurality of bacteria exhibit seven of the characteristics provided above. In some embodiments, the plurality of bacteria exhibit eight of the characteristics provided above. In some embodiments, the plurality of bacteria exhibit nine of the characteristics provided above. In some embodiments, the plurality of bacteria exhibit ten of the characteristics provided above. In some embodiments, the plurality of bacteria exhibit eleven of the characteristics provided above. In some embodiments, the plurality of bacteria exhibit twelfth of the characteristics provided above. In some embodiments, the plurality of bacteria exhibit thirteen of the characteristics provided above. In some embodiments, the plurality of bacteria exhibit fourteen of the characteristics provided above. In some embodiments, the plurality of bacteria exhibit fifteen of the characteristics provided above. In some embodiments, the plurality of bacteria exhibits 16 of the characteristics provided above. In some embodiments, the plurality of bacteria exhibits 17 of the characteristics provided above. In some embodiments, the plurality of bacteria exhibits 18 of the characteristics provided above. In some embodiments, the plurality of bacteria exhibits 19 of the characteristics provided above.In some embodiments, the plurality of bacteria exhibits 20 of the characteristics provided above. In some embodiments, the plurality of bacteria exhibits 21 of the characteristics provided above. In some embodiments, the plurality of bacteria exhibits 22 of the characteristics provided above. In some embodiments, the plurality of bacteria exhibits 23 of the characteristics provided above. In some embodiments, the plurality of bacteria exhibits 24 of the characteristics provided above. In some embodiments, the plurality of bacteria exhibits 25 of the characteristics provided above. In some embodiments, the plurality of bacteria exhibits 26 of the characteristics provided above. In some embodiments, the plurality of bacteria exhibits 27 of the characteristics provided above. In some embodiments, the plurality of bacteria exhibits 28 of the characteristics provided above. In some embodiments, the plurality of bacteria exhibits 29 of the characteristics provided above. In some embodiments, the plurality of bacteria exhibits 30 of the characteristics provided above. In some embodiments, the plurality of bacteria exhibits 31 of the characteristics provided above. In some embodiments, the plurality of bacteria exhibits 32 of the characteristics provided above. In some embodiments, the plurality of bacteria exhibits 33 of the characteristics provided above. In some embodiments, the plurality of bacteria exhibits 34 of the characteristics provided above. In some embodiments, the plurality of bacteria exhibits 35 of the characteristics provided above. In some embodiments, the plurality of bacteria exhibits 36 of the characteristics provided above. In some embodiments, the plurality of bacteria exhibits 37 of the characteristics provided above. In some embodiments, the plurality of bacteria exhibits 38 of the characteristics provided above. In some embodiments, the plurality of bacteria exhibits 39 of the characteristics provided above. In some embodiments, the plurality of bacteria exhibits 40 of the characteristics provided above. In some embodiments, the plurality of bacteria exhibits 41 of the characteristics provided above. In some embodiments, the plurality of bacteria exhibits 42 of the characteristics provided above. In some embodiments, the plurality of bacteria exhibits 43 of the characteristics provided above. In some embodiments, the plurality of bacteria exhibits 44 of the characteristics provided above. In some embodiments, the plurality of bacteria exhibits 45 of the characteristics provided above. In some embodiments, the plurality of bacteria exhibits 46 of the characteristics provided above. In some embodiments, the plurality of bacteria exhibits 47 of the characteristics provided above.In some embodiments, the plurality of bacteria exhibits 48 of the characteristics provided above. In some embodiments, the plurality of bacteria exhibits 49 of the characteristics provided above. In some embodiments, the plurality of bacteria exhibits 50 of the characteristics provided above. In some embodiments, the plurality of bacteria exhibits all of the characteristics provided above. Bacterial compositions that have been constructed to specifically exhibit one or more of the characteristics described above are also referred to herein as "designed compositions" (DEs) (or variants thereof). Non-limiting examples of designed compositions are provided in Figure 1. Compositions were designed to optimize function using a core strain (i.e., strain core) and a set of R-group additives.

[0071] In some embodiments, the plurality of bacteria was derived from a cultured consortium. In some embodiments, the plurality of bacteria was derived from a spore preparation from a donor.

[0072] In some embodiments, the plurality of bacteria comprises species of bacteria (also referred to herein as "bacterial species") that are capable of colonizing when administered to a subject. For example, in some embodiments, the plurality of bacteria comprises species of bacteria that are capable of long-term colonization when administered to a subject ("long-term colonizers"). In some embodiments, the plurality of bacteria comprises species of bacteria that are capable of transient colonization when administered to a subject ("transient colonizers"). In some embodiments, the plurality of bacteria comprises both long-term and transient colonizers.

[0073] In some embodiments, the plurality of bacteria comprises a bacterial species capable of having anti-inflammatory activity. Non-limiting examples of such anti-inflammatory activity include (a) inhibiting TNF-α-induced IL-8 secretion in epithelial cells in vitro, (b) the ability to down-regulate the expression of inflammatory genes (e.g., CXCL1, CXCL2, CXCL3, CXCL11, ICAM1), or (c) both (a) and (b). Thus, in some embodiments, the plurality of bacteria comprises a bacterial species capable of inhibiting TNF-α-induced IL-8 secretion in epithelial cells in vitro. In some embodiments, the plurality of bacteria comprises a bacterial species capable of down-regulating the expression of one or more inflammatory genes. In some embodiments, the plurality of bacteria comprises both a bacterial species capable of inhibiting TNF-α-induced IL-8 secretion in epithelial cells in vitro and a bacterial species capable of down-regulating the expression of one or more inflammatory genes. In some embodiments, the plurality of bacteria comprises a bacterial species that is capable of both inhibiting TNF-α-induced IL-8 secretion and downregulating expression of one or more inflammatory genes in epithelial cells in vitro, hi some embodiments, the plurality of bacteria comprises a bacterial species that is unable to induce pro-inflammatory activity.

[0074] In some embodiments, the plurality of bacteria comprises bacterial species capable of producing metabolic products useful for treating a disease or disorder described herein. For example, in some embodiments, the plurality of bacteria comprises bacterial species capable of producing secondary bile acids. Non-limiting examples of secondary bile acids include 7α-dehydroxylase and bile salt hydrolase activity. In some embodiments, the plurality of bacteria comprises bacterial species capable of producing tryptophan metabolites. Non-limiting examples of tryptophan metabolites include indole, 3-methylindole, and indolepropionic acid. In some embodiments, the plurality of bacteria comprises bacterial species capable of producing short-chain fatty acids. Non-limiting examples of short-chain fatty acids include butyrate and propionate. In some embodiments, the plurality of bacteria comprises bacterial species capable of producing medium-chain fatty acids. Non-limiting examples of medium-chain fatty acids include valerate and hexanoate. In some embodiments, the plurality of bacteria comprises bacterial species capable of producing vitamin B. Non-limiting examples of B vitamins include thiamine (B1) and pyridoxamine (B6). Thus, in some embodiments, a bacterial composition useful in the present disclosure comprises a plurality of bacteria, wherein the plurality of bacteria comprises one or more bacterial species capable of producing (a) secondary bile acids, (b) tryptophan metabolites, (c) short-chain fatty acids, (d) medium-chain fatty acids, (e) vitamin B, or (f) any combination of (a)-(e).

[0075] In some embodiments, the plurality of bacteria comprises a bacterial species capable of restoring and / or maintaining epithelial integrity, e.g., as determined by a primary epithelial cell monolayer barrier integrity assay. In some embodiments, the plurality of bacteria comprises a bacterial species capable of inhibiting HDAC activity. In some embodiments, the plurality of bacteria comprises a bacterial species capable of expressing catalase activity. In some embodiments, the plurality of bacteria comprises a bacterial species capable of possessing alpha-fucosidase activity. In some embodiments, the plurality of bacteria comprises a bacterial species capable of reducing fecal calprotectin levels. In some embodiments, the plurality of bacteria comprises a bacterial species incapable of activating a toll-like receptor pathway (e.g., TLR4 or TLR5). In some embodiments, the plurality of bacteria comprises a bacterial species capable of activating a toll-like receptor pathway (e.g., TLR2). In some embodiments, the plurality of bacteria comprises a bacterial species capable of restoring colonization resistance. In some embodiments, the plurality of bacteria comprises a bacterial species capable of utilizing a wide range of carbon sources. In some embodiments, the plurality of bacteria comprises a bacterial species capable of reducing carriage of a VRE pathogen. In some embodiments, the plurality of bacteria comprises a bacterial species capable of reducing carriage of CRE (e.g., carbapenem-resistant Klebsiella pneumonia) pathogens. In some embodiments, the plurality of bacteria comprises a bacterial species capable of reducing clearance of E. coli (e.g., carbapenem-resistant Escherichia coli) pathogens. In some embodiments, the plurality of bacteria comprises a bacterial species capable of reducing expression of claudin-2. In some embodiments, the plurality of bacteria comprises a bacterial species associated with a healthy human gut microbiome. In some embodiments, the plurality of bacteria comprises a bacterial species associated with reduced abundance in patients with liver disease (e.g., cirrhosis). In some embodiments, the plurality of bacteria comprises a bacterial species that fails to associate with toxin and hemolysin genes associated with Clostridial pathogens and does not produce significant cytopathic effects in vitro. In some embodiments, the plurality of bacteria comprises a bacterial species that is susceptible to multiple clinically relevant antibiotics. In some embodiments, the plurality of bacteria comprises a bacterial species that fails to associate with genes likely involved in both observed antibiotic resistance and transmissibility. In some embodiments, the plurality of bacteria comprises bacterial species capable of inhibiting epithelial cell apoptosis.In some embodiments, the plurality of bacteria comprises bacterial species that can down-regulate one or more genes that are induced in IFN-γ-treated colon organoids.Non-limiting examples of such genes include genes related to inflammatory chemokine signaling, NF-κB signaling, TNF family signaling, type I interferon signaling, type II interferon signaling, TLR signaling, lymphocyte trafficking, Th17 cell differentiation, Th1 differentiation, Th2 differentiation, apoptosis, inflammasome, autophagy, oxidative stress, MHC class I and II antigen presentation, complement, mTor, nod-like receptor signaling, PI3K signaling, or combinations thereof.In some embodiments, the plurality of bacteria comprises bacterial species that can reduce the expression of one or more inhibitory receptors on CD8+ T cells.Non-limiting examples of inhibitory receptors include TIGIT, TIM-3, and LAG-3.In some embodiments, the plurality of bacteria comprises bacterial species that can increase the expression of one or more genes / proteins that are related to CD8+ T cell activation and / or function. Non-limiting examples of such genes include CD45RO, CD69, IL-24, TNF-α, perforin, and IFN-γ. In some embodiments, the plurality of bacteria is capable of enhancing and / or ameliorating resistance to chemotherapeutic agents (e.g., those that may cause and / or be associated with neutropenia). Non-limiting examples of such chemotherapeutic agents are provided elsewhere in this application. In some embodiments, the plurality of bacteria comprises a bacterial species capable of inducing an IL-10 / IL-6 cytokine ratio in macrophages that favors anti-inflammatory IL-10. In some embodiments, the plurality of bacteria comprises a bacterial species capable of inducing a similar pathogen defense response in macrophages with less inflammatory response than a donor-derived spore-based composition (i.e., a spore-based composition). In some embodiments, the plurality of bacteria comprises a bacterial species capable of increasing the amount of an anti-inflammatory mediator. Non-limiting examples of such anti-inflammatory mediators include IL-1 receptor antagonist (IL-1RA), IL-4, IL-10, IL-11, IL-13, and TGF-β. In some embodiments, the plurality of bacteria comprises bacterial species that can reduce colonic inflammation.In some embodiments, the plurality of bacteria comprises bacterial species capable of treating and / or preventing a disease or disorder, such as one associated with gastrointestinal dysbiosis. In some embodiments, the plurality of bacteria comprises bacterial species capable of increasing the diversity of the gastrointestinal microbiome of a subject. In some embodiments, the plurality of bacteria comprises bacterial species capable of improving the integrity of the mucosal and / or epithelial barrier of a subject compared to a reference control (e.g., an untreated patient or a subject prior to treatment). In some embodiments, the plurality of bacteria comprises bacterial species capable of promoting mucosal healing. In some embodiments, the plurality of bacteria comprises bacterial species capable of reducing the incidence of infection. In some embodiments, the plurality of bacteria comprises bacterial species capable of reducing the need for antibiotics in a subject. In some embodiments, the plurality of bacteria comprises bacterial species capable of reducing the amount of an infectious disease biomarker in the stool of a subject. In some embodiments, the plurality of bacteria comprises bacterial species capable of increasing the amount of a biomarker of the administered species in the stool of a subject. In some embodiments, the plurality of bacteria comprises bacterial species capable of targeted delivery of many (e.g., 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9% of the administered species relative to the number of colony forming units administered) or all of the species administered to the subject's intestine. In some embodiments, the plurality of bacteria comprises bacterial species capable of exerting a therapeutic effect following a single administration of a composition or pharmaceutical composition described herein to a subject. In some embodiments, the plurality of bacteria comprises bacterial species that can be co-administered with an additional agent described herein without substantially reducing the therapeutic effect of the administered species. In some embodiments, the plurality of bacteria comprises bacterial species that can be co-administered with a carrier or excipient described herein without substantially reducing the therapeutic effect of the administered species. In some embodiments, the plurality of bacteria comprises bacterial species that can utilize lactulose. In some embodiments, the plurality of bacteria comprises a bacterial species that comprises a lantibiotic operon. It will be apparent to one skilled in the art that a bacterial species that comprises a lantibiotic operon may be capable of producing a lantibiotic. Thus, in some embodiments, the plurality of bacteria comprises a bacterial species that is capable of producing a lantibiotic.

[0076] In some embodiments, a bacterial composition useful in the present disclosure comprises a plurality of bacteria, wherein the plurality of bacteria comprises a first bacterial species and a second bacterial species, wherein the first species and the second species are not the same. In some embodiments, the first bacterial species is selected from the following bacterial species: Anaerotruncus colihominis, Blautia coccoides (also referred to herein as "Blautia pseudococcoides"), Blautia hominis, Blautia obeum, Blautia wexlerae, Butyricicoccus sp2 (also referred to herein as "Intestinibacillus massiliensis"), Clostridium aldenense (also referred to herein as "Enterocloster aldenensis"), Clostridium bolteae (also referred to herein as "Enterocloster bolteae"), Clostridium innocuum, Clostridium scindens, Clostridium symbiosum (also referred to herein as "Clostridium transplantifaecale"), Dorea longicatena, Eisenbergiella tayi (also referred to herein as "Eisenbergiella massiliensis), Emergencia timonensis, Erysipelatoclostridium ramosum (also referred to herein as "Thomasclavelia ramosa"), Eubacterium callanderi, Faecalicatena cortorta, Faecalicatena orotica, Flavonifractor plautii, Hungatella effluvii (also referred to herein as "Hungatella hathewayi"), Intestinimonas butyriciproducens, Intestinimonas massiliensis, Lactonifactor longoviformis, Lawsonibacter_sp7 (also referred to herein as "Clostridiumphoceensis), Massilimaliae timonensis, Murimonas intestini, Niameybacter sp1 (also referred to herein as "Niameybacter massiliensis"), Ruminococcaceae NG13 sp6 (also referred to herein as "Clostridium leptum"), or Turicibacter sanguinis. In some embodiments, the second bacterial species is selected from the following bacterial species: Anaerotruncus colihominis, Blautia coccoides, Blautia hominis, Blautia obeum, Blautia wexlerae, Butyricicoccus sp2, Clostridium aldenense, Clostridium bolteae, Clostridium innocuum, Clostridium scindens, Clostridium symbiosum, Dorea longicatena, Eisenbergiella tayi, Emergencia timonensis, Erysipelatoclostridium ramosum, Eubacterium callanderi, Faecalicatena cortorta, Faecalicatena orotica, Flavonifractor plautii, Hungatella effluvii, Intestinimonas butyriciproducens, Intestinimonas massiliensis, Lactonifactor In some embodiments, both the first and second species are selected from: Anaerotruncus colihominis, Blautia coccoides, Blautia hominis, Blautia obeum, Blautiawexlerae, Butyricicoccus sp2, Clostridium aldenense, Clostridium bolteae, Clostridium innocuum, Clostridium scindens, Clostridium symbiosum, Dorea longicatena, Eisenbergiella tayi, Emergencia timonensis, Erysipelatoclostridium ramosum, Eubacterium callanderi, Faecalicatena cortorta, Faecalicatena orotica, Flavonifractor plautii, Hungatella effluvii, Intestinimonas butyriciproducens, Intestinimonas massiliensis, Lactonifactor longoviformis, Lawsonibacter_sp7, Massilimaliae timonensis, Murimonas intestini, Niameybacter sp1, Ruminococcaceae NG13 sp6, or Turicibacter sanguinis.

[0077] Thus, in some embodiments, the bacterial compositions provided herein comprise a plurality of bacteria, wherein the plurality of bacteria comprises one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi. In some embodiments, the plurality of bacteria comprises each of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.

[0078] In some embodiments, the plurality of bacteria further comprises Emergencia timonensis. Thus, in some embodiments, a bacterial composition useful in the present disclosure comprises a plurality of bacteria, which includes Emergencia timonensis and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi. In some embodiments, the plurality of bacteria comprises each of the following: Emergencia timonensis, Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.

[0079] In some embodiments, the plurality of bacteria further comprises Intestinimonas butyriciproducens, Clostridium symbiosum, Clostridium scindens, or Emergencia timonensis. In some embodiments, the plurality of bacteria comprises Intestinimonas butyriciproducens, Clostridium symbiosum, Clostridium scindens, or Emergencia timonensis and one or more of the following: Intestinimonas butyriciproducens and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi. In some embodiments, the plurality of bacteria comprises each of the following: Intestinimonas butyriciproducens, Clostridium symbiosum, Clostridium scindens, Emergencia timonensis, Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.

[0080] In some embodiments, the plurality of bacteria further comprises Intestinimonas butyriciproducens. Thus, in some embodiments, the bacterial composition comprises a plurality of bacteria, which include Intestinimonas butyriciproducens and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi. In some embodiments, the plurality of bacteria comprises each of the following: Intestinimonas butyriciproducens, Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.

[0081] In some embodiments, the plurality of bacteria further comprises Clostridium symbiosum. In some embodiments, the plurality of bacteria comprises Clostridium symbiosum and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi. In some embodiments, the plurality of bacteria comprises each of the following: Clostridium symbiosum, Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.

[0082] In some embodiments, the plurality of bacteria further comprises Clostridium scindens. Thus, in some embodiments, the plurality of bacteria comprises Clostridium scindens and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi. In some embodiments, the plurality of bacteria comprises each of the following: Clostridium scindens, Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.

[0083] In some embodiments, the plurality of bacteria further comprises Faecalicatena cortorta or Lactonifactor longoviformis. Thus, in some embodiments, the plurality of bacteria comprises Faecalicatena cortorta or Lactonifactor longoviformis and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi. In some embodiments, the plurality of bacteria includes each of the following: Faecalicatena cortorta, Lactonifactor longoviformis, Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.

