Microbial Consortium

Abstract

The gastrointestinal tract contains various biological niches along its longitudinal length, and these niches have different physical, chemical, and nutrient compositions. Microbial species, including specific microbial communities, are highly responsive to their local environment and produce numerous bioactive molecules that facilitate host engraftment, intermicrobial communication, nutrient metabolism, and the inclusion or exclusion of competing microbial species. This disclosure provides a microbial consortium, including a complete microbiome replacement capable of stable engraftment in the gastrointestinal tract for the treatment of IBD, ulcerative colitis, and Crohn's disease, as well as methods for constructing and using it.

Description

[Technical Field]

[0001] Cross-reference of related applications This application claims priority to U.S. Provisional Patent Application No. 63 / 451,442, filed on 10 March 2023, and to U.S. Provisional Patent Application No. 63 / 469,080, filed on 26 May 2023, with the contents of each of those applications incorporated in whole and priority claimed to each of them.

[0002] Sequence List This application includes a sequence listing submitted electronically in XML format, which is incorporated herein by reference in its entirety. The XML copy, created on March 7, 2024, is named 0915920112.xml and has a size of 393,216 bytes.

[0003] This disclosure relates to a microbial consortium for the treatment of dysbiosis of the intestines and / or irritable bowel disease. [Background technology]

[0004] The gastrointestinal tract contains various biological niches along its longitudinal length, and these niches have different physical, chemical, and nutrient compositions. As a result of these diverse conditions, specific microbial communities are established within particular biological niches. Microbial species containing specific microbial communities are highly responsive to their local environment and produce numerous bioactive molecules that facilitate host engraftment, intermicrobial communication, nutrient metabolism, and the inclusion or exclusion of competing microbial species. Adding further complexity, substantial diversity of microbial species and strains exists in the human gastrointestinal tract between individuals, which is attributable to several factors including genetics, diet, antibiotic and antifungal use, surgical interventions (e.g., gastric bypass / colectomy), the presence of inflammatory bowel disease and / or irritable bowel syndrome, as well as other environmental influences. However, despite this inter-individual diversity, the functional attributes of various human gut microbiota are relatively consistent among healthy adults, including core metabolic pathways involved in carbohydrate metabolism, amino acid metabolism, fermentation, and oxidative phosphorylation.

[0005] The regulation of microbial species in the gastrointestinal tract through the use of antibiotics, antifungal agents, and more recently, fecal microbiota transplantation ("FMT"), has become a clinically investigated approach for the treatment and / or prevention of certain diseases and disorders. For example, Dodd et al. (Nature, 2007, 551:648-652) proposed FMT as a therapeutic method to modulate levels of aromatic amino acid metabolites in the serum of gnotobiotic mice, which affect intestinal permeability and systemic immunity. As modalities for treating various diseases and / or conditions, there is a need for microbial compositions containing multiple microbial species that possess improved therapeutic efficacy and the ability to efficiently engraft and grow in the host and metabolize pathogenic substrates into non-pathogenic metabolites within various biological niches and diverse gastrointestinal environments of different individuals. Furthermore, there is an unmet need for disease treatment using complex microbial communities that can engraft in the human gastrointestinal tract and function symbiotically for the degradation of disease-related metabolic substrates. [Prior art documents] [Non-patent literature]

[0006] [Non-Patent Document 1] Dodd et al.Nature,2007,551:648-652 [Overview of the Initiative]