[0084] In some embodiments, the plurality of bacteria further comprises Faecalicatena cortorta. In such embodiments, the plurality of bacteria comprises Faecalicatena cortorta and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi. In some embodiments, the plurality of bacteria includes each of the following: Faecalicatena cortorta, Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.

[0085] In some embodiments, the plurality of bacteria further comprises Lactonifactor longoviformis. In some embodiments, the plurality of bacteria comprises Lactonifactor longoviformis and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi. In some embodiments, the plurality of bacteria comprises each of the following: Lactonifactor longoviformis, Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi.

[0086] In some embodiments, the plurality of bacteria further comprises Massilimaliae timonensis, Hungatella effluvii, or Butyricicoccus sp 2. In some embodiments, the plurality of bacteria comprises Massilimaliae timonensis, Hungatella effluvii, or Butyricicoccus sp 2 and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi. In some embodiments, the plurality of bacteria comprises each of the following: Massilimaliae timonensis, Hungatella effluvii, Butyricicoccus sp2, Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi.

[0087] In some embodiments, the plurality of bacteria further comprises Massilimaliae timonensis. In some embodiments, the plurality of bacteria comprises Massilimaliae timonensis and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi. In some embodiments, the plurality of bacteria comprises each of the following: Massilimaliae timonensis, Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.

[0088] In some embodiments, the plurality of bacteria further comprises Hungatella effluvii. In some embodiments, the plurality of bacteria comprises Hungatella effluvii and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi. In some embodiments, the plurality of bacteria comprises each of the following: Hungatella effluvii, Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi.

[0089] In some embodiments, the plurality of bacteria further comprises Butyricicoccus sp 2. In some embodiments, the plurality of bacteria comprises Butyricicoccus sp 2 and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi. In some embodiments, the plurality of bacteria comprises each of the following: Butyricicoccus sp2, Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.

[0090] In some embodiments, the plurality of bacteria further comprises Intestinimonas massiliensis, Niameybacter sp1, or Turicibacter sanguinis. In some embodiments, the plurality of bacteria comprises Intestinimonas massiliensis, Niameybacter sp1, or Turicibacter sanguinis and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi. In some embodiments, the plurality of bacteria comprises each of the following: Intestinimonas massiliensis, Niameybacter sp1, Turicibacter sanguinis, Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.

[0091] In some embodiments, the plurality of bacteria further comprises Intestinimonas massiliensis. In some embodiments, the plurality of bacteria comprises Intestinimonas massiliensis and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi. In some embodiments, the plurality of bacteria comprises each of the following: Intestinimonas massiliensis, Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.

[0092] In some embodiments, the plurality of bacteria further comprises Niameybacter sp 1. In some embodiments, the plurality of bacteria comprises Niameybacter sp 1 and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi. In some embodiments, the plurality of bacteria includes each of the following: Niameybacter sp1, Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.

[0093] In some embodiments, the plurality of bacteria further comprises Turicibacter sanguinis. In some embodiments, the plurality of bacteria comprises Turicibacter sanguinis and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi. In some embodiments, the plurality of bacteria comprises each of the following: Turicibacter sanguinis and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.

[0094] In some embodiments, the plurality of bacteria further comprises Ruminococcaceae NG13 sp6. In some embodiments, the plurality of bacteria comprises Ruminococcaceae NG13 sp6 and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi. In some embodiments, the plurality of bacteria comprises each of the following: Ruminococcaceae NG13 sp6, Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.

[0095] In some embodiments, the plurality of bacteria further comprises Dorea longicatena. In some embodiments, the plurality of bacteria comprises Dorea longicatena and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi. In some embodiments, the plurality of bacteria comprises each of the following: Dorea longicatena, Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.

[0096] In some embodiments, the plurality of bacteria further comprises Blautia obeum. In some embodiments, the plurality of bacteria comprises Blautia obeum and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi. In some embodiments, the plurality of bacteria comprises each of the following: Blautia obeum, Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.

[0097] In some embodiments, the plurality of bacteria further comprises Lawsonibacter_sp 7. In some embodiments, the plurality of bacteria comprises Lawsonibacter_sp 7 and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi. In some embodiments, the plurality of bacteria comprises each of the following: Lawsonibacter_sp7, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.

[0098] In some embodiments, the plurality of bacteria further comprises Blautia hominis. In some embodiments, the plurality of bacteria comprises Blautia hominis and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi. In some embodiments, the plurality of bacteria comprises each of the following: Blautia hominis, Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.

[0099] In some embodiments, the plurality of bacteria further comprises Blautia wexlerae. In some embodiments, the plurality of bacteria comprises Blautia wexlerae and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi. In some embodiments, the plurality of bacteria comprises each of the following: Blautia wexlerae, Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.

[0100] In some embodiments, the plurality of bacteria further comprises Eubacterium callanderi. In some embodiments, the plurality of bacteria comprises Eubacterium callanderi and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi. In some embodiments, the plurality of bacteria comprises each of the following: Eubacterium callanderi, Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.

[0101] In some embodiments, the plurality of bacteria includes (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Emergencia timonensis, (10) Clostridium aldenense, (11) Intestinimonas butyriciproducens, (12) Eisenbergiella tayi, (13) Clostridium symbiosum, and (14) Clostridium scindens. In some embodiments, the plurality of bacteria consists essentially of (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Emergencia timonensis, (10) Clostridium aldenense, (11) Intestinimonas butyriciproducens, (12) Eisenbergiella tayi, (13) Clostridium symbiosum, and (14) Clostridium scindens.In some embodiments, the plurality of bacteria consists of (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Emergencia timonensis, (10) Clostridium aldenense, (11) Intestinimonas butyriciproducens, (12) Eisenbergiella tayi, (13) Clostridium symbiosum, and (14) Clostridium scindens.

[0102] In some embodiments, the plurality of bacteria includes (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, and (14) Emergencia timonensis. In some embodiments, the plurality of bacteria consists essentially of (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, and (14) Emergencia timonensis.In some embodiments, the plurality of bacteria consists of (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, and (14) Emergencia timonensis.

[0103] In some embodiments, the plurality of bacteria are (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergencia timonensis, (15) Faecalicatena cortorta, (16) Lactonifactor longoviformis, and (17) Ruminococcaceae NG13 Contains sp6.

[0104] In some embodiments, the plurality of bacteria are (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergencia timonensis, (15) Faecalicatena cortorta, (16) Lactonifactor longoviformis, and (17) Ruminococcaceae NG13 Consists essentially of sp6. In some embodiments, the plurality of bacteria are (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergencia timonensis, (15) Faecalicatena cortorta, (16) Lactonifactor longoviformis, and (17) Ruminococcaceae NG13 It consists of sp6.

[0105] In some embodiments, the plurality of bacteria includes (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergencia timonensis, (15) Faecalicatena cortorta, (16) Lactonifactor longoviformis, (17) Massilimaliae timonensis, (18) Hungatella effluvii, and (19) Butyricicoccus sp2.In some embodiments, the plurality of bacteria are (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergencia timonensis, (15) Faecalicatena cortorta, (16) Lactonifactor longoviformis, (17) Massilimaliae timonensis, (18) Hungatella effluvii, and (19) Butyricicoccus sp2.In some embodiments, the plurality of bacteria consists of (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergencia timonensis, (15) Faecalicatena cortorta, (16) Lactonifactor longoviformis, (17) Massilimaliae timonensis, (18) Hungatella effluvii, and (19) Butyricicoccus sp2.

[0106] In some embodiments, the plurality of bacteria are: (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergencia timonensis, (15) Faecalicatena cortorta, (16) Lactonifactor longoviformis, (17) Massilimaliae timonensis, (18) Hungatella effluvii, (19) Butyricicoccus sp2, (20) Intestinimonas massiliensis, (21) Niameybacter sp1, and (22) Turicibacter including bloodIn some embodiments, the plurality of bacteria consists essentially of (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergencia timonensis, (15) Faecalicatena cortorta, (16) Lactonifactor longoviformis, (17) Massilimaliae timonensis, (18) Hungatella effluvii, (19) Butyricicoccus sp2, (20) Intestinimonas massiliensis, (21) Niameybacter sp1, and (22) Turicibacter sanguinis.In some embodiments, the plurality of bacteria are: (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergencia timonensis, (15) Faecalicatena cortorta, (16) Lactonifactor longoviformis, (17) Massilimaliae timonensis, (18) Hungatella effluvii, (19) Butyricicoccus sp2, (20) Intestinimonas massiliensis, (21) Niameybacter sp1, and (22) Turicibacter consisting of blood

[0107] In some embodiments, the plurality of bacteria includes (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Emergencia timonensis, (10) Clostridium aldenense, (11) Eisenbergiella tayi, (12) Dorea longicatena, and (13) Blautia obeum. In some embodiments, the plurality of bacteria consists essentially of (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Emergencia timonensis, (10) Clostridium aldenense, (11) Eisenbergiella tayi, (12) Dorea longicatena, and (13) Blautia obeum.In some embodiments, the plurality of bacteria consists of (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Emergencia timonensis, (10) Clostridium aldenense, (11) Eisenbergiella tayi, (12) Dorea longicatena, and (13) Blautia obeum.

[0108] In some embodiments, the plurality of bacteria includes (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergencia timonensis, (15) Blautia obeum, and (16) Lawsonibacter_sp7. In some embodiments, the plurality of bacteria consists essentially of (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergencia timonensis, (15) Blautia obeum, and (16) Lawsonibacter_sp7.In some embodiments, the plurality of bacteria consists of (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergencia timonensis, (15) Blautia obeum, and (16) Lawsonibacter_sp7.

[0109] In some embodiments, the plurality of bacteria are (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergencia timonensis, (15) Faecalicatena cortorta, (16) Lactonifactor longoviformis, (17) Ruminococcaceae NG13 sp6, (18) Blautia obeum, and (19) Lawsonibacter_sp7.In some embodiments, the plurality of bacteria are (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergencia timonensis, (15) Faecalicatena cortorta, (16) Lactonifactor longoviformis, (17) Ruminococcaceae NG13 sp6, (18) Blautia obeum, and (19) Lawsonibacter_sp7.In some embodiments, the plurality of bacteria are (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergencia timonensis, (15) Faecalicatena cortorta, (16) Lactonifactor longoviformis, (17) Ruminococcaceae NG13 sp6, (18) Blautia obeum, and (19) Lawsonibacter_sp7.

[0110] In some embodiments, the plurality of bacteria includes (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, and (13) Emergencia timonensis. In some embodiments, the plurality of bacteria consists essentially of (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, and (13) Emergencia timonensis.In some embodiments, the plurality of bacteria consists of (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, and (13) Emergencia timonensis.

[0111] In some embodiments, the plurality of bacteria includes (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergencia timonensis, (15) Faecalicatena cortorta, (16) Lactonifactor longoviformis, (17) Intestinimonas massiliensis, (18) Niameybacter sp1, and (19) Turicibacter sanguinis.In some embodiments, the plurality of bacteria are (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergencia timonensis, (15) Faecalicatena cortorta, (16) Lactonifactor longoviformis, (17) Intestinimonas massiliensis, (18) Niameybacter sp1, and (19) Turicibacter sanguinis.In some embodiments, the plurality of bacteria consists of (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergencia timonensis, (15) Faecalicatena cortorta, (16) Lactonifactor longoviformis, (17) Intestinimonas massiliensis, (18) Niameybacter sp1, and (19) Turicibacter sanguinis.

[0112] In some embodiments, the plurality of bacteria includes (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia hominis, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Emergencia timonensis, (10) Clostridium aldenense, (11) Eisenbergiella tayi, (12) Clostridium scindens, (13) Dorea longicatena, (14) Blautia obeum, (15) Blautia wexlerae, and (16) Eubacterium callanderi. In some embodiments, the plurality of bacteria consists essentially of (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia hominis, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Emergencia timonensis, (10) Clostridium aldenense, (11) Eisenbergiella tayi, (12) Clostridium scindens, (13) Dorea longicatena, (14) Blautia obeum, (15) Blautia wexlerae, and (16) Eubacterium callanderi.In some embodiments, the plurality of bacteria consists of (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia hominis, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Emergencia timonensis, (10) Clostridium aldenense, (11) Eisenbergiella tayi, (12) Clostridium scindens, (13) Dorea longicatena, (14) Blautia obeum, (15) Blautia wexlerae, and (16) Eubacterium callanderi.

[0113] In some embodiments, Anaerotruncus colihominis comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, or SEQ ID NO:81. In some embodiments, Anaerotruncus colihominis comprises a 16S rDNA sequence set forth in SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, or SEQ ID NO:81. In some embodiments, Blautia coccoides comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, or SEQ ID NO:78. In some embodiments, Blautia coccoides comprises a 16S rDNA sequence set forth in SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, or SEQ ID NO:78. In some embodiments, Blautia hominis comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:29, SEQ ID NO:32, SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, or SEQ ID NO:37. In some embodiments, Blautia hominis comprises a 16S rDNA sequence set forth in SEQ ID NO:29, SEQ ID NO:32, SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, or SEQ ID NO:37. In some embodiments, Blautia obeum comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:26, SEQ ID NO:158, SEQ ID NO:159, SEQ ID NO:160, SEQ ID NO:161, SEQ ID NO:162, or SEQ ID NO:163.In some embodiments, Blautia obeum comprises a 16S rDNA sequence set forth in SEQ ID NO:26, SEQ ID NO:158, SEQ ID NO:159, SEQ ID NO:160, SEQ ID NO:161, SEQ ID NO:162, or SEQ ID NO: 163. In some embodiments, Blautia wexlerae comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:30, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41, SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO:166, SEQ ID NO:167, SEQ ID NO:168, SEQ ID NO:169, SEQ ID NO:170, SEQ ID NO:171, or SEQ ID NO:172. In some embodiments, Blautia wexlerae comprises a 16S rDNA sequence set forth in SEQ ID NO:30, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41, SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO:166, SEQ ID NO:167, SEQ ID NO:168, SEQ ID NO:169, SEQ ID NO:170, SEQ ID NO:171, or SEQ ID NO:172. In some embodiments, Butyricicoccus sp2 comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:20 or SEQ ID NO:132. In some embodiments, Butyricicoccus sp2 comprises a 16S rDNA sequence set forth in SEQ ID NO:20 or SEQ ID NO:132. In some embodiments, Clostridium aldenense comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104. In some embodiments, Clostridium aldenense comprises a 16S rDNA sequence set forth in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104.In some embodiments, Clostridium bolteae comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:2, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:69, or SEQ ID NO:70. In some embodiments, Clostridium bolteae comprises a 16S rDNA sequence set forth in SEQ ID NO:2, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:69, or SEQ ID NO:70. In some embodiments, Clostridium innocuum comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:1, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, or SEQ ID NO:65. In some embodiments, Clostridium innocuum comprises a 16S rDNA sequence set forth in SEQ ID NO:1, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, or SEQ ID NO:65. In some embodiments, Clostridium scindens comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:14, SEQ ID NO:111, SEQ ID NO:112, SEQ ID NO:113, or SEQ ID NO:114. In some embodiments, Clostridium scindens comprises a 16S rDNA sequence set forth in SEQ ID NO:14, SEQ ID NO:111, SEQ ID NO:112, SEQ ID NO:113, or SEQ ID NO:114. In some embodiments, the Clostridium symbiosum comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 13 or SEQ ID NO: 110. In some embodiments, the Clostridium symbiosum comprises a 16S rDNA sequence set forth in SEQ ID NO: 13 or SEQ ID NO: 110.In some embodiments, Dorea longicatena further comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:25, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, SEQ ID NO:54, SEQ ID NO:55, SEQ ID NO:56, SEQ ID NO:57, SEQ ID NO:58, SEQ ID NO:59, SEQ ID NO:60, SEQ ID NO:152, SEQ ID NO:153, SEQ ID NO:154, SEQ ID NO:155, SEQ ID NO:156, or SEQ ID NO:157. In some embodiments, Dorea longicatena comprises a 16S rDNA sequence set forth in SEQ ID NO:25, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, SEQ ID NO:54, SEQ ID NO:55, SEQ ID NO:56, SEQ ID NO:57, SEQ ID NO:58, SEQ ID NO:59, SEQ ID NO:60, SEQ ID NO:152, SEQ ID NO:153, SEQ ID NO:154, SEQ ID NO:155, SEQ ID NO:156, or SEQ ID NO:157. In some embodiments, Eisenbergiella tayi comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109. In some embodiments, Eisenbergiella tayi comprises a 16S rDNA sequence set forth in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109. In some embodiments, Emergencia timonensis comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 9, SEQ ID NO: 97, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 15, SEQ ID NO: 115, or SEQ ID NO: 116. In some embodiments, the Emergencia timonensis comprises the 16S rDNA sequence set forth in SEQ ID NO:9, SEQ ID NO:97, SEQ ID NO:98, SEQ ID NO:99, SEQ ID NO:15, SEQ ID NO:115, or SEQ ID NO:116.In some embodiments, Erysipelatoclostridium ramosum comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:7, SEQ ID NO:87, SEQ ID NO:88, SEQ ID NO:89, SEQ ID NO:90, or SEQ ID NO:91. In some embodiments, Erysipelatoclostridium ramosum comprises a 16S rDNA sequence set forth in SEQ ID NO:7, SEQ ID NO:87, SEQ ID NO:88, SEQ ID NO:89, SEQ ID NO:90, or SEQ ID NO:91. In some embodiments, the Eubacterium callanderi further comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:31, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:173, SEQ ID NO:174, SEQ ID NO:175, SEQ ID NO:176, or SEQ ID NO: 177. In some embodiments, the Eubacterium callanderi comprises a 16S rDNA sequence set forth in SEQ ID NO:31, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:173, SEQ ID NO:174, SEQ ID NO:175, SEQ ID NO:176, or SEQ ID NO:177. In some embodiments, Faecalicatena cortorta comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 16, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 119, or SEQ ID NO: 120. In some embodiments, Faecalicatena cortorta comprises a 16S rDNA sequence set forth in SEQ ID NO: 16, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 119, or SEQ ID NO: 120.In some embodiments, Faecalicatena orotica comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:8, SEQ ID NO:92, SEQ ID NO:93, SEQ ID NO:94, SEQ ID NO:95, SEQ ID NO:96. In some embodiments, Faecalicatena orotica comprises a 16S rDNA sequence set forth in SEQ ID NO:8, SEQ ID NO:92, SEQ ID NO:93, SEQ ID NO:94, SEQ ID NO:95, or SEQ ID NO:96. In some embodiments, Flavonifractor plautii comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:3. In some embodiments, Flavonifractor plautii comprises a 16S rDNA sequence set forth in SEQ ID NO:3. In some embodiments, the Hungatella effluvia is SEQ ID NO: 19, SEQ ID NO: 126, SEQ ID NO: 127, ... In some embodiments, the Hungatella effluvia comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:128, SEQ ID NO:129, SEQ ID NO:130, or SEQ ID NO:131. In some embodiments, the Hungatella effluvia comprises a 16S rDNA sequence set forth in SEQ ID NO:19, SEQ ID NO:126, SEQ ID NO:127, SEQ ID NO:128, SEQ ID NO:129, SEQ ID NO:130, or SEQ ID NO:131. In some embodiments, the Intestinimonas butyriciproducens comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:11 or SEQ ID NO:105. In some embodiments, the Intestinimonas butyriciproducens comprises a 16S rDNA sequence set forth in SEQ ID NO:11 or SEQ ID NO:105. In some embodiments, Intestinimonas massiliensis comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:21 or SEQ ID NO:133. In some embodiments, Intestinimonas massiliensis comprises a 16S rDNA sequence set forth in SEQ ID NO:21 or SEQ ID NO:133. In some embodiments, Lactonifactor longoviformis comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:17, SEQ ID NO:28, or SEQ ID NO:165. In some embodiments, Lactonifactor longoviformis comprises a 16S rDNA sequence set forth in SEQ ID NO:17, SEQ ID NO:28, or SEQ ID NO:165. In some embodiments, Lactonifactor longoviformis comprises the 16S rDNA sequence set forth in SEQ ID NO:17, SEQ ID NO:121, SEQ ID NO:122, SEQ ID NO:123, or SEQ ID NO:124.In some embodiments, Lactonifactor longoviformis comprises a 16S rDNA sequence set forth in SEQ ID NO:28 or SEQ ID NO: 165. In some embodiments, Lawsonibacter_sp7 comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:27 or SEQ ID NO: 164. In some embodiments, Lawsonibacter_sp7 comprises a 16S rDNA sequence set forth in SEQ ID NO:27 or SEQ ID NO: 164. In some embodiments, Massilimaliae timonensis comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:18 or SEQ ID NO:125. In some embodiments, Massilimaliae timonensis comprises a 16S rDNA sequence set forth in SEQ ID NO: 18 or SEQ ID NO: 125. In some embodiments, Murimonas intestini comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86. In some embodiments, Murimonas intestini comprises a 16S rDNA sequence set forth in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86. In some embodiments, Niameybacter sp1 comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 22 or SEQ ID NO: 134. In some embodiments, the Niameybacter sp1 comprises the 16S rDNA sequence set forth in SEQ ID NO:22 or SEQ ID NO:134.In some embodiments, Ruminococcaceae NG13 sp6 comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:24, SEQ ID NO:149, SEQ ID NO:150, or SEQ ID NO: 151. In some embodiments, Ruminococcaceae NG13 sp6 comprises a 16S rDNA sequence set forth in SEQ ID NO:24, SEQ ID NO:149, SEQ ID NO:150, or SEQ ID NO:151. In some embodiments, Turicibacter sanguinis comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:23, SEQ ID NO:135, SEQ ID NO:136, SEQ ID NO:137, SEQ ID NO:138, SEQ ID NO:139, SEQ ID NO:140, SEQ ID NO:141, SEQ ID NO:142, SEQ ID NO:143, SEQ ID NO:144, SEQ ID NO:145, SEQ ID NO:146, SEQ ID NO:147, or SEQ ID NO: 148. In some embodiments, Turicibacter sanguinis comprises a 16S rDNA sequence set forth in SEQ ID NO:23, SEQ ID NO:135, SEQ ID NO:136, SEQ ID NO:137, SEQ ID NO:138, SEQ ID NO:139, SEQ ID NO:140, SEQ ID NO:141, SEQ ID NO:142, SEQ ID NO:143, SEQ ID NO:144, SEQ ID NO:145, SEQ ID NO:146, SEQ ID NO:147, or SEQ ID NO:148.

[0114] As is apparent from the present disclosure, any of the bacterial species provided herein can be described based on its 16S rDNA sequence. Thus, in some embodiments, the bacterial compositions useful in the present disclosure include a plurality of bacteria, and the plurality of bacteria can be selected from the group consisting of SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, SEQ ID NO:81, SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, SEQ ID NO:78, SEQ ID NO:26, SEQ ID NO:158, SEQ ID NO:159, SEQ ID NO:160, SEQ ID NO:161, SEQ ID NO:162, SEQ ID NO:163, SEQ ID NO:20, SEQ ID NO:132, SEQ ID NO:10, SEQ ID NO:100, SEQ ID NO:101, SEQ ID NO:10266, SEQ ID NO:10367, SEQ ID NO:10468, SEQ ID NO:69, SEQ ID NO:70, SEQ ID NO:1, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, SEQ ID NO:65, SEQ ID NO:14, SEQ ID NO:111, SEQ ID NO:112, SEQ ID NO:113, SEQ ID NO:114, SEQ ID NO:13, SEQ ID NO:110, SEQ ID NO:25, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, SEQ ID NO:54, SEQ ID NO:55, SEQ ID NO:56, SEQ ID NO:57, SEQ ID NO:58, SEQ ID NO:59, SEQ ID NO:60, SEQ ID NO:152, SEQ ID NO:153, SEQ ID NO:154, SEQ ID NO:155, SEQ ID NO:156, SEQ ID NO: No. 157, SEQ ID NO:12, SEQ ID NO:9, SEQ ID NO:97, SEQ ID NO:98, SEQ ID NO:99, SEQ ID NO:15, SEQ ID NO:115, SEQ ID NO:116, SEQ ID NO:7, SEQ ID NO:87, SEQ ID NO:88, SEQ ID NO:89, SEQ ID NO:90, SEQ ID NO:91, SEQ ID NO:16, SEQ ID NO:117, SEQ ID NO:118, SEQ ID NO:119, SEQ ID NO:120, SEQ ID NO:8, SEQ ID NO:92, SEQ ID NO:93, SEQ ID NO:94, SEQ ID NO:95, SEQ ID NO:96, SEQ ID NO:3, SEQ ID NO:71, SEQ ID NO:72, SEQ ID NO:73, SEQ ID NO:19, SEQ ID NO:126, SEQ ID NO:127, SEQ ID NO: No. 128, SEQ ID NO: 129, SEQ ID NO: 130, SEQ ID NO: 131, SEQ ID NO: 11, SEQ ID NO: 105, SEQ ID NO: 21, SEQ ID NO: 133, SEQ ID NO: 17, SEQ ID NO: 121, SEQ ID NO: 122, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 28, SEQ ID NO: 165, SEQ ID NO: 27, SEQ ID NO: 164, SEQ ID NO: 18, SEQ ID NO: 125, SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 86, SEQ ID NO: 22, SEQ ID NO: 134, SEQ ID NO: 24, SEQ ID NO: 149, SEQ ID NO: 150, SEQ ID NO: 151, SEQ ID NO: 23,16S set forth in any one of SEQ ID NO:135, SEQ ID NO:136, SEQ ID NO:137, SEQ ID NO:138, SEQ ID NO:139, SEQ ID NO:140, SEQ ID NO:141, SEQ ID NO:142, SEQ ID NO:143, SEQ ID NO:144, SEQ ID NO:145, SEQ ID NO:146, SEQ ID NO:147, SEQ ID NO:148, SEQ ID NO:29, SEQ ID NO:32, SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, or SEQ ID NO:37, SEQ ID NO:30, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41, SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO:166, SEQ ID NO:167, SEQ ID NO:168, SEQ ID NO:169, SEQ ID NO:170, SEQ ID NO:171, SEQ ID NO:172, SEQ ID NO:31, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:173, SEQ ID NO:174, SEQ ID NO:175, SEQ ID NO:176, or SEQ ID NO:177 16S rDNA sequences having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the rDNA sequence.

[0115] In some embodiments, the plurality of bacteria comprises a 16S gene set forth in any one of SEQ ID NO:1, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, SEQ ID NO:65, SEQ ID NO:2, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:69, SEQ ID NO:70, SEQ ID NO:3, SEQ ID NO:71, SEQ ID NO:72, SEQ ID NO:73, SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, SEQ ID NO:78, SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, SEQ ID NO:81, SEQ ID NO:6, SEQ ID NO:82, SEQ ID NO:83, SEQ ID NO:84, SEQ ID NO:85, SEQ ID NO:86, SEQ ID NO:7, SEQ ID NO:87, SEQ ID NO:88, SEQ ID NO:89, SEQ ID NO:90, SEQ ID NO:91, SEQ ID NO:8, SEQ ID NO:92, SEQ ID NO:93, SEQ ID NO:94, SEQ ID NO:95, SEQ ID NO:96, SEQ ID NO:10, SEQ ID NO:100, SEQ ID NO:101, SEQ ID NO:102, SEQ ID NO:103, SEQ ID NO:104, SEQ ID NO:12, SEQ ID NO:106, SEQ ID NO:107, SEQ ID NO:108, or SEQ ID NO:109. rDNA sequences having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence.

[0116] In some embodiments, the plurality of bacteria further comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:9, SEQ ID NO:97, SEQ ID NO:98, or SEQ ID NO:99. Thus, in some embodiments, the plurality of bacteria comprises a first 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:9, SEQ ID NO:97, SEQ ID NO:98, or SEQ ID NO:99. rDNA sequences and the 16S set forth in any one of SEQ ID NO:1, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, SEQ ID NO:65, SEQ ID NO:2, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:69, SEQ ID NO:70, SEQ ID NO:3, SEQ ID NO:71, SEQ ID NO:72, SEQ ID NO:73, SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, SEQ ID NO:78, SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, SEQ ID NO:81, SEQ ID NO:6, SEQ ID NO:82, SEQ ID NO:83, SEQ ID NO:84, SEQ ID NO:85, SEQ ID NO:86, SEQ ID NO:7, SEQ ID NO:87, SEQ ID NO:88, SEQ ID NO:89, SEQ ID NO:90, SEQ ID NO:91, SEQ ID NO:8, SEQ ID NO:92, SEQ ID NO:93, SEQ ID NO:94, SEQ ID NO:95, SEQ ID NO:96, SEQ ID NO:10, SEQ ID NO:100, SEQ ID NO:101, SEQ ID NO:102, SEQ ID NO:103, SEQ ID NO:104, SEQ ID NO:12, SEQ ID NO:106, SEQ ID NO:107, SEQ ID NO:108, or SEQ ID NO:109. and a second 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the rDNA sequence.

[0117] In some embodiments, the plurality of bacteria includes each of the following:

[0118] (a) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:9, SEQ ID NO:97, SEQ ID NO:98, or SEQ ID NO:99;

[0119] (b) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:1, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, or SEQ ID NO:65;

[0120] (c) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:2, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:69, or SEQ ID NO:70;

[0121] (d) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:3, SEQ ID NO:71, SEQ ID NO:72, or SEQ ID NO:73;

[0122] (e) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, or SEQ ID NO:78;

[0123] (f) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, or SEQ ID NO:81;

[0124] (g) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:6, SEQ ID NO:82, SEQ ID NO:83, SEQ ID NO:84, SEQ ID NO:85, or SEQ ID NO:86;

[0125] (h) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:7, SEQ ID NO:87, SEQ ID NO:88, SEQ ID NO:89, SEQ ID NO:90, or SEQ ID NO:91;

[0126] (i) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:8, SEQ ID NO:92, SEQ ID NO:93, SEQ ID NO:94, SEQ ID NO:95, or SEQ ID NO:96;

[0127] (j) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:10, SEQ ID NO:100, SEQ ID NO:101, SEQ ID NO:102, SEQ ID NO:103, or SEQ ID NO:104; and

[0128] (k) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109.

[0129] In some embodiments, the plurality of bacteria further comprises: (a) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:11 or SEQ ID NO:105; (b) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:13 or SEQ ID NO:110; (c) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:14, SEQ ID NO:111, SEQ ID NO:112, SEQ ID NO:113, or SEQ ID NO:114. rDNA sequence, or (d) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:15, SEQ ID NO:115, or SEQ ID NO:116.

[0130] Thus, in some embodiments, the plurality of bacteria comprises a first 16S sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:11 or SEQ ID NO:105. rDNA sequences and the 16S set forth in any one of SEQ ID NO:1, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, SEQ ID NO:65, SEQ ID NO:2, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:69, SEQ ID NO:70, SEQ ID NO:3, SEQ ID NO:71, SEQ ID NO:72, SEQ ID NO:73, SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, SEQ ID NO:78, SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, SEQ ID NO:81, SEQ ID NO:6, SEQ ID NO:82, SEQ ID NO:83, SEQ ID NO:84, SEQ ID NO:85, SEQ ID NO:86, SEQ ID NO:7, SEQ ID NO:87, SEQ ID NO:88, SEQ ID NO:89, SEQ ID NO:90, SEQ ID NO:91, SEQ ID NO:8, SEQ ID NO:92, SEQ ID NO:93, SEQ ID NO:94, SEQ ID NO:95, SEQ ID NO:96, SEQ ID NO:10, SEQ ID NO:100, SEQ ID NO:101, SEQ ID NO:102, SEQ ID NO:103, SEQ ID NO:104, SEQ ID NO:12, SEQ ID NO:106, SEQ ID NO:107, SEQ ID NO:108, or SEQ ID NO:109. and a second 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the rDNA sequence.

[0131] In some embodiments, the plurality of bacteria includes each of the following:

[0132] (a) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 11 or SEQ ID NO: 105;

[0133] (b) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:1, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, or SEQ ID NO:65;

[0134] (c) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:2, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:69, or SEQ ID NO:70;

[0135] (d) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:3, SEQ ID NO:71, SEQ ID NO:72, or SEQ ID NO:73;

[0136] (e) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, or SEQ ID NO:78;

[0137] (f) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, or SEQ ID NO:81;

[0138] (g) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:6, SEQ ID NO:82, SEQ ID NO:83, SEQ ID NO:84, SEQ ID NO:85, or SEQ ID NO:86;

[0139] (h) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:7, SEQ ID NO:87, SEQ ID NO:88, SEQ ID NO:89, SEQ ID NO:90, or SEQ ID NO:91;

[0140] (i) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:8, SEQ ID NO:92, SEQ ID NO:93, SEQ ID NO:94, SEQ ID NO:95, or SEQ ID NO:96;

[0141] (j) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:10, SEQ ID NO:100, SEQ ID NO:101, SEQ ID NO:102, SEQ ID NO:103, or SEQ ID NO:104; and

[0142] (k) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109.

[0143] In some embodiments, the bacterial composition comprises a first 16S polypeptide having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:13 or SEQ ID NO:110. rDNA sequences and the 16S set forth in any one of SEQ ID NO:1, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, SEQ ID NO:65, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:71, SEQ ID NO:72, SEQ ID NO:73, SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, SEQ ID NO:78, SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, SEQ ID NO:81, SEQ ID NO:6, SEQ ID NO:82, SEQ ID NO:83, SEQ ID NO:84, SEQ ID NO:85, SEQ ID NO:86, SEQ ID NO:7, SEQ ID NO:87, SEQ ID NO:88, SEQ ID NO:89, SEQ ID NO:90, SEQ ID NO:91, SEQ ID NO:8, SEQ ID NO:92, SEQ ID NO:93, SEQ ID NO:94, SEQ ID NO:95, SEQ ID NO:96, SEQ ID NO:10, SEQ ID NO:100, SEQ ID NO:101, SEQ ID NO:102, SEQ ID NO:103, SEQ ID NO:104, SEQ ID NO:12, SEQ ID NO:106, SEQ ID NO:107, SEQ ID NO:108, or SEQ ID NO:109. and a second 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the rDNA sequence.

[0144] In some embodiments, the plurality of bacteria includes each of the following:

[0145] (a) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 13 or SEQ ID NO: 110;

[0146] (b) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:1, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, or SEQ ID NO:65;

[0147] (c) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:2, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:69, or SEQ ID NO:70;

[0148] (d) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:3, SEQ ID NO:71, SEQ ID NO:72, or SEQ ID NO:73;

[0149] (e) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, or SEQ ID NO:78;

[0150] (f) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, or SEQ ID NO:81;

[0151] (g) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:6, SEQ ID NO:82, SEQ ID NO:83, SEQ ID NO:84, SEQ ID NO:85, or SEQ ID NO:86;

[0152] (h) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:7, SEQ ID NO:87, SEQ ID NO:88, SEQ ID NO:89, SEQ ID NO:90, or SEQ ID NO:91;

[0153] (i) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:8, SEQ ID NO:92, SEQ ID NO:93, SEQ ID NO:94, SEQ ID NO:95, or SEQ ID NO:96;

[0154] (j) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:10, SEQ ID NO:100, SEQ ID NO:101, SEQ ID NO:102, SEQ ID NO:103, or SEQ ID NO:104; and

[0155] (k) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109.

[0156] In some embodiments, the bacterial composition comprises a first 16S polypeptide having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:14, SEQ ID NO:111, SEQ ID NO:112, SEQ ID NO:113, or SEQ ID NO:114. rDNA sequences and the 16S set forth in any one of SEQ ID NO:1, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, SEQ ID NO:65, SEQ ID NO:2, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:69, SEQ ID NO:70, SEQ ID NO:3, SEQ ID NO:71, SEQ ID NO:72, SEQ ID NO:73, SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, SEQ ID NO:78, SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, SEQ ID NO:81, SEQ ID NO:6, SEQ ID NO:82, SEQ ID NO:83, SEQ ID NO:84, SEQ ID NO:85, SEQ ID NO:86, SEQ ID NO:7, SEQ ID NO:87, SEQ ID NO:88, SEQ ID NO:89, SEQ ID NO:90, SEQ ID NO:91, SEQ ID NO:8, SEQ ID NO:92, SEQ ID NO:93, SEQ ID NO:94, SEQ ID NO:95, SEQ ID NO:96, SEQ ID NO:10, SEQ ID NO:100, SEQ ID NO:101, SEQ ID NO:102, SEQ ID NO:103, SEQ ID NO:104, SEQ ID NO:12, SEQ ID NO:106, SEQ ID NO:107, SEQ ID NO:108, or SEQ ID NO:109. and a second 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the rDNA sequence.

[0157] In some embodiments, the plurality of bacteria includes each of the following:

[0158] (a) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:14, SEQ ID NO:111, SEQ ID NO:112, SEQ ID NO:113, or SEQ ID NO:114;

[0159] (b) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:1, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, or SEQ ID NO:65;

[0160] (c) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:2, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:69, or SEQ ID NO:70;

[0161] (d) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:3, SEQ ID NO:71, SEQ ID NO:72, or SEQ ID NO:73;

[0162] (e) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, or SEQ ID NO:78;

[0163] (f) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, or SEQ ID NO:81;

[0164] (g) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequences set forth in SEQ ID NO:6, SEQ ID NO:82, SEQ ID NO:83, SEQ ID NO:84, SEQ ID NO:85, SEQ ID NO:86;

[0165] (h) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:7, SEQ ID NO:87, SEQ ID NO:88, SEQ ID NO:89, SEQ ID NO:90, or SEQ ID NO:91;

[0166] (i) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:8, SEQ ID NO:92, SEQ ID NO:93, SEQ ID NO:94, SEQ ID NO:95, or SEQ ID NO:96;

[0167] (j) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:10, SEQ ID NO:100, SEQ ID NO:101, SEQ ID NO:102, SEQ ID NO:103, or SEQ ID NO:104; and

[0168] (k) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109.