[0007] This disclosure provides methods for preventing, reducing, and / or treating dysbiosis in a subject. In certain embodiments, the method is a) Clostridium citroniae, Bacteroides salyersiae, Blautia obeum, Parabacteroides merdae, Parabacteroides distasonis, Anaerostipes hadrus, Lachnospiraceae sp.FBI00033, Eubacterium eligens, Bifidobacterium dentium, Blautia wexlerae, Fusicatenibacter saccharivorans, Bacteroides nordii, Dorea formicigenerans, Dorea longicatena, Bacteroides stercorirosoris, Bifidobacterium longum, Bacteroides kribbi, Lachnospiraceae sp.FBI00071, Bacteroides thetaiotaomicron, Clostridium clostridioforme, Clostridium scindens, Roseburia hominis, Clostridium fessum, Coprococcus comes, Blautia faecis, Hungatella hathewayi, Bacteroides stercoris, Collinsella aerofaciens, Hungatella effluvii, Bifidobacterium adolescentis, Bifidobacterium catenulatum, Lactobacillus rogosae, Bacteroides faecis, Bacteroides finegoldii、Clostridiaceae sp.FBI00191, Ruminococcus faecis, Lachnoclostridium pacaense, Clostridium bolteae, Longicatena caecimuris, Eggerthella lenta, Blautia massiliensis, Bacteroides xylanisolvens, Bacteroides vulgatus, Megasphaera massiliensis, Butyricimonas faecihominis, Eisenbergiella tayi, Acidaminococcus intestini, Emergencia timonensis, Bifidobacterium pseudocatenulatum, Eubacterium hallii, Anaerofustis stercorihominis, Eubacterium ventriosum, Blautia hydrogenotrophica, and Lachnospiraceae sp. FBI00290, or their functional equivalents, or. b) FBI00001, FBI00002, FBI00010, FBI00013, FBI00029, FBI00032, FBI00033, FBI00034, FBI00043, FBI00044, FBI00048, FBI00050, FBI00051, FBI00057, FBI00059 , FBI00060, FBI00070, FBI00071, FBI00076, FBI00079, FBI00087, FBI00093, FBI00102, FBI00109, FBI00117, FBI00120, FBI00125, FBI00127, FBI00128, FBI00145, The procedure involves administering an effective amount of a microbial consortium or its pharmaceutically acceptable composition containing FBI00162, FBI00174, FBI00184, FBI00190, FBI00191, FBI00194, FBI00198, FBI00199, FBI00200, FBI00201, FBI00205, FBI00206, FBI00211, FBI00220, FBI00221, FBI00236, FBI00245, FBI00248, FBI00251, FBI00254, FBI00267, FBI00278, FBI00288, and FBI00290, or their functional equivalents.

[0008] In certain embodiments, a microbial consortium or its pharmaceutical composition is a) Acutalibacter timonensis, Alistipes onderdonkii, Bacteroides uniformis, Eubacterium rectale, Alistipes timonensis, Bacteroides kribbi, Coprococcus eutactus, Bilophila wadsworthia, Bacteroides caccae, Alistipes shahii, Parasutterella excrementihominis, Paraprevotella clara, Sutterella wadsworthensis, Sutterella massiliensis, Porphyromonas asaccharolytica, Ruminococcus bromii, Monoglobus pectinolyticus, Ruminococcaceae sp.FBI00097, Gordonibacter pamelaeae, Bacteroides uniformis, Gordonibacter pamelaeae, Bacteroides fragilis, Phascolarctobacterium faecium, Monoglobus pectinolyticus, Clostridium aldenense, Ruthenibacterium lactatiformans, Bacteroides ovatus, Bifidobacterium bifidum, Anaerotruncus massiliensis, Clostridium aldenense, Sutterella wadsworthensis, Catabacter hongkongensis, Alistipes senegalensis、Ruminococcaceae sp.FBI00233, Alistipes shahii, Dielma fastidiosa, Eubacterium siraeum, Faecalibacterium prausnitzii, Turicibacter sanguinis, Eubacterium rectale, Bacteroides caccae, Methanobrevibacter smithii, Barnesiella intestinihominis, Alistipes onderdonkii, and Methanobrevibacter smithii, or their functional equivalents. b) Bifidobacterium adolescentis, Bifidobacterium longum, Bifidobacterium pseudocatenulatum, Bacteroides thetaiotaomicron, Coprococcus comes, Fusicatenibacter saccharivorans, Eggerthella lenta, Eubacterium eligens, Bacteroides xylanisolvens, Lactobacillus rogosae, Clostridium citoniae, Collinsella aerofaciens, Blautia obeum, Eggerthella lenta, Blautia wexlerae, Lachnoclostridium pacaense, Bacteroides vulgatus, Parabacteroides merdae, Dorea formicigenerans, Ruminococcus faecis, Roseburia hominis, Anaerostipes hadrus, Bifidobacterium adolescentis, Bifidobacterium pseudocatenulatum, Clostridium bolteae, Eisenbergiella tayi, Dorea longicatena, Eggerthella lenta, Bacteroides stercoris, Hungatella hathawayi, and Bacteroides xylanisolvens, or their functional equivalents, and / or c) Alistipes putredinis, Dialister succinatiphilus, Akkermansia muciniphila, Ruminococcus bromii, Dialister invisus, Bacteroides massiliensis, Bilophila wadsworthia, Holdemanella biformis, Parasutterella excrementihominis, Alistipes sp.FBI00180, Bacteroides coprocola, Alistipes sp.FBI00238, Alistipes putredinis, Eubacterium xylanophilum, and Senegalimassilia anaerobia, or their functional equivalents, further comprising:

[0009] In certain embodiments, a microbial consortium or its pharmaceutical composition is a) FBI00004, FBI00012, FBI00015, FBI00018, FBI00019, FBI00021, FBI00038, FBI00040, FBI00046, FBI00061, FBI00066, FBI00 075, FBI00077, FBI00080, FBI00081, FBI00085, FBI00092, FBI00097, FBI00099, FBI00112, FBI00132, FBI00137, FBI00140, FBI 00149, FBI00151, FBI00176, FBI00189, FBI00197, FBI00208, FBI00212, FBI00224, FBI00226, FBI00229, FBI00233, FBI00235, FBI00237, FBI00243, FBI00244, FBI00258, FBI00260, FBI00263, FBI00270, FBI00273, FBI00277, and FBI00292, or their functional equivalents, b) FBI00009, FBI00011, FBI00016, FBI00020, FBI00025, FBI00027, FBI00030, FBI00047, FB I00052, FBI00053, FBI00056, FBI00062, FBI00078, FBI00096, FBI00104, FBI00110, FBI0011 1, FBI00113, FBI00115, FBI00116, FBI00123, FBI00124, FBI00126, FBI00135, FBI00147, FBI00159, FBI00167, FBI00170, FBI00232, FBI00255, and FBI00271, or their functional equivalents, and / or c) FBI00022, FBI00049, FBI00068, FBI00069, FBI00152, FBI00165, FBI00171, FBI00175, FBI00177, FBI00180, FBI00182, FBI00238, FBI00269, FBI00274, and FBI00281, or their functional equivalents, further included.

[0010] In certain embodiments, the microbial consortium or its pharmaceutical composition further comprises a first strain of Oxalobacter formigenes or FBI00067. In certain embodiments, the microbial consortium or its pharmaceutical composition further comprises a second strain of Oxalobacter formigenes or FBI00133. In certain embodiments, the microbial consortium or its pharmaceutical composition further comprises a third strain of Oxalobacter formigenes or FBI00289.