[0169] In some embodiments, the bacterial composition comprises a first 16S polypeptide having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:15, SEQ ID NO:115, or SEQ ID NO:116. rDNA sequences and the 16S set forth in any one of SEQ ID NO:1, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, SEQ ID NO:65, SEQ ID NO:2, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:69, SEQ ID NO:70, SEQ ID NO:3, SEQ ID NO:71, SEQ ID NO:72, SEQ ID NO:73, SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, SEQ ID NO:78, SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, SEQ ID NO:81, SEQ ID NO:6, SEQ ID NO:82, SEQ ID NO:83, SEQ ID NO:84, SEQ ID NO:85, SEQ ID NO:86, SEQ ID NO:7, SEQ ID NO:87, SEQ ID NO:88, SEQ ID NO:89, SEQ ID NO:90, SEQ ID NO:91, SEQ ID NO:8, SEQ ID NO:92, SEQ ID NO:93, SEQ ID NO:94, SEQ ID NO:95, SEQ ID NO:96, SEQ ID NO:10, SEQ ID NO:100, SEQ ID NO:101, SEQ ID NO:102, SEQ ID NO:103, SEQ ID NO:104, SEQ ID NO:12, SEQ ID NO:106, SEQ ID NO:107, SEQ ID NO:108, or SEQ ID NO:109. and a second 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the rDNA sequence.

[0170] In some embodiments, the plurality of bacteria includes each of the following:

[0171] (a) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 15, SEQ ID NO: 115, or SEQ ID NO: 116;

[0172] (b) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:1, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, or SEQ ID NO:65;

[0173] (c) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:2, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:69, or SEQ ID NO:70;

[0174] (d) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:3, SEQ ID NO:71, SEQ ID NO:72, or SEQ ID NO:73;

[0175] (e) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, or SEQ ID NO:78;

[0176] (f) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, or SEQ ID NO:81;

[0177] (g) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequences set forth in SEQ ID NO:6, SEQ ID NO:82, SEQ ID NO:83, SEQ ID NO:84, SEQ ID NO:85, SEQ ID NO:86;

[0178] (h) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:7, SEQ ID NO:87, SEQ ID NO:88, SEQ ID NO:89, SEQ ID NO:90, or SEQ ID NO:91;

[0179] (i) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:8, SEQ ID NO:92, SEQ ID NO:93, SEQ ID NO:94, SEQ ID NO:95, or SEQ ID NO:96;

[0180] (j) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:10, SEQ ID NO:100, SEQ ID NO:101, SEQ ID NO:102, SEQ ID NO:103, or SEQ ID NO:104; and

[0181] (k) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109.

[0182] In some embodiments, the plurality of bacteria includes each of the following:

[0183] (a) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 11 or SEQ ID NO: 105;

[0184] (b) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 13 or SEQ ID NO: 110;

[0185] (c) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:14, SEQ ID NO:111, SEQ ID NO:112, SEQ ID NO:113, or SEQ ID NO:114;

[0186] (d) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 15, SEQ ID NO: 115, or SEQ ID NO: 116;

[0187] (e) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:1, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, or SEQ ID NO:65;

[0188] (f) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:2, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:69, or SEQ ID NO:70;

[0189] (g) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:3, SEQ ID NO:71, SEQ ID NO:72, or SEQ ID NO:73;

[0190] (h) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, or SEQ ID NO:78;

[0191] (i) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, or SEQ ID NO:81;

[0192] (j) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequences set forth in SEQ ID NO:6, SEQ ID NO:82, SEQ ID NO:83, SEQ ID NO:84, SEQ ID NO:85, SEQ ID NO:86;

[0193] (k) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:7, SEQ ID NO:87, SEQ ID NO:88, SEQ ID NO:89, SEQ ID NO:90, or SEQ ID NO:91;

[0194] (l) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:8, SEQ ID NO:92, SEQ ID NO:93, SEQ ID NO:94, SEQ ID NO:95, or SEQ ID NO:96;

[0195] (m) a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO:10, SEQ ID NO:100, SEQ ID NO:101, SEQ ID NO:102, SEQ ID NO:103, or SEQ ID NO:104; and

[0196] (n) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109.

[0197] In some embodiments, the plurality of bacteria further comprises: (a) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:16, SEQ ID NO:117, SEQ ID NO:118, SEQ ID NO:119, or SEQ ID NO:120, or (b) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:17, SEQ ID NO:121, SEQ ID NO:122, SEQ ID NO:123, SEQ ID NO:124, SEQ ID NO:28, or SEQ ID NO:165.

[0198] In some embodiments, the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 16, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 119, or SEQ ID NO: 120. Thus, in some embodiments, the plurality of bacteria comprises a first 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 16, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 119, or SEQ ID NO: 120. rDNA sequences and the 16S set forth in any one of SEQ ID NO:1, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, SEQ ID NO:65, SEQ ID NO:2, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:69, SEQ ID NO:70, SEQ ID NO:3, SEQ ID NO:71, SEQ ID NO:72, SEQ ID NO:73, SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, SEQ ID NO:78, SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, SEQ ID NO:81, SEQ ID NO:6, SEQ ID NO:82, SEQ ID NO:83, SEQ ID NO:84, SEQ ID NO:85, SEQ ID NO:86, SEQ ID NO:7, SEQ ID NO:87, SEQ ID NO:88, SEQ ID NO:89, SEQ ID NO:90, SEQ ID NO:91, SEQ ID NO:8, SEQ ID NO:92, SEQ ID NO:93, SEQ ID NO:94, SEQ ID NO:95, SEQ ID NO:96, SEQ ID NO:10, SEQ ID NO:100, SEQ ID NO:101, SEQ ID NO:102, SEQ ID NO:103, SEQ ID NO:104, SEQ ID NO:12, SEQ ID NO:106, SEQ ID NO:107, SEQ ID NO:108, or SEQ ID NO:109. and a second 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the rDNA sequence.

[0199] In some embodiments, the plurality of bacteria includes each of the following:

[0200] (1) A 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 16, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 119, or SEQ ID NO: 120;

[0201] (2) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65;

[0202] (3) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70;

[0203] (4) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73;

[0204] (5) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78;

[0205] (6) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81;

[0206] (7) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86;

[0207] (8) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91;

[0208] (9) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96;

[0209] (10) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104; and

[0210] (11) SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109. A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity.

[0211] In some embodiments, the plurality of bacteria comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 17, SEQ ID NO: 121, SEQ ID NO: 122, SEQ ID NO: 123, or SEQ ID NO: 124. Thus, in some embodiments, the plurality of bacteria comprises a first 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 17, SEQ ID NO: 121, SEQ ID NO: 122, SEQ ID NO: 123, or SEQ ID NO: 124. rDNA sequences and the 16S set forth in any one of SEQ ID NO:1, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, SEQ ID NO:65, SEQ ID NO:2, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:69, SEQ ID NO:70, SEQ ID NO:3, SEQ ID NO:71, SEQ ID NO:72, SEQ ID NO:73, SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, SEQ ID NO:78, SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, SEQ ID NO:81, SEQ ID NO:6, SEQ ID NO:82, SEQ ID NO:83, SEQ ID NO:84, SEQ ID NO:85, SEQ ID NO:86, SEQ ID NO:7, SEQ ID NO:87, SEQ ID NO:88, SEQ ID NO:89, SEQ ID NO:90, SEQ ID NO:91, SEQ ID NO:8, SEQ ID NO:92, SEQ ID NO:93, SEQ ID NO:94, SEQ ID NO:95, SEQ ID NO:96, SEQ ID NO:10, SEQ ID NO:100, SEQ ID NO:101, SEQ ID NO:102, SEQ ID NO:103, SEQ ID NO:104, SEQ ID NO:12, SEQ ID NO:106, SEQ ID NO:107, SEQ ID NO:108, or SEQ ID NO:109. and a second 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the rDNA sequence.

[0212] In some embodiments, the plurality of bacteria includes each of the following:

[0213] (1) A 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 17, SEQ ID NO: 121, SEQ ID NO: 122, SEQ ID NO: 123, or SEQ ID NO: 124;

[0214] (2) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65;

[0215] (3) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70;

[0216] (4) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73;

[0217] (5) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78;

[0218] (6) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81;

[0219] (7) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86;

[0220] (8) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91;

[0221] (9) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96;

[0222] (10) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104; and

[0223] (11) SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109. A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity.

[0224] In some embodiments, the plurality of bacteria comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 28. For example, in some embodiments, the plurality of bacteria comprises a first 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 28 or SEQ ID NO: 165. rDNA sequences and 16S sequences set forth in any one of SEQ ID NO:1, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, SEQ ID NO:65, SEQ ID NO:2, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:69, SEQ ID NO:70, SEQ ID NO:3, SEQ ID NO:71, SEQ ID NO:72, SEQ ID NO:73, SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, SEQ ID NO:78, SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, SEQ ID NO:81, SEQ ID NO:6, SEQ ID NO:82, SEQ ID NO:83, SEQ ID NO:84, SEQ ID NO:85, SEQ ID NO:86, SEQ ID NO:7, SEQ ID NO:87, SEQ ID NO:88, SEQ ID NO:89, SEQ ID NO:90, or SEQ ID NO:91, SEQ ID NO:8, SEQ ID NO:92, SEQ ID NO:93, SEQ ID NO:94, SEQ ID NO:95, SEQ ID NO:96, SEQ ID NO:10, SEQ ID NO:100, SEQ ID NO:101, SEQ ID NO:102, SEQ ID NO:103, SEQ ID NO:104, SEQ ID NO:12, SEQ ID NO:106, SEQ ID NO:107, SEQ ID NO:108, or SEQ ID NO:109. and a second 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the rDNA sequence.

[0225] In some embodiments, the plurality of bacteria includes each of the following:

[0226] (1) A 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 28 or SEQ ID NO: 165;

[0227] (2) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65;

[0228] (3) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70;

[0229] (4) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73;

[0230] (5) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78;

[0231] (6) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81;

[0232] (7) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86;

[0233] (8) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91;

[0234] (9) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96;

[0235] (10) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104; and

[0236] (11) SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109. A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity.

[0237] In some embodiments, the plurality of bacteria includes each of the following:

[0238] (1) A 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 16, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 119, or SEQ ID NO: 120;

[0239] (2) A 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 17, SEQ ID NO: 121, SEQ ID NO: 122, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 28, or SEQ ID NO: 165;

[0240] (3) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65;

[0241] (4) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70;

[0242] (5) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73;

[0243] (6) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78;

[0244] (7) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81;

[0245] (8) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86;

[0246] (9) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91;

[0247] (10) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96;

[0248] (11) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104; and

[0249] (12) SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109. A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity.

[0250] In some embodiments, the bacteria provided herein further comprise: (a) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 18 or SEQ ID NO: 125; (b) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 19, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 128, SEQ ID NO: 129, SEQ ID NO: 130, or SEQ ID NO: 131; or (c) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 20 or SEQ ID NO: 132.

[0251] In some embodiments, the plurality of bacteria comprises a first 16S sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:18 or SEQ ID NO:125. rDNA sequences and the 16S set forth in any one of SEQ ID NO:1, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, SEQ ID NO:65, SEQ ID NO:2, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:69, SEQ ID NO:70, SEQ ID NO:3, SEQ ID NO:71, SEQ ID NO:72, SEQ ID NO:73, SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, SEQ ID NO:78, SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, SEQ ID NO:81, SEQ ID NO:6, SEQ ID NO:82, SEQ ID NO:83, SEQ ID NO:84, SEQ ID NO:85, SEQ ID NO:86, SEQ ID NO:7, SEQ ID NO:87, SEQ ID NO:88, SEQ ID NO:89, SEQ ID NO:90, SEQ ID NO:91, SEQ ID NO:8, SEQ ID NO:92, SEQ ID NO:93, SEQ ID NO:94, SEQ ID NO:95, SEQ ID NO:96, SEQ ID NO:10, SEQ ID NO:100, SEQ ID NO:101, SEQ ID NO:102, SEQ ID NO:103, SEQ ID NO:104, SEQ ID NO:12, SEQ ID NO:106, SEQ ID NO:107, SEQ ID NO:108, or SEQ ID NO:109. and a second 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the rDNA sequence.

[0252] In some embodiments, the plurality of bacteria includes each of the following:

[0253] (1) A 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 18 or SEQ ID NO: 125;

[0254] (2) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65;

[0255] (3) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70;

[0256] (4) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73;

[0257] (5) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78;

[0258] (6) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81;

[0259] (7) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86;

[0260] (8) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91;

[0261] (9) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96;

[0262] (10) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104; and

[0263] (11) SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109. A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity.

[0264] In some embodiments, the plurality of bacteria comprises a first 16S sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:19, SEQ ID NO:126, SEQ ID NO:127, SEQ ID NO:128, SEQ ID NO:129, SEQ ID NO:130, or SEQ ID NO:131. rDNA sequences and the 16S set forth in any one of SEQ ID NO:1, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, SEQ ID NO:65, SEQ ID NO:2, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:69, SEQ ID NO:70, SEQ ID NO:3, SEQ ID NO:71, SEQ ID NO:72, SEQ ID NO:73, SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, SEQ ID NO:78, SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, SEQ ID NO:81, SEQ ID NO:6, SEQ ID NO:82, SEQ ID NO:83, SEQ ID NO:84, SEQ ID NO:85, SEQ ID NO:86, SEQ ID NO:7, SEQ ID NO:87, SEQ ID NO:88, SEQ ID NO:89, SEQ ID NO:90, SEQ ID NO:91, SEQ ID NO:8, SEQ ID NO:92, SEQ ID NO:93, SEQ ID NO:94, SEQ ID NO:95, SEQ ID NO:96, SEQ ID NO:10, SEQ ID NO:100, SEQ ID NO:101, SEQ ID NO:102, SEQ ID NO:103, SEQ ID NO:104, SEQ ID NO:12, SEQ ID NO:106, SEQ ID NO:107, SEQ ID NO:108, or SEQ ID NO:109. and a second 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the rDNA sequence.

[0265] In some embodiments, the plurality of bacteria includes each of the following:

[0266] (1) A 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 19, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 128, SEQ ID NO: 129, SEQ ID NO: 130, or SEQ ID NO: 131;

[0267] (2) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65;

[0268] (3) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70;

[0269] (4) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73;

[0270] (5) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78;

[0271] (6) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81;

[0272] (7) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86;

[0273] (8) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91;

[0274] (9) SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, SEQ ID NO: 96. A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity;

[0275] (10) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104; and

[0276] (11) SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109. A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity.

[0277] In some embodiments, the plurality of bacteria comprises a first 16S sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:20 or SEQ ID NO:132. rDNA sequences and the 16S set forth in any one of SEQ ID NO:1, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, SEQ ID NO:65, SEQ ID NO:2, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:69, SEQ ID NO:70, SEQ ID NO:3, SEQ ID NO:71, SEQ ID NO:72, SEQ ID NO:73, SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, SEQ ID NO:78, SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, SEQ ID NO:81, SEQ ID NO:6, SEQ ID NO:82, SEQ ID NO:83, SEQ ID NO:84, SEQ ID NO:85, SEQ ID NO:86, SEQ ID NO:7, SEQ ID NO:87, SEQ ID NO:88, SEQ ID NO:89, SEQ ID NO:90, SEQ ID NO:91, SEQ ID NO:8, SEQ ID NO:92, SEQ ID NO:93, SEQ ID NO:94, SEQ ID NO:95, SEQ ID NO:96, SEQ ID NO:10, SEQ ID NO:100, SEQ ID NO:101, SEQ ID NO:102, SEQ ID NO:103, SEQ ID NO:104, SEQ ID NO:12, SEQ ID NO:106, SEQ ID NO:107, SEQ ID NO:108, or SEQ ID NO:109. and a second 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the rDNA sequence.

[0278] In some embodiments, the plurality of bacteria includes each of the following:

[0279] (1) A 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 20 or SEQ ID NO: 132;

[0280] (2) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65;

[0281] (3) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70;

[0282] (4) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73;

[0283] (5) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78;

[0284] (6) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81;

[0285] (7) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86;

[0286] (8) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91;

[0287] (9) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96;

[0288] (10) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104; and

[0289] (11) SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109. A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity.

[0290] In some embodiments, the plurality of bacteria includes each of the following:

[0291] (1) A 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 18 or SEQ ID NO: 125;

[0292] (2) A 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 19, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 128, SEQ ID NO: 129, SEQ ID NO: 130, or SEQ ID NO: 131;

[0293] (3) A 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 20 or SEQ ID NO: 132;

[0294] (4) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65;

[0295] (5) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70;

[0296] (6) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73;

[0297] (7) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78;

[0298] (8) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81;

[0299] (9) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86;

[0300] (10) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91;

[0301] (11) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity with the 16S rDNA sequence set forth in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96;

[0302] (12) A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity to the 16S rDNA sequence set forth in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104; and

[0303] (13) SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109. A 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% sequence identity.

[0304] In some embodiments, the plurality of bacteria comprises (a) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:21 or SEQ ID NO:133, (b) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:22 or SEQ ID NO:134, or (c) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:23, SEQ ID NO:135, SEQ ID NO:136, SEQ ID NO:137, SEQ ID NO:138, SEQ ID NO:139, SEQ ID NO:140, SEQ ID NO:141, SEQ ID NO:142, SEQ ID NO:143, SEQ ID NO:144, SEQ ID NO:145, SEQ ID NO:146, SEQ ID NO:147, or SEQ ID NO:148. Contains rDNA sequenc...

Claims

1. 1. A method of treating chronic liver disease in a subject in need thereof, comprising administering to the subject a composition comprising a plurality of bacteria, wherein the plurality of bacteria comprises a first bacterial species and a second bacterial species, wherein the first species and the second species are not the same, and wherein the first species and the second species are selected from the group consisting of Anaerotruncus colihominis, Blautia coccoides, Blautia hominis, Blautia obeum, Blautia wexlerae, Butyricicoccus sp2, Clostridium aldenense, Clostridium bolteae, Clostridium innocuum, Clostridium sindens, and Clostridium spp. symbiosum, Dorea longicatena, Eisenbergiella tayi, Emergencia timonensis, Erysipelate clostridium ramosum, Eubacterium Callanderi, Faecalicatena cortorta, Faecalicatena orotica, Flavonifractor plautii, Hungatella effluvii, Intestinimonas butyriciproducens, Intestinimonas massiliensis, Lactonifactor longoviformis, Lawsonibacter sp7, Massilimaliae timonensis, Murimonas intestini, Niameybacter sp1, Ruminococcus aureus NG13 sp6, or Turicibacter sanguinis.

2. 2. The method of claim 1, wherein treating chronic liver disease comprises (i) reducing or preventing the occurrence of an infectious disease in the subject, (ii) reducing or preventing symptoms of the chronic liver disease in the subject, or (iii) both (i) and (ii).

3. 3. The method of claim 1 or 2, wherein the chronic liver disease is caused by and / or associated with toxins (e.g., long-term alcohol and / or drug abuse), infectious diseases, metabolic disorders, autoimmune diseases, genetic abnormalities, or a combination thereof.

4. 3. The method of claim 1 or 2, wherein the chronic liver disease is idiopathic.

5. 5. The method of any one of claims 1 to 4, wherein the chronic liver disease comprises cirrhosis, liver fibrosis, alcoholic liver disease, non-alcoholic fatty liver disease (NAFLD), non-alcoholic steatohepatitis (NASH), hepatitis (including viral and alcoholic hepatitis), primary biliary cirrhosis (PBC), primary sclerosing cholangitis (PSC), alpha-1 antitrypsin deficiency, hereditary hemochromatosis, Wilson's disease, autoimmune hepatitis (AIH), Budd-Chiari syndrome, and combinations thereof.

6. 6. The method of any one of claims 1 to 5, wherein the chronic liver disease comprises abdominal fluid accumulation (ascites), vomiting, gallstones, itching, jaundice, kidney failure, muscle loss, loss of appetite, bruising, spider veins in the skin, fatigue, weight loss, confusion, swelling of the legs (e.g., ankles), portal hypertension, hepatic encephalopathy, and combinations thereof.

7. 1. A method of treating neutropenia in a subject in need thereof, comprising administering to the subject a composition comprising a plurality of bacteria, wherein the plurality of bacteria comprises a first bacterial species and a second bacterial species, wherein the first species and the second species are not the same, and wherein the first species and the second species are selected from the group consisting of Anaerotruncus colihominis, Blautia coccoides, Blautia hominis, Blautia obeum, Blautia wexlerae, Butyricicoccus sp2, Clostridium aldenense, Clostridium bolteae, Clostridium innocuum, Clostridium sindens, and Clostridium symbiosum, Dorea longicatena, Eisenbergiella tayi, Emergencia timonensis, Erysipelate clostridium ramosum, Eubacterium Callanderi, Faecalicatena cortorta, Faecalicatena orotica, Flavonifractor plautii, Hungatella effluvii, Intestinimonas butyriciproducens, Intestinimonas massiliensis, Lactonifactor longoviformis, Lawsonibacter sp7, Massilimaliae timonensis, Murimonas intestini, Niameybacter sp1, Ruminococcus aureus NG13 sp6, or Turicibacter sanguinis.

8. 8. The method of claim 7, wherein treating neutropenia comprises (i) reducing or preventing the occurrence of an infection in the subject, (ii) reducing or preventing the symptoms of neutropenia in the subject, or (iii) both (i) and (ii).

9. 9. The method of claim 7 or 8, wherein the neutropenia comprises cancer neutropenia.

10. 1. A method of treating a disease or disorder associated with solid organ transplantation in a subject in need thereof, comprising administering to the subject a composition comprising a plurality of bacteria, wherein the plurality of bacteria comprises a first bacterial species and a second bacterial species, wherein the first species and the second species are not the same, and wherein the first species and the second species are selected from the group consisting of Anaerotruncus colihominis, Blautia coccoides, Blautia hominis, Blautia obeum, Blautia wexlerae, Butyricicoccus sp2, Clostridium aldenense, Clostridium bolteae, Clostridium innocuum, and Clostridium sp2. scindens, Clostridium symbiosum, Dorea longicatena, Eisenbergiella tayi, Emergencia timonensis, Erysipelatoclostridium ramosum, Eubacterium callanderi, Faecalicatena cortorta, Faecalicatena orotica, Flavonifractor plautii, Hungatella effluvii, Intestinimonas butyriciproducens, Intestinimonas massiliensis, Lactonifactor longoviformis, Lawsonibacter sp7, Massilimaliae timonensis, Murimonas intestini, Niameybacter sp1, Ruminococcus aureus NG13 sp6, or Turicibacter sanguinis.

11. 11. The method of claim 10, wherein treating a disease or disorder associated with solid organ transplantation comprises (i) reducing or preventing the occurrence of an infection in the subject, (ii) reducing or preventing symptoms of the disease or disorder associated with solid organ transplantation in the subject, or (iii) both (i) and (ii).

12. 12. The method of claim 10 or 11, wherein the solid organ transplant comprises a liver transplant.

13. 13. The method of any one of claims 1 to 12, wherein the first species and / or the second species is selected from Clostridium innocuum, Clostridium bolteae, Flavonifractor platii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi.

14. 14. The method of any one of claims 1 to 13, wherein the plurality of bacteria comprises each of Clostridium innocuum, Clostridium bolteae, Flavonifractor platii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.

15. 15. The method of claim 13 or 14, wherein the plurality of bacteria further comprises Emergencia timonensis.

16. The method of any one of claims 13 to 15, wherein the plurality of bacteria further comprises Intestinimonas butyriciproducens.

17. The method of any one of claims 13 to 16, wherein the plurality of bacteria further comprises Clostridium symbiosum.

18. The method of any one of claims 13 to 17, wherein the plurality of bacteria further comprises Clostridium scindens.

19. The method of any one of claims 13 to 18, wherein the plurality of bacteria further comprises Faecalicatena cortorta.

20. 20. The method of any one of claims 13 to 19, wherein the plurality of bacteria further comprises Lactonifactor longoviformis.

21. 21. The method of any one of claims 13 to 20, wherein the plurality of bacteria further comprises Massilimaliae timonensis.

22. 22. The method of any one of claims 13 to 21, wherein the plurality of bacteria further comprises Hungatellella effluvii.

23. 23. The method of any one of claims 13 to 22, wherein the plurality of bacteria further comprises Butyricicoccus sp2.

24. 24. The method of any one of claims 13 to 23, wherein the plurality of bacteria further comprises Intestinimonas massiliensis.

25. The method of any one of claims 13 to 24, wherein the plurality of bacteria further comprises Niameybacter sp1.

26. 26. The method of any one of claims 13 to 25, wherein the plurality of bacteria further comprises Turicibacter sanguinis.

27. 27. The method of any one of claims 13 to 26, wherein the plurality of bacteria further comprises Ruminococcus NG13 sp6.

28. 28. The method of any one of claims 13 to 27, wherein the plurality of bacteria further comprises Dorea longicatena.

29. 29. The method of any one of claims 13 to 28, wherein the plurality of bacteria further comprises Blautia obeum.

30. The method of any one of claims 13 to 29, wherein the plurality of bacteria further comprises Lawsonibacter_sp7.

31. 31. The method of any one of claims 13 to 30, wherein the plurality of bacteria further comprises Blautia hominis.

32. 32. The method of any one of claims 13 to 31, wherein the plurality of bacteria further comprises Blautia wexlerae.

33. 33. The method of any one of claims 13 to 32, wherein the plurality of bacteria further comprises Eubacterium callanderi.

34. The plurality of bacteria is selected from the following bacterial species: (a) (1) Clostridium innocuum, (2) Clostridium boltea, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecaliatena orotica, (9) Emergence timonensis, (10) Clostridium aleeeeeeeeeees, (11) foreceliingeseringes (b) (1) Clostridium innocuum, (2) Clostridium boltea, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecaliatena orotica, (9) Clostridium aldenense, (10) Intestinimonas Butyric acid production, (11) Eisenbergia tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, and (14) Emergensia timonensis, (c) (1) Clostridium innocuum, (2) Clostridium boltea, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecaliatena orotica, (9) Clostridium aldenense, (10) Intestinimonas Butyric production, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergence timonensis, (15) Faecalitatena cortorta, (16) Lactonifactor longoviformis, and (17) Ruminococcaceae Ng13 sp6, (d) (1) Clostridium innocuum, (2) Clostridium boltea, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecaliatena orotica, (9) Clostridium aldenense, (10) Intestinimonas Butyric production, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergence timonensis, (15) Faecalitatena cortorta, (16) Lactonifactor longoviformis, (17) Massimalia timonensis, (18) H ungatella effluvfy、119BOyricicoccus sp2、 (e) (1) Clostridium innocuum, (2) Clostridium boltae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecaliatena orotica, (9) Clostridium aldenense, (10) Intestinimonas Butyric production, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergence timonensis, (15) Faecalitatena cortorta, (16) Lactonifactor longoviformis, (17) Massimalia timonensis, (18) H Uncategorized, (19) Butyricococcus sp2, (20) Interstitial mycobacteria, (21) Ni ameybacter sp1、222222222 (f) (1) Clostridium innocuum, (2) Clostridium boltea, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecaliatena orotica, (9) Emergence timonensis, (10) Clostridium aldenense, (11) Eisenbergiella tayi, (12) Dorea longicatena, and (13) Blautia obeum, (') (1) Clostridium innocuum, (2) Clostridium boltea, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecaliatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyricipróducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergence timonensis、(11)Blautia obeum、116)Lawsonibacter_sp7、 (h) (1) Clostridium innocuum, (2) Clostridium boltea, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecaliatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyricipróducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergence timonensis, (15) Faecalicatena cortorta, (16) Lactonifactor longovifformis, (17) Рuminococcaceae NG13 sp6, (18) Blautiaガレッック、はなは(19)Lawsonibacter_sp7、 (1) Clostridium innocuum, (2) Clostridium boltea, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecaliatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyricipróducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, and (13) Emergencia timonensis, (j) (1) Clostridium innocuum, (2) Clostridium boltea, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecaliatena orotica, (9) Clostridium aldenense, (10) Intestinimonas Butyric production, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergence timonensis, (15) Faecalicathena cortorta, (16) Lactonifactor longoviformis, (17) Intestinmonas massiliensis, (18) Ni ameybacter sp1、111111111 (k) (1) Clostridium innocum, (2) Clostridium volteae, (3) Flavonifractor plautii, (4) Blautia hominis, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Emergencia timonensis, (10) Clostridium aldenense, (11) Eisenbergiella tayi, (12) Clostridium scindens, (13) Dorea longicatena, (14) Blautia obeum, (15) Blautia wexlerae, and (16) Eubacterium callanderi 13. The method of any one of claims 1 to 12, comprising, consisting essentially of, or consisting of:

35. (a) the Anaerotruncus colihominis comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, or SEQ ID NO:81; (b) the Blautia coccoides comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, or SEQ ID NO:78; or (c) the Blautia hominis comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:29, SEQ ID NO:32, SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, or SEQ ID NO:37; or (d) the Blautia obeum comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:26; (e) the Blautia wexlerae comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:30, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41, SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO:166, SEQ ID NO:167, SEQ ID NO:168, SEQ ID NO:169, SEQ ID NO:170, SEQ ID NO:171, or SEQ ID NO:172; or (f) the Butyricicoccus sp2 comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 20 or SEQ ID NO: 132; (g) the Clostridium aldenense comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104; (h) the Clostridium bolteae comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:2, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:69, or SEQ ID NO:70; (i) the Clostridium innocuum comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65; (j) the Clostridium scindens comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 14, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, or SEQ ID NO: 114; (k) the Clostridium symbiosum comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 13 or SEQ ID NO: 110; (l) the Dorea longicatena comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:25, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, SEQ ID NO:54, SEQ ID NO:55, SEQ ID NO:56, SEQ ID NO:57, SEQ ID NO:58, SEQ ID NO:59, SEQ ID NO:60, SEQ ID NO:152, SEQ ID NO:153, SEQ ID NO:154, SEQ ID NO:155, SEQ ID NO:156, or SEQ ID NO:157; or (m) the Eisenbergiella tayi comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109; (n) the Emergencia timonensis comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:9, SEQ ID NO:97, SEQ ID NO:98, SEQ ID NO:99, SEQ ID NO:15, SEQ ID NO:115, or SEQ ID NO:116; (o) the Erysipelatoclostridium ramosum comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:7, SEQ ID NO:87, SEQ ID NO:88, SEQ ID NO:89, SEQ ID NO:90, or SEQ ID NO:91; (p) the Eubacterium callanderi comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:31, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:173, SEQ ID NO:174, SEQ ID NO:175, SEQ ID NO:176, or SEQ ID NO:177; (q) the Faecalicatena cortorta comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 16; (r) the Faecalicatena orotica comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:8, SEQ ID NO:92, SEQ ID NO:93, SEQ ID NO:94, SEQ ID NO:95, or SEQ ID NO:96; (s) the Flavonifractor platii comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 3; (t) the Hungatella effluvia comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 19, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 128, SEQ ID NO: 129, SEQ ID NO: 130, or SEQ ID NO: 131; (u) the Intestinimonas butyriciproducens comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 11 or SEQ ID NO: 105; (v) the Intestinimonas massiliensis comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 21; (w) the Lactonifactor longoviformis comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 17, SEQ ID NO: 121, SEQ ID NO: 122, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 28, or SEQ ID NO: 165; (x) the Lawsonibacter_sp7 comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 27 or SEQ ID NO: 164; (y) the Massilimaliae timonensis comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 18 or SEQ ID NO: 125; (z) the Murimonas intestini comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:6, SEQ ID NO:82, SEQ ID NO:83, SEQ ID NO:84, SEQ ID NO:85, or SEQ ID NO:86; (aa) the Niameybacter sp1 comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 22 or SEQ ID NO: 134; (bb) the Ruminococcaceae NG13 sp6 comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:24, SEQ ID NO:149, SEQ ID NO:150, or SEQ ID NO:151; or (cc) the Turicibacter sanguinis comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:23, SEQ ID NO:135, SEQ ID NO:136, SEQ ID NO:137, SEQ ID NO:138, SEQ ID NO:139, SEQ ID NO:140, SEQ ID NO:141, SEQ ID NO:142, SEQ ID NO:143, SEQ ID NO:144, SEQ ID NO:145, SEQ ID NO:146, SEQ ID NO:147, or SEQ ID NO:

148.

36. (a) the Anaerotruncus colihominis comprises a 16S rDNA sequence set forth in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81; (b) the Blautia coccoides comprises the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78; (c) the Blautia hominis comprises the 16S rDNA sequence set forth in SEQ ID NO: 29, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 36, or SEQ ID NO: 37; (d) the Blautia obeum comprises the 16S rDNA sequence set forth in SEQ ID NO: 26, SEQ ID NO: 158, SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 161, SEQ ID NO: 162, or SEQ ID NO: 163; (e) the Blautia wexlerae comprises the 16S rDNA sequence set forth in SEQ ID NO:30, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41, SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO:166, SEQ ID NO:167, SEQ ID NO:168, SEQ ID NO:169, SEQ ID NO:170, SEQ ID NO:171, or SEQ ID NO:172; (f) The Butyricicoccus sp2 comprises the 16S rDNA sequence set forth in SEQ ID NO: 20 or SEQ ID NO: 132; (g) the Clostridium aldenense comprises the 16S rDNA sequence set forth in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104; (h) the Clostridium bolteae comprises the 16S rDNA sequence set forth in SEQ ID NO: 22 or SEQ ID NO: 134; (i) The Clostridium innocuum comprises a 16S rDNA sequence set forth in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65; (j) the Clostridium scindens comprises the 16S rDNA sequence set forth in SEQ ID NO: 14, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, or SEQ ID NO: 114; (k) The Clostridium symbiosum comprises the 16S rDNA sequence shown in SEQ ID NO: 13 or SEQ ID NO: 110; (l) the Dorea longicatena comprises the 16S rDNA sequence set forth in SEQ ID NO:25, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, SEQ ID NO:54, SEQ ID NO:55, SEQ ID NO:56, SEQ ID NO:57, SEQ ID NO:58, SEQ ID NO:59, SEQ ID NO:60, SEQ ID NO:152, SEQ ID NO:153, SEQ ID NO:154, SEQ ID NO:155, SEQ ID NO:156, or SEQ ID NO:157; (m) the Eisenbergiella tayi comprises a 16S rDNA sequence set forth in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109; (n) the Emergencia timonensis comprises a 16S rDNA sequence set forth in SEQ ID NO: 9, SEQ ID NO: 97, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 15, SEQ ID NO: 115, or SEQ ID NO: 116; (O) the Erysipelatoclostridium ramosum comprises a 16S rDNA sequence set forth in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91; (p) the Eubacterium callanderi comprises a 16S rDNA sequence set forth in SEQ ID NO: 31, SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 173, SEQ ID NO: 174, SEQ ID NO: 175, SEQ ID NO: 176, or SEQ ID NO: 177; (q) the Faecalicatena cortorta comprises the 16S rDNA sequence shown in SEQ ID NO: 16; (r) the Faecalicatena orotica comprises a 16S rDNA sequence set forth in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96; (s) the Flavonifractor platii comprises the 16S rDNA sequence shown in SEQ ID NO: 3; (t) the Hungatella effluvia comprises a 16S rDNA sequence set forth in SEQ ID NO: 19, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 128, SEQ ID NO: 129, SEQ ID NO: 130, or SEQ ID NO: 131; (u) the Intestinimonas butyriciproducens comprises the 16S rDNA sequence shown in SEQ ID NO: 11 or SEQ ID NO: 105; (v) The Intestinimonas massiliensis comprises the 16S rDNA sequence shown in SEQ ID NO: 21; (w) the Lactonifactor longoviformis comprises the 16S rDNA sequence set forth in SEQ ID NO: 17, SEQ ID NO: 121, SEQ ID NO: 122, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 28, or SEQ ID NO: 165; (x) the Lawsonibacter_sp7 comprises the 16S rDNA sequence set forth in SEQ ID NO: 27 or SEQ ID NO: 164; (y) the Massilimaliae timonensis comprises the 16S rDNA sequence set forth in SEQ ID NO: 18 or SEQ ID NO: 125; (z) the Murimonas intestini comprises the 16S rDNA sequence set forth in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86; (aa) the Niameybacter sp1 comprises the 16S rDNA sequence shown in SEQ ID NO: 22 or SEQ ID NO: 134; (bb) the Ruminococcaceae NG13 sp6 comprises the 16S rDNA sequence set forth in SEQ ID NO: 24, SEQ ID NO: 149, SEQ ID NO: 150, or SEQ ID NO: 151; or (cc) the Turicibacter sanguinis comprises the 16S rDNA sequence set forth in SEQ ID NO:23, SEQ ID NO:135, SEQ ID NO:136, SEQ ID NO:137, SEQ ID NO:138, SEQ ID NO:139, SEQ ID NO:140, SEQ ID NO:141, SEQ ID NO:142, SEQ ID NO:143, SEQ ID NO:144, SEQ ID NO:145, SEQ ID NO:146, SEQ ID NO:147, or SEQ ID NO:

148. The method of any one of claims 1 to 35.

37. 1. A method of treating chronic liver disease in a subject in need thereof, comprising administering to the subject a composition comprising a first bacterial species and a second bacterial species, wherein said first species and said second species are not the same, and said first species and said second species are independently selected from the group consisting of SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, SEQ ID NO:81, SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, SEQ ID NO:78, SEQ ID NO:26, SEQ ID NO:158, SEQ ID NO:159, SEQ ID NO:160, SEQ ID NO:161, SEQ ID NO:162, SEQ ID NO:163, SEQ ID NO:20, SEQ ID NO:132, SEQ ID NO: 10, SEQ ID NO:100, SEQ ID NO:101, SEQ ID NO:10266, SEQ ID NO:10367, SEQ ID NO:10468, SEQ ID NO:69, SEQ ID NO:70, SEQ ID NO:1, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, SEQ ID NO:65, SEQ ID NO:14, SEQ ID NO:111, SEQ ID NO:112, SEQ ID NO:113, SEQ ID NO:114, SEQ ID NO:13, SEQ ID NO:110, SEQ ID NO:25, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, SEQ ID NO:54, SEQ ID NO:55, SEQ ID NO:56, SEQ ID NO:57, SEQ ID NO:58, SEQ ID NO:59, SEQ ID NO:60, SEQ ID NO:152, SEQ ID NO:153, SEQ ID NO:154, SEQ ID NO:155, SEQ ID NO:156, SEQ ID NO:157, SEQ ID NO:12, SEQ ID NO:106, SEQ ID NO:107, SEQ ID NO:108, SEQ ID NO:109, SEQ ID NO:9, SEQ ID NO:97, SEQ ID NO:98, SEQ ID NO:99, SEQ ID NO:15, SEQ ID NO:7, SEQ ID NO:87, SEQ ID NO:88, SEQ ID NO:89, SEQ ID NO:90, SEQ ID NO:91, SEQ ID NO:16, SEQ ID NO:8, SEQ ID NO:92, SEQ ID NO:93, SEQ ID NO:94, SEQ ID NO:95, SEQ ID NO:96, SEQ ID NO:3, SEQ ID NO:71, SEQ ID NO:72, SEQ ID NO:73, SEQ ID NO:19, SEQ ID NO:126, SEQ ID NO:12 7, SEQ ID NO:128, SEQ ID NO:129, SEQ ID NO:130, SEQ ID NO:131, SEQ ID NO:11, SEQ ID NO:105, SEQ ID NO:21, SEQ ID NO:133, SEQ ID NO:17, SEQ ID NO:121, SEQ ID NO:122, SEQ ID NO:123, SEQ ID NO:124, SEQ ID NO:28, SEQ ID NO:27, SEQ ID NO:164, SEQ ID NO:18, SEQ ID NO:125, SEQ ID NO:6, SEQ ID NO:82, SEQ ID NO:83, SEQ ID NO:84, SEQ ID NO:85, SEQ ID NO:86, SEQ ID NO:22, SEQ ID NO:134, SEQ ID NO:24, SEQ ID NO:149, SEQ ID NO:150, SEQ ID NO:151, SEQ ID NO:23, SEQ ID NO:135, SEQ ID NO:136,SEQ ID NO:137, SEQ ID NO:138, SEQ ID NO:139, SEQ ID NO:140, SEQ ID NO:141, SEQ ID NO:142, SEQ ID NO:143, SEQ ID NO:144, SEQ ID NO:145, SEQ ID NO:146, SEQ ID NO:147, SEQ ID NO:148, SEQ ID NO:29, SEQ ID NO:32, SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, or SEQ ID NO:37, SEQ ID NO:30, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41, SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO:166, The method comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to any one of the sequences set forth in SEQ ID NO:167, SEQ ID NO:168, SEQ ID NO:169, SEQ ID NO:170, SEQ ID NO:171, SEQ ID NO:172, SEQ ID NO:31, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:173, SEQ ID NO:174, SEQ ID NO:175, SEQ ID NO:176, or SEQ ID NO:

177.