[0011] In certain embodiments, a microbial consortium or its pharmaceutical composition is a) Clostridium citroniae, Bacteroides salyersiae, Blautia obeum, Parabacteroides merdae, Parabacteroides distasonis, Anaerostipes hadrus, Lachnospiraceae sp.FBI00033, Eubacterium eligens, Bifidobacterium dentium, Blautia wexlerae, Fusicatenibacter saccharivorans, Bacteroides nordii, Dorea formicigenerans, Dorea longicatena, Bacteroides stercorirosoris, Bifidobacterium longum, Bacteroides kribbi, Lachnospiraceae sp.FBI00071, Bacteroides thetaiotaomicron, Clostridium clostridioforme, Clostridium scindens, Roseburia hominis, Clostridium fessum, Coprococcus comes, Blautia faecis, Hungatella hathewayi, Bacteroides stercoris, Collinsella aerofaciens, Hungatella effluvii, Bifidobacterium adolescentis, Bifidobacterium catenulatum, Lactobacillus rogosae, Bacteroides faecis, Bacteroides finegoldii、Clostridiaceae sp.FBI00191, Ruminococcus faecis, Lachnoclostridium pacaense, Clostridium bolteae, Longicatena caecimuris, Eggerthella lenta, Blautia massiliensis, Bacteroides xylanisolvens, Bacteroides vulgatus, Megasphaera massiliensis, Butyricimonas faecihominis, Eisenbergiella tayi, Acidaminococcus intestini, Emergencia timonensis, Bifidobacterium pseudocatenulatum, Eubacterium hallii, Anaerofustis stercorihominis, Eubacterium ventriosum, Blautia hydrogenotrophica, and Lachnospiraceae sp. FBI00290, or their functional equivalents. b) Acutalibacter timonensis, Alistipes onderdonkii, Bacteroides uniformis, Eubacterium rectale, Alistipes timonensis, Bacteroides kribbi, Coprococcus eutactus, Bilophila wadsworthia, Bacteroides caccae, Alistipes shahii, Parasutterella excrementihominis, Paraprevotella clara, Sutterella wadsworthensis, Sutterella massiliensis, Porphyromonas asaccharolytica, Ruminococcus bromii, Monoglobus pectinolyticus, Ruminococcaceae sp.FBI00097, Gordonibacter pamelaeae, Bacteroides uniformis, Gordonibacter pamelaeae, Bacteroides fragilis, Phascolarctobacterium faecium, Monoglobus pectinolyticus, Clostridium aldenense, Ruthenibacterium lactatiformans, Bacteroides ovatus, Bifidobacterium bifidum, Anaerotruncus massiliensis, Clostridium aldenense, Sutterella wadsworthensis, Catabacter hongkongensis, Alistipes senegalensis、Ruminococcaceae sp.FBI00233, Alistipes shahii, Dielma fastidiosa, Eubacterium siraeum, Faecalibacterium prausnitzii, Turicibacter sanguinis, Eubacterium rectale, Bacteroides caccae, Methanobrevibacter smithii, Barnesiella intestinihominis, Alistipes onderdonkii, and Methanobrevibacter smithii, or their functional equivalents. c) Bifidobacterium adolescentis, Bifidobacterium longum, Bifidobacterium pseudocatenulatum, Bacteroides thetaiotaomicron, Coprococcus comes, Fusicatenibacter saccharivorans, Eggerthella lenta, Eubacterium eligens, Bacteroides xylanisolvens, Lactobacillus rogosae, Clostridium citoniae, Collinsella aerofaciens, Blautia obeum, Eggerthella lenta, Blautia wexlerae, Lachnoclostridium pacaense, Bacteroides vulgatus, Parabacteroides merdae, Dorea formicigenerans, Ruminococcus faecis, Roseburia hominis, Anaerostipes hadrus, Bifidobacterium adolescentis, Bifidobacterium pseudocatenulatum, Clostridium bolteae, Eisenbergiella tayi, Dorea longicatena, Eggerthella lenta, Bacteroides stercoris, Hungatella hathawayi, and Bacteroides xylanisolvens, or their functional equivalents, and d) Alistipes putredinis, Dialister succinatiphilus, Akkermansia muciniphila, Ruminococcus bromii, Dialister invisus, Bacteroides massiliensis, Bilophila wadsworthia, Holdemanella biformis, Parasutterella excrementihominis, Alistipes sp.FBI00180, Bacteroides coprocola, Alistipes sp. FBI00238, Alistipes putredinis, Eubacterium xylanophilum, and Senegalimassilia anaerobia, or their functional equivalents.