38. 38. The method of claim 37, wherein treating the chronic liver disease comprises (i) reducing or preventing the occurrence of an infection in the subject, (ii) reducing or preventing symptoms of the chronic liver disease in the subject, or (iii) both (i) and (ii).

39. 38. The method of claim 36 or 37, wherein the chronic liver disease comprises cirrhosis.

40. 40. The method of claim 39, wherein the cirrhosis comprises decompensated cirrhosis.

41. 38. The method of claim 36 or 37, wherein the chronic liver disease comprises hepatic encephalopathy.

42. 1. A method of treating neutropenia in a subject in need thereof, comprising administering to the subject a composition comprising a first bacterial species and a second bacterial species, wherein said first species and said second species are not the same, and said first species and said second species are independently selected from the group consisting of SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, SEQ ID NO:81, SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, SEQ ID NO:78, SEQ ID NO:26, SEQ ID NO:158, SEQ ID NO:159, SEQ ID NO:160, SEQ ID NO:161, SEQ ID NO:162, SEQ ID NO:163, SEQ ID NO:20, SEQ ID NO:132, SEQ ID NO: No. 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 10266, SEQ ID NO: 10367, SEQ ID NO: 10468, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 14, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, SEQ ID NO: 114, SEQ ID NO: 13, SEQ ID NO: 110, SEQ ID NO: 25, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56, SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 152 , SEQ ID NO:153, SEQ ID NO:154, SEQ ID NO:155, SEQ ID NO:156, SEQ ID NO:157, SEQ ID NO:12, SEQ ID NO:106, SEQ ID NO:107, SEQ ID NO:108, SEQ ID NO:109, SEQ ID NO:9, SEQ ID NO:97, SEQ ID NO:98, SEQ ID NO:99, SEQ ID NO:15, SEQ ID NO:115, SEQ ID NO:116, SEQ ID NO:7, SEQ ID NO:87, SEQ ID NO:88, SEQ ID NO:89, SEQ ID NO:90, SEQ ID NO:91, SEQ ID NO:16, SEQ ID NO:8, SEQ ID NO:92, SEQ ID NO:93, SEQ ID NO:94, SEQ ID NO:95, SEQ ID NO:96, SEQ ID NO:3, SEQ ID NO:71, SEQ ID NO:72, SEQ ID NO:73 19, SEQ ID NO:126, SEQ ID NO:127, SEQ ID NO:128, SEQ ID NO:129, SEQ ID NO:130, SEQ ID NO:131, SEQ ID NO:11, SEQ ID NO:105, SEQ ID NO:21, SEQ ID NO:133, SEQ ID NO:17, SEQ ID NO:121, SEQ ID NO:122, SEQ ID NO:123, SEQ ID NO:124, SEQ ID NO:28, SEQ ID NO:27, SEQ ID NO:164, SEQ ID NO:18, SEQ ID NO:125, SEQ ID NO:6, SEQ ID NO:82, SEQ ID NO:83, SEQ ID NO:84, SEQ ID NO:85, SEQ ID NO:86, SEQ ID NO:22, SEQ ID NO:134, SEQ ID NO:24, SEQ ID NO:149, SEQ ID NO:150, SEQ ID NO:151, SEQ ID NO:23,SEQ ID NO:135, SEQ ID NO:136, SEQ ID NO:137, SEQ ID NO:138, SEQ ID NO:139, SEQ ID NO:140, SEQ ID NO:141, SEQ ID NO:142, SEQ ID NO:143, SEQ ID NO:144, SEQ ID NO:145, SEQ ID NO:146, SEQ ID NO:147, SEQ ID NO:148, SEQ ID NO:29, SEQ ID NO:32, SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, or SEQ ID NO:37, SEQ ID NO:30, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41, SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, The method comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to any one of the sequences set forth in SEQ ID NO:166, SEQ ID NO:167, SEQ ID NO:168, SEQ ID NO:169, SEQ ID NO:170, SEQ ID NO:171, SEQ ID NO:172, SEQ ID NO:31, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:173, SEQ ID NO:174, SEQ ID NO:175, SEQ ID NO:176, or SEQ ID NO:

177.

43. 43. The method of claim 42, wherein treating neutropenia comprises (i) reducing or preventing the occurrence of an infection in the subject, (ii) reducing or preventing the symptoms of neutropenia in the subject, or (iii) both (i) and (ii).

44. 44. The method of claim 42 or 43, wherein the neutropenia comprises cancer neutropenia.

45. 1. A method of treating a disease or disorder associated with solid organ transplantation in a subject in need thereof, comprising administering to the subject a composition comprising a first bacterial species and a second bacterial species, wherein said first species and said second species are not the same, and said first species and said second species are independently selected from the group consisting of SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, SEQ ID NO:81, SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, SEQ ID NO:78, SEQ ID NO:26, SEQ ID NO:158, SEQ ID NO:159, SEQ ID NO:160, SEQ ID NO:161, SEQ ID NO:162, SEQ ID NO:163, SEQ ID NO:20, SEQ ID NO:132, SEQ ID NO:10, SEQ ID NO:100, SEQ ID NO:101, SEQ ID NO:10266, SEQ ID NO:10367, SEQ ID NO:10468, SEQ ID NO:69, SEQ ID NO:70, SEQ ID NO:1, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, SEQ ID NO:65, SEQ ID NO:14, SEQ ID NO:111, SEQ ID NO:112, SEQ ID NO:113, SEQ ID NO:114, SEQ ID NO:13, SEQ ID NO:110, SEQ ID NO:25, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, SEQ ID NO:54, SEQ ID NO:55, SEQ ID NO:56, SEQ ID NO:57, SEQ ID NO:58, SEQ ID NO: No. 59, SEQ ID NO: 60, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO: 155, SEQ ID NO: 156, SEQ ID NO: 157, SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 9, SEQ ID NO: 97, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 15, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, SEQ ID NO: 91, SEQ ID NO: 16, SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, SEQ ID NO: 96, SEQ ID NO: 3 71, SEQ ID NO:72, SEQ ID NO:73, SEQ ID NO:19, SEQ ID NO:126, SEQ ID NO:127, SEQ ID NO:128, SEQ ID NO:129, SEQ ID NO:130, SEQ ID NO:131, SEQ ID NO:11, SEQ ID NO:105, SEQ ID NO:21, SEQ ID NO:133, SEQ ID NO:17, SEQ ID NO:121, SEQ ID NO:122, SEQ ID NO:123, SEQ ID NO:124, SEQ ID NO:28, SEQ ID NO:27, SEQ ID NO:164, SEQ ID NO:18, SEQ ID NO:125, SEQ ID NO:6, SEQ ID NO:82, SEQ ID NO:83, SEQ ID NO:84, SEQ ID NO:85, SEQ ID NO:86, SEQ ID NO:22, SEQ ID NO:134, SEQ ID NO:24, SEQ ID NO:149,SEQ ID NO:150, SEQ ID NO:151, SEQ ID NO:23, SEQ ID NO:135, SEQ ID NO:136, SEQ ID NO:137, SEQ ID NO:138, SEQ ID NO:139, SEQ ID NO:140, SEQ ID NO:141, SEQ ID NO:142, SEQ ID NO:143, SEQ ID NO:144, SEQ ID NO:145, SEQ ID NO:146, SEQ ID NO:147, SEQ ID NO:148, SEQ ID NO:29, SEQ ID NO:32, SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, or SEQ ID NO:37, SEQ ID NO:30, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41, SEQ ID NO:42, SEQ ID NO: No. 43, SEQ ID NO: 44, SEQ ID NO: 166, SEQ ID NO: 167, SEQ ID NO: 168, SEQ ID NO: 169, SEQ ID NO: 170, SEQ ID NO: 171, SEQ ID NO: 172, SEQ ID NO: 31, SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 173, SEQ ID NO: 174, SEQ ID NO: 175, SEQ ID NO: 176, or SEQ ID NO:

177. The method of claim 1, wherein the 16S rDNA sequence has at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to any one of the sequences set forth in SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 166, SEQ ID NO: 167, SEQ ID NO: 168, SEQ ID NO: 169, SEQ ID NO: 170, SEQ ID NO: 171, SEQ ID NO: 172, SEQ ID NO: 31, SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 173, SEQ ID NO: 174, SEQ ID NO: 175, SEQ ID NO: 176, or SEQ ID NO:

177.

46. 46. ​​The method of claim 45, wherein treating a disease or disorder associated with solid organ transplantation comprises (i) reducing or preventing the occurrence of an infection in the subject, (ii) reducing or preventing symptoms of the disease or disorder associated with solid organ transplantation in the subject, or (iii) both (i) and (ii).

47. 47. The method of claim 45 or 46, wherein the solid organ transplant comprises a liver transplant.

48. The first species and / or the second species is SEQ ID NO:1, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, SEQ ID NO:65, SEQ ID NO:2, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:69, SEQ ID NO:70, SEQ ID NO:3, SEQ ID NO:71, SEQ ID NO:72, SEQ ID NO:73, SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, SEQ ID NO:78, SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, SEQ ID NO:81, SEQ ID NO:6, SEQ ID NO:82, SEQ ID NO:83, SEQ ID NO:84, SEQ ID NO:85, SEQ ID NO:8 ...79, SEQ ID NO:80, SEQ ID NO:81, SEQ ID NO:6, SEQ ID NO:82, SEQ ID NO:83, SEQ ID NO:84, SEQ ID NO:85, SEQ ID NO:86, SEQ ID NO:77, SEQ ID NO:78, SEQ ID NO:79, SEQ ID NO:80, SEQ ID NO:81, SEQ ID NO:6, SEQ ID NO:82, SEQ ID NO:83, SEQ ID NO:84 48. The method of any one of claims 37-47, comprising a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in any one of SEQ ID NO: 87, SEQ ID NO:88, SEQ ID NO:89, SEQ ID NO:90, SEQ ID NO:91, SEQ ID NO:8, SEQ ID NO:92, SEQ ID NO:93, SEQ ID NO:94, SEQ ID NO:95, SEQ ID NO:96, SEQ ID NO:10, SEQ ID NO:100, SEQ ID NO:101, SEQ ID NO:102, SEQ ID NO:103, SEQ ID NO:104, SEQ ID NO:12, SEQ ID NO:106, SEQ ID NO:107, SEQ ID NO:108, or SEQ ID NO:

109.

49. The plurality of bacteria is selected from the group consisting of: (a) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:1, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, SEQ ID NO:65, or (b) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:2, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:69, or SEQ ID NO:70; (c) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73; (d) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, or SEQ ID NO:78; (e) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, or SEQ ID NO:81; (f) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:6, SEQ ID NO:82, SEQ ID NO:83, SEQ ID NO:84, SEQ ID NO:85, or SEQ ID NO:86; (g) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:7, SEQ ID NO:87, SEQ ID NO:88, SEQ ID NO:89, SEQ ID NO:90, or SEQ ID NO:91; (h) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:8, SEQ ID NO:92, SEQ ID NO:93, SEQ ID NO:94, SEQ ID NO:95, or SEQ ID NO:96; (i) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104; and (j) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO:

109. The method of any one of claims 37 to 48, comprising each of:

50. 50. The method of claim 48 or 49, wherein the plurality of bacteria further comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:9, SEQ ID NO:97, SEQ ID NO:98, SEQ ID NO:

99.

51. 51. The method of any one of claims 48-50, wherein the plurality of bacteria further comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:15, SEQ ID NO:115, or SEQ ID NO:

116.

52. 52. The method of any one of claims 48-51, wherein the plurality of bacteria further comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:11, or SEQ ID NO:

105.

53. 53. The method of any one of claims 48-52, wherein the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:13 or SEQ ID NO:

110.

54. 54. The method of any one of claims 48-53, wherein the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:14, SEQ ID NO:111, SEQ ID NO:112, SEQ ID NO:113, or SEQ ID NO:

114.

55. 55. The method of any one of claims 48-54, wherein the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:

16.

56. 56. The method of any one of claims 48-55, wherein the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:

17.

57. 57. The method of any one of claims 48-56, wherein the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:

28.

58. 58. The method of any one of claims 48-57, wherein the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:18 or SEQ ID NO:

125.

59. 59. The method of any one of claims 48-58, wherein the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:19, SEQ ID NO:126, SEQ ID NO:127, SEQ ID NO:128, SEQ ID NO:129, SEQ ID NO:130, or SEQ ID NO:

131.

60. 60. The method of any one of claims 48-59, wherein the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:20 or SEQ ID NO:

132.

61. 61. The method of any one of claims 48-60, wherein the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:21 or SEQ ID NO:

133.

62. 62. The method of any one of claims 48-61, wherein the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:22 or SEQ ID NO:

134.

63. 63. The method of any one of claims 48-62, wherein the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:23, SEQ ID NO:135, SEQ ID NO:136, SEQ ID NO:137, SEQ ID NO:138, SEQ ID NO:139, SEQ ID NO:140, SEQ ID NO:141, SEQ ID NO:142, SEQ ID NO:143, SEQ ID NO:144, SEQ ID NO:145, SEQ ID NO:146, SEQ ID NO:147, or SEQ ID NO:

148.

64. 64. The method of any one of claims 48-63, wherein the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:24, SEQ ID NO:149, SEQ ID NO:150, or SEQ ID NO:

151.

65. 65. The method of any one of claims 48-64, wherein the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:25, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, SEQ ID NO:54, SEQ ID NO:55, SEQ ID NO:56, SEQ ID NO:57, SEQ ID NO:58, SEQ ID NO:59, SEQ ID NO:60, SEQ ID NO:152, SEQ ID NO:153, SEQ ID NO:154, SEQ ID NO:155, SEQ ID NO:156, or SEQ ID NO:

157.

66. 66. The method of any one of claims 48-65, wherein the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:26, SEQ ID NO:158, SEQ ID NO:159, SEQ ID NO:160, SEQ ID NO:161, SEQ ID NO:162, or SEQ ID NO:

163.

67. 67. The method of any one of claims 48-66, wherein the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:27 or SEQ ID NO:

164.

68. 68. The method of any one of claims 48-67, wherein the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:29, SEQ ID NO:32, SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, or SEQ ID NO:

37.

69. 69. The method of any one of claims 48-68, wherein the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:30, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41, SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO:166, SEQ ID NO:167, SEQ ID NO:168, SEQ ID NO:169, SEQ ID NO:170, SEQ ID NO:171, or SEQ ID NO:

172.

70. 70. The method of any one of claims 48-69, wherein the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:31, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:173, SEQ ID NO:174, SEQ ID NO:175, SEQ ID NO:176, or SEQ ID NO:

177.