[0012] In certain embodiments, a microbial consortium or its pharmaceutical composition is a) FBI00001, FBI00002, FBI00010, FBI00013, FBI00029, FBI00032, FBI00033, FBI00034, FBI00043, FBI00044, FBI00048, FBI00050, FBI00051, FBI0005 7, FBI00059, FBI00060, FBI00070, FBI00071, FBI00076, FBI00079, FBI00087, FBI00093, FBI00102, FBI00109, FBI00117, FBI00120, FBI00125, FBI0012 7, FBI00128, FBI00145, FBI00162, FBI00174, FBI00184, FBI00190, FBI00191, FBI00194, FBI00198, FBI00199, FBI00200, FBI00201, FBI00205, FBI00206, FBI00211, FBI00220, FBI00221, FBI00236, FBI00245, FBI00248, FBI00251, FBI00254, FBI00267, FBI00278, FBI00288, and FBI00290, or their functional equivalents, b) FBI00004, FBI00012, FBI00015, FBI00018, FBI00019, FBI00021, FBI00038, FBI00040, FBI00046, FBI00061, FBI00066, FBI00 075, FBI00077, FBI00080, FBI00081, FBI00085, FBI00092, FBI00097, FBI00099, FBI00112, FBI00132, FBI00137, FBI00140, FBI 00149, FBI00151, FBI00176, FBI00189, FBI00197, FBI00208, FBI00212, FBI00224, FBI00226, FBI00229, FBI00233, FBI00235, FBI00237, FBI00243, FBI00244, FBI00258, FBI00260, FBI00263, FBI00270, FBI00273, FBI00277, and FBI00292, or their functional equivalents, c) FBI00009, FBI00011, FBI00016, FBI00020, FBI00025, FBI00027, FBI00030, FBI00047, FBI00052, FBI00053, FBI00056, FBI00062, FBI00078, FBI00096, FBI00104, FBI00110, FBI00 111, FBI00113, FBI00115, FBI00116, FBI00123, FBI00124, FBI00126, FBI00135, FBI00147, FBI00159, FBI00167, FBI00170, FBI00232, FBI00255, and FBI00271, or their functional equivalents, and d) FBI00022, FBI00049, FBI00068, FBI00069, FBI00152, FBI00165, FBI00171, FBI00175, FBI00177, FBI00180, FBI00182, FBI00238, FBI00269, FBI00274, and FBI00281, or their functional equivalents.

[0013] In certain embodiments, the microbial consortium or its pharmaceutical composition further comprises a first strain of Oxalobacter formigenes or FBI00067, a second strain of Oxalobacter formigenes or FBI00133, and a third strain of Oxalobacter formigenes or FBI00289. In certain embodiments, the microbial consortium or its pharmaceutical composition further comprises a first strain of Oxalobacter formigenes or FBI00067, a second strain of Oxalobacter formigenes or FBI00133, and a third strain of Oxalobacter formigenes or FBI00289. In certain embodiments, the microbial consortium or its pharmaceutical composition is FB-001 or its functional equivalent. In certain embodiments, the microbial consortium or its pharmaceutical composition is FB-003 or its functional equivalent.

[0014] In certain embodiments, the microbial consortium or its pharmaceutical composition increases microbial diversity in the gastrointestinal tract. In certain embodiments, the microbial consortium or its pharmaceutical composition increases short-chain fatty acids (SCFAs). In certain embodiments, the microbial consortium or its pharmaceutical composition increases secondary bile acids. In certain embodiments, the microbial consortium or its pharmaceutical composition reduces bacterial pathogens in the target gastrointestinal tract.

[0015] In a particular embodiment, the microbial consortium or its pharmaceutical composition is approximately 5 × 10 9 ~Approx. 5×10 12 Contains several living cells. In certain embodiments, the microbial consortium or its pharmaceutical composition contains about 5 × 10 9 ~Approx. 5×10 10 Contains several living cells. In certain embodiments, the microbial consortium or its pharmaceutical composition contains about 5 × 10 10 ~Approx. 5×10 11contains viable cells. In certain embodiments, the microbial consortium or its pharmaceutical composition contains from about 5×10 11 to about 5×10 12 viable cells. In certain embodiments, the microbial consortium or its pharmaceutical composition contains up to about 10 11 viable cells. In certain embodiments, the microbial consortium or its pharmaceutical composition contains up to about 10 12 viable cells.

[0016] In certain embodiments, the method includes administering a loading dose and one or more maintenance doses. In certain embodiments, the loading dose is administered for 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 days. In certain embodiments, the loading dose is administered for 2 to 3 days, 3 to 5 days, 4 to 6 days, or 5 to 7 days. In certain embodiments, the one or more maintenance doses are administered for at least 21 days after the last loading dose.