71. The plurality of bacteria is selected from the group consisting of: (a) (1) 16S rDNA sequence shown in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65, (2) 16S rDNA sequence shown in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70, (3) 16S rDNA sequence shown in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73, (4) 16S rDNA sequence shown in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78, (5) 16S rDNA sequence shown in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81, (6) 16S rDNA sequence shown in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86, (7) 16S rDNA sequence shown in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91 rDNA sequence, (8) 16S rDNA sequence shown in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96, (9) 16S rDNA sequence shown in SEQ ID NO: 9, SEQ ID NO: 97, SEQ ID NO: 98, SEQ ID NO: 99, (10) 16S rDNA sequence shown in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104, (11) 16S rDNA sequence shown in SEQ ID NO: 11 or SEQ ID NO: 105, (12) 16S rDNA sequence shown in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109, (13) 16S rDNA sequence shown in SEQ ID NO: 13 or SEQ ID NO: 110, (14) 16S rDNA sequence shown in SEQ ID NO: 14, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, or SEQ ID NO: 114 rDNA sequence, and (15) a 16S rDNA sequence set forth in SEQ ID NO: 15, SEQ ID NO: 115, or SEQ ID NO: 116; (b) (1) the 16S rDNA sequence shown in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65; (2) the 16S rDNA sequence shown in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70; (3) the 16S rDNA sequence shown in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73; (4) the 16S rDNA sequence shown in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78; (5) the 16S rDNA sequence shown in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81; (6) the 16S rDNA sequence shown in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86; (7) the 16S rDNA sequence shown in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91 rDNA sequence, (8) a 16S rDNA sequence shown in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96, (9) a 16S rDNA sequence shown in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104, (10) a 16S rDNA sequence shown in SEQ ID NO: 11 or SEQ ID NO: 105, (11) a 16S rDNA sequence shown in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109, (12) a 16S rDNA sequence shown in SEQ ID NO: 13 or SEQ ID NO: 110, (13) a 16S rDNA sequence shown in SEQ ID NO: 14, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, or SEQ ID NO: 114, and (14) a 16S rDNA sequence shown in SEQ ID NO: 15, SEQ ID NO: 115, or SEQ ID NO: 116, (c) (1) 16S rDNA sequence shown in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, (2) 16S rDNA sequence shown in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70, (3) 16S rDNA sequence shown in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73, (4) 16S rDNA sequence shown in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78, (5) 16S rDNA sequence shown in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81, (6) 16S rDNA sequence shown in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86, (7) 16S rDNA sequence shown in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91 rDNA sequence, (8) 16S rDNA sequence shown in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96, (9) 16S rDNA sequence shown in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104, (10) 16S rDNA sequence shown in SEQ ID NO: 11 or SEQ ID NO: 105, (11) 16S rDNA sequence shown in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109, (12) 16S rDNA sequence shown in SEQ ID NO: 13 or SEQ ID NO: 110, (13) 16S rDNA sequence shown in SEQ ID NO: 14, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, or SEQ ID NO: 114, (14) 16S rDNA sequence shown in SEQ ID NO: 15, SEQ ID NO: 115, or SEQ ID NO: 116, (15) 16S rDNA sequence shown in SEQ ID NO: 16 rDNA sequence, (16) the 16S rDNA sequence shown in SEQ ID NO: 28 or SEQ ID NO: 165, and (17) the 16S rDNA sequence shown in SEQ ID NO: 24, SEQ ID NO: 149, SEQ ID NO: 150, or SEQ ID NO: 151; (d) (1) the 16S rDNA sequence shown in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65; (2) the 16S rDNA sequence shown in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70; (3) the 16S rDNA sequence shown in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73; (4) the 16S rDNA sequence shown in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78; (5) the 16S rDNA sequence shown in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81; (6) the 16S rDNA sequence shown in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86; (7) the 16S rDNA sequence shown in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91 rDNA sequence, (8) 16S rDNA sequence shown in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96, (9) 16S rDNA sequence shown in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104, (10) 16S rDNA sequence shown in SEQ ID NO: 11 or SEQ ID NO: 105, (11) 16S rDNA sequence shown in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109, (12) 16S rDNA sequence shown in SEQ ID NO: 13 or SEQ ID NO: 110, (13) 16S rDNA sequence shown in SEQ ID NO: 14, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, or SEQ ID NO: 114, (14) 16S rDNA sequence shown in SEQ ID NO: 15, SEQ ID NO: 115, or SEQ ID NO: 116, (15) 16S rDNA sequence shown in SEQ ID NO: 16 rDNA sequence, (16) the 16S rDNA sequence shown in SEQ ID NO: 17, SEQ ID NO: 121, SEQ ID NO: 122, SEQ ID NO: 123, or SEQ ID NO: 124, and (17) the 16S rDNA sequence shown in SEQ ID NO: 24, SEQ ID NO: 149, SEQ ID NO: 150, or SEQ ID NO: 151; (e) (1) the 16S rDNA sequence shown in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65; (2) the 16S rDNA sequence shown in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70; (3) the 16S rDNA sequence shown in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73; (4) the 16S rDNA sequence shown in SEQ ID NO: 4, or SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78; (5) the 16S rDNA sequence shown in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81; (6) the 16S rDNA sequence shown in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86; (7) the 16S rDNA sequence shown in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91 rDNA sequence, (8) 16S rDNA sequence shown in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96, (9) 16S rDNA sequence shown in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104, (10) 16S rDNA sequence shown in SEQ ID NO: 11 or SEQ ID NO: 105, (11) 16S rDNA sequence shown in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109, (12) 16S rDNA sequence shown in SEQ ID NO: 13 or SEQ ID NO: 110, (13) 16S rDNA sequence shown in SEQ ID NO: 14, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, or SEQ ID NO: 114, (14) 16S rDNA sequence shown in SEQ ID NO: 15, SEQ ID NO: 115, or SEQ ID NO: 116, (15) 16S rDNA sequence shown in SEQ ID NO: 16 rDNA sequence, (16) the 16S rDNA sequence shown in SEQ ID NO: 17, SEQ ID NO: 121, SEQ ID NO: 122, SEQ ID NO: 123, or SEQ ID NO: 124, and (17) the 16S rDNA sequence shown in SEQ ID NO: 24, SEQ ID NO: 149, SEQ ID NO: 150, or SEQ ID NO: 151; (f) (1) a 16S rDNA sequence shown in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65; (2) a 16S rDNA sequence shown in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70; (3) a 16S rDNA sequence shown in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73; (4) a 16S rDNA sequence shown in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78; (5) a 16S rDNA sequence shown in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81; (6) a 16S rDNA sequence shown in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86; (7) a 16S rDNA sequence shown in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO:

91. rDNA sequence, (8) 16S rDNA sequence shown in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96, (9) 16S rDNA sequence shown in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104, (10) 16S rDNA sequence shown in SEQ ID NO: 11 or SEQ ID NO: 105, (11) 16S rDNA sequence shown in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109, (12) 16S rDNA sequence shown in SEQ ID NO: 13 or SEQ ID NO: 110, (13) 16S rDNA sequence shown in SEQ ID NO: 14, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, or SEQ ID NO: 114, (14) 16S rDNA sequence shown in SEQ ID NO: 15, SEQ ID NO: 115, or SEQ ID NO: 116, (15) 16S rDNA sequence shown in SEQ ID NO: 16 rDNA sequence, (16) 16S rDNA sequence shown in SEQ ID NO: 17, SEQ ID NO: 121, SEQ ID NO: 122, SEQ ID NO: 123, or SEQ ID NO: 124, (17) 16S rDNA sequence shown in SEQ ID NO: 18 or SEQ ID NO: 125, (18) 16S rDNA sequence shown in SEQ ID NO: 19, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 128, SEQ ID NO: 129, SEQ ID NO: 130, or SEQ ID NO: 131rDNA sequence, and (19) the 16S rDNA sequence shown in SEQ ID NO: 20 or SEQ ID NO: 132; (g) (1) the 16S rDNA sequence shown in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65; (2) the 16S rDNA sequence shown in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70; (3) the 16S rDNA sequence shown in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73; (4) the 16S rDNA sequence shown in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78; (5) the 16S rDNA sequence shown in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81; (6) the 16S rDNA sequence shown in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86; (7) the 16S rDNA sequence shown in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91 rDNA sequence, (8) 16S rDNA sequence shown in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96, (9) 16S rDNA sequence shown in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104, (10) 16S rDNA sequence shown in SEQ ID NO: 11 or SEQ ID NO: 105, (11) 16S rDNA sequence shown in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109, (12) 16S rDNA sequence shown in SEQ ID NO: 13 or SEQ ID NO: 110, (13) 16S rDNA sequence shown in SEQ ID NO: 14, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, or SEQ ID NO: 114, (14) 16S rDNA sequence shown in SEQ ID NO: 15, SEQ ID NO: 115, or SEQ ID NO: 116, (15) 16S rDNA sequence shown in SEQ ID NO: 16 rDNA sequence, (16) 16S rDNA sequence shown in SEQ ID NO: 17, SEQ ID NO: 121, SEQ ID NO: 122, SEQ ID NO: 123, or SEQ ID NO: 124, (17) 16S rDNA sequence shown in SEQ ID NO: 18 or SEQ ID NO: 125, (18) 16S rDNA sequence shown in SEQ ID NO: 19, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 128, SEQ ID NO: 129, SEQ ID NO: 130, or SEQ ID NO: 131rDNA sequence, (19) the 16S rDNA sequence shown in SEQ ID NO: 20 or SEQ ID NO: 132, (20) the 16S rDNA sequence shown in SEQ ID NO: 21 or SEQ ID NO: 133, (21) the 16S rDNA sequence shown in SEQ ID NO: 22 or SEQ ID NO: 134, and (22) the 16S rDNA sequence shown in SEQ ID NO: 23, SEQ ID NO: 135, SEQ ID NO: 136, SEQ ID NO: 137, SEQ ID NO: 138, SEQ ID NO: 139, SEQ ID NO: 140, SEQ ID NO: 141, SEQ ID NO: 142, SEQ ID NO: 143, SEQ ID NO: 144, SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NO: 147, or SEQ ID NO: 148, (h) (1) the 16S rDNA sequence shown in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65; (2) the 16S rDNA sequence shown in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70; (3) the 16S rDNA sequence shown in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73; (4) the 16S rDNA sequence shown in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78; (5) the 16S rDNA sequence shown in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81; (6) the 16S rDNA sequence shown in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86; (7) the 16S rDNA sequence shown in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91 rDNA sequence, (8) 16S rDNA sequence shown in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96, (9) 16S rDNA sequence shown in SEQ ID NO: 9, SEQ ID NO: 97, SEQ ID NO: 98, SEQ ID NO: 99, (10) 16S rDNA sequence shown in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104, (11) 16S rDNA sequence shown in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109, (12) 16S rDNA sequence shown in SEQ ID NO: 25, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56, SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO: 155, SEQ ID NO: 156, or SEQ ID NO: 157 rDNA sequence, and (13) a 16S rDNA sequence set forth in SEQ ID NO: 26, SEQ ID NO: 158, SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 161, SEQ ID NO: 162, or SEQ ID NO: 163; (i) (1) 16S rDNA sequence shown in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65, (2) 16S rDNA sequence shown in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70, (3) 16S rDNA sequence shown in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73, (4) 16S rDNA sequence shown in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78, (5) 16S rDNA sequence shown in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81, (6) 16S rDNA sequence shown in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86, (7) 16S rDNA sequence shown in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91 rDNA sequence, (8) 16S rDNA sequence shown in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96, (9) 16S rDNA sequence shown in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104, (10) 16S rDNA sequence shown in SEQ ID NO: 11 or SEQ ID NO: 105, (11) 16S rDNA sequence shown in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109, (12) 16S rDNA sequence shown in SEQ ID NO: 13 or SEQ ID NO: 110, (13) 16S rDNA sequence shown in SEQ ID NO: 14, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, or SEQ ID NO: 114, (14) 16S rDNA sequence shown in SEQ ID NO: 15, SEQ ID NO: 115, or SEQ ID NO: 116 rDNA sequence, (15) the 16S rDNA sequence shown in SEQ ID NO: 26, SEQ ID NO: 158, SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 161, SEQ ID NO: 162, or SEQ ID NO: 163, and (16) the 16S rDNA sequence shown in SEQ ID NO: 27 or SEQ ID NO: 164; (j) (1) 16S rDNA sequence shown in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65; (2) 16S rDNA sequence shown in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70; (3) 16S rDNA sequence shown in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73; (4) 16S rDNA sequence shown in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78; (5) 16S rDNA sequence shown in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81; (6) 16S rDNA sequence shown in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86; (7) 16S rDNA sequence shown in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91 rDNA sequence, (8) 16S rDNA sequence shown in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96, (9) 16S rDNA sequence shown in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104, (10) 16S rDNA sequence shown in SEQ ID NO: 11 or SEQ ID NO: 105, (11) 16S rDNA sequence shown in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109, (12) 16S rDNA sequence shown in SEQ ID NO: 13 or SEQ ID NO: 110, (13) 16S rDNA sequence shown in SEQ ID NO: 14, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, or SEQ ID NO: 114, (14) 16S rDNA sequence shown in SEQ ID NO: 15, SEQ ID NO: 115, or SEQ ID NO: 116, (15) 16S rDNA sequence shown in SEQ ID NO: 16 rDNA sequence, (16) the 16S rDNA sequence shown in SEQ ID NO: 28 or SEQ ID NO: 165, (17) the 16S rDNA sequence shown in SEQ ID NO: 24, SEQ ID NO: 149, SEQ ID NO: 150, or SEQ ID NO: 151, (18) the 16S rDNA sequence shown in SEQ ID NO: 26, SEQ ID NO: 158, SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 161, SEQ ID NO: 162, or SEQ ID NO: 163rDNA sequence, and (19) the 16S rDNA sequence shown in SEQ ID NO: 27 or SEQ ID NO: 164; (k) (1) 16S rDNA sequence shown in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65; (2) 16S rDNA sequence shown in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70; (3) 16S rDNA sequence shown in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73; (4) 16S rDNA sequence shown in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78; (5) 16S rDNA sequence shown in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81; (6) 16S rDNA sequence shown in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86; (7) 16S rDNA sequence shown in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91 rDNA sequence, (8) a 16S rDNA sequence shown in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96, (9) a 16S rDNA sequence shown in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104, (10) a 16S rDNA sequence shown in SEQ ID NO: 11 or SEQ ID NO: 105, (11) a 16S rDNA sequence shown in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109, (12) a 16S rDNA sequence shown in SEQ ID NO: 13 or SEQ ID NO: 110, and (13) a 16S rDNA sequence shown in SEQ ID NO: 15, SEQ ID NO: 115, or SEQ ID NO: 116, (1) (1) 16S rDNA sequence shown in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65; (2) 16S rDNA sequence shown in SEQ ID NO: 2, or SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70; (3) 16S rDNA sequence shown in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73; (4) 16S rDNA sequence shown in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78; (5) 16S rDNA sequence shown in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81; (6) 16S rDNA sequence shown in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86; (7) 16S rDNA sequence shown in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91 rDNA sequence, (8) 16S rDNA sequence shown in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96, (9) 16S rDNA sequence shown in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104, (10) 16S rDNA sequence shown in SEQ ID NO: 11 or SEQ ID NO: 105, (11) 16S rDNA sequence shown in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109, (12) 16S rDNA sequence shown in SEQ ID NO: 13 or SEQ ID NO: 110, (13) 16S rDNA sequence shown in SEQ ID NO: 14, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, or SEQ ID NO: 114, (14) 16S rDNA sequence shown in SEQ ID NO: 15, SEQ ID NO: 115, or SEQ ID NO: 116, (15) 16S rDNA sequence shown in SEQ ID NO: 16 rDNA sequence, (16) 16S rDNA sequence shown in SEQ ID NO: 17, SEQ ID NO: 121, SEQ ID NO: 122, SEQ ID NO: 123, or SEQ ID NO: 124, (17) 16S rDNA sequence shown in SEQ ID NO: 21 or SEQ ID NO: 133, (18) 16S rDNA sequence shown in SEQ ID NO: 22 or SEQ ID NO: 134rDNA sequence, and (19) the 16S rDNA sequence set forth in SEQ ID NO: 23, SEQ ID NO: 135, SEQ ID NO: 136, SEQ ID NO: 137, SEQ ID NO: 138, SEQ ID NO: 139, SEQ ID NO: 140, SEQ ID NO: 141, SEQ ID NO: 142, SEQ ID NO: 143, SEQ ID NO: 144, SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NO: 147, or SEQ ID NO: 148; or (m) (1) 16S rDNA sequence shown in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65; (2) 16S rDNA sequence shown in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70; (3) 16S rDNA sequence shown in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73; (4) 16S rDNA sequence shown in SEQ ID NO: 29, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 36, or SEQ ID NO: 37; (5) 16S rDNA sequence shown in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81; (6) 16S rDNA sequence shown in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86; (7) 16S rDNA sequence shown in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91 rDNA sequence, (8) 16S rDNA sequence shown in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96, (9) 16S rDNA sequence shown in SEQ ID NO: 9, SEQ ID NO: 97, SEQ ID NO: 98, or SEQ ID NO: 99, (10) 16S rDNA sequence shown in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104, (11) 16S rDNA sequence shown in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109, (12) 16S rDNA sequence shown in SEQ ID NO: 14, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, or SEQ ID NO: 114 rDNA sequence, (13) 16S rDNA sequence shown in SEQ ID NO: 25, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56, SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO: 155, SEQ ID NO: 156, or SEQ ID NO: 157, (14) 16S rDNA sequence shown in SEQ ID NO: 26, SEQ ID NO: 158, SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 161, SEQ ID NO: 162, or SEQ ID NO: 163rDNA sequence, (15) SEQ ID NO: 30, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 166, SEQ ID NO: 167, SEQ ID NO: 168, SEQ ID NO: 169, SEQ ID NO: 170, SEQ ID NO: 171, or SEQ ID NO: 172; and (16) SEQ ID NO: 31, SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 173, SEQ ID NO: 174, SEQ ID NO: 175, SEQ ID NO: 176, or SEQ ID NO:

177.

71. The method of any one of claims 48 to 70, comprising, consisting essentially of, or consisting of:

72. 72. The method of any one of claims 1 to 71, wherein after said administration, colonization of the gastrointestinal tract of said subject with pathogenic microorganisms is reduced or prevented.

73. 73. The method of any one of claims 1-72, wherein after said administering, the presence of pathogenic microorganisms in the gastrointestinal tract of said subject is reduced.

74. 74. The method of claim 72 or 73, wherein the pathogenic microorganism comprises Enterococcus faecium (e.g., vancomycin-resistant), Enterococcus species, Klebsiella pneumonia (e.g., carbapenem-resistant), E. coli, Staphylococcus aureus, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter species, Enterococcus faecalis, Klebsiella oxytoca, Klebsiella aerogenes, Streptococcus species, or a combination thereof.

75. The bacteria (1) are capable of colonization (long-term and / or transient) when administered to a subject; (2) are capable of anti-inflammatory activity (e.g., inhibiting TNF-α-induced IL-8 secretion in epithelial cells in vitro, and the ability to down-regulate the expression of inflammatory genes (e.g., CXCL1, CXCL2, CXCL3, CXCL11, ICAM1)); (3) are incapable of inducing pro-inflammatory activity; (4) are capable of producing secondary bile acids (e.g., 7α-dehydroxylase and bile salt hydrolase activity); (5) are capable of producing tryptophan metabolites (e.g., indole, 3-methylindole, indolepropionic acid); (6) are capable of restoring epithelial integrity as determined by a primary epithelial cell monolayer barrier integrity assay; (7) are capable of producing short chain fatty acids (e.g., (8) capable of inhibiting HDAC activity, (9) capable of producing medium-chain fatty acids (e.g., valerate, hexanoate), (10) capable of expressing catalase activity, (11) capable of having alpha-fucosidase activity, (12) capable of producing B vitamins (e.g., thiamine (B1) and / or pyridoxamine (B6)), (13) capable of reducing fecal calprotectin levels, (14) inability to activate toll-like receptor pathways (e.g., TLR4 or TLR5), (15) capable of activating toll-like receptor pathways (e.g., TLR2), (16) capable of restoring colonization resistance, (17) capable of utilizing a wide range of carbon sources, (18) capable of reducing carriage of VRE pathogens, (19) capable of reducing carriage of CRE pathogens, (20) E. (21) can reduce carriage of E. coli pathogens, (22) can reduce expression of claudin-2, (23) can associate with healthy human gut microbiota, (24) cannot associate with toxin and hemolysin genes associated with clostridial pathogens and do not produce significant cytopathic effects in vitro, (25) are sensitive to multiple clinically relevant antibiotics, (26) cannot associate with genes likely involved in both the observed antibiotic resistance and transmissibility, (27) can inhibit epithelial cell apoptosis, (28) can inhibit one or more genes induced in IFN-γ-treated colon organoids (e.g., inflammatory chemokine signaling, NF-κB signaling, TNF family signaling, type I interferon signaling,(28) can decrease the expression of one or more inhibitory receptors (e.g., TIGIT, TIM-3, or LAG-3) on CD8+ T cells; (29) can increase the expression of one or more genes / proteins associated with CD8+ T cell activation and / or function (e.g., CD45RO, CD69, IL-24, TNF-α, perforin, or IFN-γ); (30) can enhance and / or improve chemotherapeutic drug resistance; (31) can enhance immune checkpoint receptor (ICR) expression; (32) can downregulate one or more genes / proteins associated with type II interferon signaling, TLR signaling, lymphocyte trafficking, Th17 cell differentiation, Th1 differentiation, Th2 differentiation, apoptosis, inflammasomes, autophagy, oxidative stress, MHC class I and II antigen presentation, complement, mTor, nod-like receptor signaling, PI3K signaling, or a combination thereof; (33) can decrease the expression of one or more inhibitory receptors (e.g., TIGIT, TIM-3, or LAG-3) on CD8+ T cells; (34) can increase the expression of one or more genes / proteins associated with CD8+ T cell activation and / or function (e.g., CD45RO, CD69, IL-24, TNF-α, perforin, or IFN-γ); (35) can enhance and / or improve chemotherapeutic drug resistance; (36) can enhance immune checkpoint receptor (ICR) expression; (37) can downregulate one or more genes / proteins associated with type II interferon signaling, TLR signaling, lymphocyte trafficking, Th17 cell differentiation, Th1 differentiation, Th2 differentiation, apoptosis, inflammasomes, autophagy, oxidative stress, MHC class I and II antigen presentation, complement, mTor, nod-like receptor signaling, PI3K signaling, or a combination thereof; (38) can decrease the expression of one or more inhibitor (32) can enhance the efficacy of checkpoint inhibitor therapy, (33) can promote the recruitment of CD8+ T cells to tumors, (34) can induce an IL-10 / IL-6 cytokine ratio in macrophages that favors anti-inflammatory IL-10, (35) can induce a similar pathogen defense response in macrophages with less inflammatory response than donor-derived spore-based compositions (i.e., spore-based compositions), (36) can increase the amount of anti-inflammatory mediators (e.g., IL-1 receptor antagonist (IL-1RA), IL-4, IL-10, IL-11, IL-13, TGF-β), (37) can reduce colonic inflammation, (38) can treat and / or prevent diseases or disorders, such as those associated with gastrointestinal dysbiosis, (39) can increase the diversity of the gastrointestinal microbiome in a subject, and (40) can increase the diversity of the gastrointestinal microbiome in a subject. (40) improve the integrity of the mucosal and / or epithelial barrier of the subject compared to a control (e.g., an untreated patient or a subject prior to treatment); (41) promote mucosal healing; (42) reduce the incidence of infection; (43) reduce the amount of infectious disease biomarkers in the stool of the subject; (44) increase the amount of biomarkers of the administered species in the stool of the subject; (45) increase the number of colony-forming units of the administered species relative to the number of colony-forming units administered to the intestine of the subject by more than or equal to all of the administered species (e.g., 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9%) of the administered species. (46) capable of targeted delivery of (e.g., by encapsulation or by coating one or more dosage components with an enteric polymer), (47) capable of exerting a therapeutic effect following a single administration of a composition or pharmaceutical composition described herein to a subject, (48) capable of co-administration with an additional agent described herein without substantially reducing the therapeutic effect of the administered species, (49) capable of utilizing lactulose, (50) comprising a lantibiotic operon, (51) capable of being associated with decreased abundance in patients with liver disease (e.g., cirrhosis), or (52) any combination thereof.

75. The method of any one of claims 1 to 74, further comprising an additional bacterial species having one or more characteristics selected from:

76. 76. The method of any one of claims 1 to 75, wherein each of the plurality of bacteria is capable of forming spores.

77. 77. The method of any one of claims 1 to 76, wherein each of the plurality of bacteria is in spore form.

78. 78. The method of any one of claims 1 to 77, wherein each of the plurality of bacteria is not a vegetative cell.

79. 79. The method of any one of claims 1 to 78, wherein the composition further comprises a pharmaceutically acceptable excipient.

80. 80. The method of any one of claims 1 to 79, wherein the composition is administered orally to the subject.

81. 81. The method of any one of claims 1 to 80, further comprising administering to the subject an additional agent.

82. 82. The method of claim 81, wherein the additional agent is administered simultaneously with or sequentially with the composition.

83. 83. The method of claim 81 or 82, wherein the additional agent comprises a standard of care.

84. 84. The method of claim 83, wherein the standard of care comprises lactulose, rifaximin, or both.

85. 1. A composition comprising a plurality of bacteria, the plurality of bacteria comprising a first bacterial species and a second bacterial species, the first species and the second species being different, the first species and the second species being different, and the first species and the second species being selected from the group consisting of Anaerotruncus colihominis, Blautia coccoides, Blautia hominis, Blautia obeum, Blautia wexlerae, Butyricicoccus sp2, Clostridium aldenense, Clostridium bolteae, Clostridium innocuum, Clostridium sindens, Clostridium symbiosum, Dorea longicatena, Eisenbergiella tayi, Emergencia timonensis, Erysipelatoclostridium ramosum, Eubacterium Callanderi, Faecalicatena cortorta, Faecalicatena orotica, Flavonifractor plautii, Hungatella effluvii, Intestinimonas butyriciproducens, Intestinimonas massiliensis, Lactonifactor longoviformis, Lawsonibacter sp7, Massilimaliae timonensis, Murimonas intestini, Niameybacter sp1, Ruminococcus NG13 sp6, or Turicibacter sanguinis.

86. 1. A composition comprising a plurality of bacteria, the plurality of bacteria comprising a first bacterial species and a second bacterial species, wherein the first species and the second species are not the same, the first species and the second species are not the same, and the first species and the second species are selected from the group consisting of Clostridium innocuum, Clostridium bolteae, Flavonifractor platii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella. The composition is independently selected from:

87. 87. The composition of claim 86, wherein the plurality of bacteria further comprises Emergencia timonensis.

88. 88. The composition of claim 86 or 87, wherein the plurality of bacteria further comprises Intestinimonas butyriciproducens, Clostridium symbiosum, Clostridium scindens, and / or Emergencia timonensis.

89. 88. The composition of any one of claims 86-87, wherein the plurality of bacteria further comprises Faecalicatena cortorta and / or Lactonifactor longoviformis.

90. 90. The composition of any one of claims 86-89, wherein the plurality of bacteria further comprises Massilimaliae timonensis, Hungatella effluvii, and / or Butyricicoccus sp2.

91. 91. The composition of any one of claims 86-90, wherein the plurality of bacteria further comprises Intestinimonas massiliensis, Niameybacter sp1, and / or Turicibacter sanguinis.

92. 92. The composition of any one of claims 86-91, wherein the plurality of bacteria further comprises Ruminococcus NG13 sp6.

93. 93. The composition of any one of claims 86-92, wherein the plurality of bacteria further comprises Dorea longicatena.

94. 94. The composition of any one of claims 86-93, wherein the plurality of bacteria further comprises Blautia obeum.

95. 95. The composition of any one of claims 86 to 94, wherein the plurality of bacteria further comprises Lawsonibacter_sp7.

96. 96. The composition of any one of claims 86-95, wherein the plurality of bacteria further comprises Blautia hominis.

97. 97. The composition of any one of claims 86-96, wherein the plurality of bacteria further comprises Blautia wexlerae.

98. 98. The composition of any one of claims 86-97, wherein the plurality of bacteria further comprises Eubacterium callanderi.

99. 1. A composition comprising a plurality of bacteria, wherein the plurality of bacteria comprises a first bacterial species and a second bacterial species, wherein the first species and the second species are not the same, wherein the first species and the second species are not the same, and wherein the first species and the second species are independently selected from the group consisting of SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, SEQ ID NO:81, SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, SEQ ID NO:78, SEQ ID NO:26, SEQ ID NO:158, SEQ ID NO:159, SEQ ID NO:160, SEQ ID NO:161, SEQ ID NO:162, SEQ ID NO:163, SEQ ID NO:20, SEQ ID NO:132, SEQ ID NO:10, SEQ ID NO:1 00, SEQ ID NO:101, SEQ ID NO:10266, SEQ ID NO:10367, SEQ ID NO:10468, SEQ ID NO:69, SEQ ID NO:70, SEQ ID NO:1, SEQ ID NO:14, SEQ ID NO:111, SEQ ID NO:112, SEQ ID NO:113, SEQ ID NO:114, SEQ ID NO:13, SEQ ID NO:110, SEQ ID NO:25, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, SEQ ID NO:54, SEQ ID NO:55, SEQ ID NO:56, SEQ ID NO:57, SEQ ID NO:58, SEQ ID NO:59, SEQ ID NO:60, SEQ ID NO:152, SEQ ID NO:153, SEQ ID NO:154, SEQ ID NO:155, SEQ ID NO:156, SEQ ID NO:157, SEQ ID NO: No. 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 9, SEQ ID NO: 97, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 15, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91, SEQ ID NO: 16, SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, SEQ ID NO: 96, SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 19, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 128, SEQ ID NO: 129, SEQ ID NO: 13 0, SEQ ID NO:131, SEQ ID NO:11, SEQ ID NO:105, SEQ ID NO:21, SEQ ID NO:133, SEQ ID NO:17, SEQ ID NO:121, SEQ ID NO:122, SEQ ID NO:123, SEQ ID NO:124, SEQ ID NO:28, SEQ ID NO:27, SEQ ID NO:164, SEQ ID NO:18, SEQ ID NO:125, SEQ ID NO:6, SEQ ID NO:82, SEQ ID NO:83, SEQ ID NO:84, SEQ ID NO:85, SEQ ID NO:86, SEQ ID NO:22, SEQ ID NO:134, SEQ ID NO:24, SEQ ID NO:149, SEQ ID NO:150, SEQ ID NO:151, SEQ ID NO:23, SEQ ID NO:135, SEQ ID NO:136, SEQ ID NO:137, SEQ ID NO:138, SEQ ID NO:139The composition comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in any one of SEQ ID NO:140, SEQ ID NO:141, SEQ ID NO:142, SEQ ID NO:143, SEQ ID NO:144, SEQ ID NO:145, SEQ ID NO:146, SEQ ID NO:147, SEQ ID NO:148, SEQ ID NO:29, SEQ ID NO:32, SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, or SEQ ID NO:37, SEQ ID NO:30, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41, SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO:166, SEQ ID NO:167, SEQ ID NO:168, SEQ ID NO:169, SEQ ID NO:170, SEQ ID NO:171, SEQ ID NO:172, SEQ ID NO:31, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:173, SEQ ID NO:174, SEQ ID NO:175, SEQ ID NO:176, or SEQ ID NO:

177. ,

100. 1. A composition comprising a plurality of bacteria, the plurality of bacteria comprising a first bacterial species and a second bacterial species, wherein the first species and the second species are not the same, the first species and the second species are not the same, and the first species and / or the second species are selected from the group consisting of SEQ ID NO:1, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, SEQ ID NO:65, SEQ ID NO:2, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:69, SEQ ID NO:70, SEQ ID NO:3, SEQ ID NO:71, SEQ ID NO:72, SEQ ID NO:73, SEQ ID NO:4, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:77, SEQ ID NO:78, SEQ ID NO:5, SEQ ID NO:79, SEQ ID NO:80, SEQ ID NO:8 ... The composition comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to any one of the sequences set forth in SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 86, SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, SEQ ID NO: 91, SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, SEQ ID NO: 96, SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, SEQ ID NO: 104, SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO:

109.

101. 101. The composition of claim 100, wherein the plurality of bacteria further comprises a 16S rDNA sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:9, SEQ ID NO:97, SEQ ID NO:98, or SEQ ID NO:

99.

102. The plurality of bacteria (a) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 11 or SEQ ID NO: 105; (b) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 13 or SEQ ID NO: 110; (c) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 14, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, or SEQ ID NO: 114; and / or (d) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 15, SEQ ID NO: 115, or SEQ ID NO:

116.

102. The composition of claim 100 or 101, further comprising:

103. The plurality of bacteria (a) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 16; and / or (b) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 17, SEQ ID NO: 121, SEQ ID NO: 122, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 28, or SEQ ID NO:

165. The composition of any one of claims 100 to 102, further comprising:

104. The plurality of bacteria (a) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 18 or SEQ ID NO: 125; (b) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 19, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 128, SEQ ID NO: 129, SEQ ID NO: 130, or SEQ ID NO: 131; and / or (c) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 20 or SEQ ID NO:

132. The composition of any one of claims 100 to 103, further comprising:

105. The plurality of bacteria (a) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:21 or SEQ ID NO:133; (b) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO: 22 or SEQ ID NO: 134; and / or (c) SEQ ID NO: 23, SEQ ID NO: 135, SEQ ID NO: 136, SEQ ID NO: 137, SEQ ID NO: 138, SEQ ID NO: 139, SEQ ID NO: 140, SEQ ID NO: 141, SEQ ID NO: 142, SEQ ID NO: 143, SEQ ID NO: 144, SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NO: 147, or SEQ ID NO:

148. A 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity. The composition of any one of claims 96 to 100, further comprising:

106. 102. The composition of any one of claims 96-101, wherein the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:24, SEQ ID NO:149, SEQ ID NO:150, or SEQ ID NO:

151.

107. 107. The composition of any one of claims 100-106, wherein the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:25, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, SEQ ID NO:54, SEQ ID NO:55, SEQ ID NO:56, SEQ ID NO:57, SEQ ID NO:58, SEQ ID NO:59, SEQ ID NO:60, SEQ ID NO:152, SEQ ID NO:153, SEQ ID NO:154, SEQ ID NO:155, SEQ ID NO:156, or SEQ ID NO:

157.

108. 108. The composition of any one of claims 100-107, wherein the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:26, SEQ ID NO:158, SEQ ID NO:159, SEQ ID NO:160, SEQ ID NO:161, SEQ ID NO:162, or SEQ ID NO:

163.

109. 109. The composition of any one of claims 100-108, wherein the plurality of bacteria further comprises a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence set forth in SEQ ID NO:27 or SEQ ID NO:

164.

110. The plurality of bacteria (a) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to any one of the sequences set forth in SEQ ID NO:29, SEQ ID NO:32, SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, or SEQ ID NO:37; (b) a 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to any one of SEQ ID NO:30, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41, SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO:166, SEQ ID NO:167, SEQ ID NO:168, SEQ ID NO:169, SEQ ID NO:170, SEQ ID NO:171, or SEQ ID NO:172; and / or (c) SEQ ID NO: 31, SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 173, SEQ ID NO: 174, SEQ ID NO: 175, SEQ ID NO: 176, or SEQ ID NO:

177. A 16S rDNA sequence having at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to any one of the sequences set forth in SEQ ID NO: 173, SEQ ID NO: 174, SEQ ID NO: 175, SEQ ID NO: 176, or SEQ ID NO:

177. The composition of any one of claims 100 to 109, further comprising:

111. The bacteria (1) are capable of colonizing (long-term and / or transient) when administered to a subject; (2) have anti-inflammatory activity (e.g., the ability to inhibit TNF-α-induced IL-8 secretion in epithelial cells in vitro and down-regulate the expression of inflammatory genes (e.g., CXCL1, CXCL2, CXCL3, CXCL11, ICAM1)); (3) are unable to induce pro-inflammatory activity; (4) are capable of producing secondary bile acids (e.g., 7α-dehydroxylase and bile salt hydrolase activity); (5) are capable of producing tryptophan metabolites (e.g., indole, 3-methylindole, indolepropionic acid); (6) are capable of restoring and / or maintaining epithelial integrity (e.g., as determined by a primary epithelial cell monolayer barrier integrity assay); and (7) are capable of regulating short-chain lipids. (8) capable of producing fatty acids (e.g., butyrate, propionate), (9) capable of inhibiting HDAC activity, (10) capable of producing medium-chain fatty acids (e.g., valerate, hexanoate), (11) capable of expressing catalase activity, (12) capable of producing B vitamins (e.g., thiamine (B1) and / or pyridoxamine (B6)), (13) capable of reducing fecal calprotectin levels, (14) inability to activate toll-like receptor pathways (e.g., TLR4 or TLR5), (15) capable of activating toll-like receptor pathways (e.g., TLR2), (16) capable of restoring colonization resistance, (17) capable of utilizing a wide range of carbon sources, (18) capable of reducing carriage of VRE pathogens, (19) capable of reducing carriage of CRE pathogens, (20) E. (21) can reduce E. coli pathogen carriage, (22) can reduce the expression of claudin-2, (23) can associate with healthy human gut microbiota, (24) cannot associate with toxin and hemolysin genes associated with clostridial pathogens and do not produce significant cytopathic effects in vitro, (25) are sensitive to multiple clinically relevant antibiotics, (26) cannot associate with genes likely involved in both the observed antibiotic resistance and transmissibility, (27) can inhibit epithelial cell apoptosis, (28) can inhibit one or more genes induced in IFN-γ-treated colon organoids (e.g., inflammatory chemokine signaling, NF-κB signaling, TNF family signaling,(28) can decrease the expression of one or more inhibitory receptors (e.g., TIGIT, TIM-3, or LAG-3) on CD8+ T cells; (29) can increase the expression of one or more genes / proteins associated with CD8+ T cell activation and / or function (e.g., CD45RO, CD69, IL-24, TNF-α, perforin, or IFN-γ); (30) can enhance and / or ameliorate chemotherapeutic drug resistance. (31) can enhance the efficacy of immune checkpoint inhibitor therapy, (32) can promote the recruitment of CD8+ T cells to tumors, (33) can induce an IL-10 / IL-6 cytokine ratio in macrophages that favors anti-inflammatory IL-10, (34) can induce a similar pathogen defense response in macrophages with less inflammatory response than donor-derived spore-based compositions (i.e., spore-based compositions), (35) can increase the amount of anti-inflammatory mediators (e.g., IL-1 receptor antagonist (IL-1RA), IL-4, IL-10, IL-11, IL-13, TGF-β), (36) can reduce colonic inflammation, (37) can treat and / or prevent diseases or disorders, such as those associated with gastrointestinal dysbiosis, (38) can increase the diversity of the gastrointestinal microbiome in a subject, (39) see, (40) improve the integrity of the mucosal and / or epithelial barrier of the subject compared to a control (e.g., an untreated patient or a subject prior to treatment); (41) promote mucosal healing; (42) reduce the incidence of infection; (43) reduce the amount of infectious disease biomarkers in the stool of the subject; (44) increase the amount of biomarkers of the administered species in the stool of the subject; (45) increase the number of colony-forming units of the administered species relative to the number of colony-forming units administered to the intestine of the subject by more than or equal to all of the administered species (e.g., 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9%) of the administered species. (46) capable of targeted delivery of (e.g., by encapsulation or by coating one or more dosage components with an enteric polymer), (47) capable of exerting a therapeutic effect following a single administration of a composition or pharmaceutical composition described herein to a subject, (48) capable of co-administration with an additional agent described herein without substantially reducing the therapeutic effect of the administered species, (49) capable of utilizing lactulose, (50) comprising a lantibiotic operon, (51) capable of being associated with decreased abundance in patients with liver disease (e.g., cirrhosis), or (52) any combination thereof.

111. The composition of any one of claims 85 to 110, further comprising an additional bacterial species having one or more characteristics selected from:

112. 12. The composition of any one of claims 85 to 11, wherein each of the plurality of bacteria is capable of forming spores.

113. 113. The composition of any one of claims 85-112, wherein each of the plurality of bacteria is in spore form.

114. 114. The composition of any one of claims 85-113, wherein each of the plurality of bacteria is not a vegetative cell.

115. The composition of any one of claims 85 to 114, further comprising a pharmaceutically acceptable excipient.

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