[0017] In certain embodiments, the method further comprises administering an antibacterial agent, antiviral agent, antifungal agent, anti-inflammatory agent, immunosuppressant, and / or prebiotic. In certain embodiments, the antibacterial agent is selected from the group consisting of ciprofloxacin, levaquin, phloxin, tequin, avelox, norflox, cephalexin, cefuroxime, cefadroxil, cefazolin, cephalothin, cefaclor, cephamandol, cefoxitin, cefprodil, ceftoviprole, amoxicillin, ampicillin, penicillin V, dicloxacillin, carbenicillin, vancomycin, and methicillin, tetracycline, minocycline, oxytetracycline, doxycycline, ertapenem, doripenem, imipenem / cilastatin, and meropenem. In certain embodiments, the antiviral agents include abacavir, acyclovir, adefovir, amprenavir, atazanavir, cidofovir, darunavir, delavirdin, didanosine, docosanol, efavirenz, elvitegravir, emtricitabine, enfuvirtide, etravirine, famciclovir, foscamet, homivirsen, ganciclovir, indinavir, and idoxuridine. The drug is selected from the group consisting of lamivudine, lopinavir maraviloc, mk-2048, nelfinavir, nevirapine, nilmatrelvir, penciclovir, raltegravir, rilpivirine, ritonavir, saquinavir, stabudine, tenofovir trifluridine, valacyclovir, valganciclovir, vidarabine, ivacitabine, amantadine, oseltamivir, rimantidine, tipranavir, zalcitabine, zanamivir, and zidovudine.In certain embodiments, the antifungal agent is selected from the group consisting of miconazole, ketoconazole, clotrimazole, econazole, omoconazole, bifonazole, butoconazole, fenticonazole, isoconazole, oxiconazole, sertaconazole, sulconazole, thioconazole, fluconazole, itraconazole, isabconazole, ravconazole, posaconazole, voriconazole, terconazole, albaconazole, abafungin, terbinafine, naftifine, butenafine, anidurafungin, caspofungin, micafungin, polygodial, benzoic acid, cyclopirox, tolnaphthate, undecylenic acid, flucytosine or 5-fluorocytosine, griseofulvin, and haloprozin. In certain embodiments, the anti-inflammatory and / or immunosuppressant is selected from the group consisting of cyclophosphamide, mycophenolate mofetil, corticosteroids, mesalazine, mesalamine, sulfasalazine, sulfasalazine derivatives, cyclosporine A, mercaptopurine, azathioprine, prednisone, methotrexate, antihistamines, glucocorticoids, epinephrine, theophylline, cromolyn sodium, anti-leukotrienes, anticholinergics, monoclonal anti-IgE, immunomodulatory peptides, immunomodulatory small molecules, immunomodulatory cytokines, immunomodulatory antibodies, and vaccines. In certain embodiments, the prebiotic is selected from the group consisting of amino acids, biotin, fructooligosaccharides, galactooligosaccharides, inulin, lactulose, mannan-oligosaccharides, oligofructose-concentrated inulin, oligofructose, oligodextrose, tagatose, transgalactooligosaccharides, and xylooligosaccharides.

[0018] In certain embodiments, the microbial consortium or its pharmaceutical composition is present in the food product.

[0019] This disclosure also provides methods for restoring a microbiome in a subject and / or restoring a healthy microbiome. In certain embodiments, the method is a) Clostridium citroniae, Bacteroides salyersiae, Blautia obeum, Parabacteroides merdae, Parabacteroides distasonis, Anaerostipes hadrus, Lachnospiraceae sp.FBI00033, Eubacterium eligens, Bifidobacterium dentium, Blautia wexlerae, Fusicatenibacter saccharivorans, Bacteroides nordii, Dorea formicigenerans, Dorea longicatena, Bacteroides stercorirosoris, Bifidobacterium longum, Bacteroides kribbi, Lachnospiraceae sp.FBI00071, Bacteroides thetaiotaomicron, Clostridium clostridioforme, Clostridium scindens, Roseburia hominis, Clostridium fessum, Coprococcus comes, Blautia faecis, Hungatella hathewayi, Bacteroides stercoris, Collinsella aerofaciens, Hungatella effluvii, Bifidobacterium adolescentis, Bifidobacterium catenulatum, Lactobacillus rogosae, Bacteroides faecis, Bacteroides finegoldii、Clostridiaceae sp.FBI00191, Ruminococcus faecis, Lachnoclostridium pacaense, Clostridium bolteae, Longicatena caecimuris, Eggerthella lenta, Blautia massiliensis, Bacteroides xylanisolvens, Bacteroides vulgatus, Megasphaera massiliensis, Butyricimonas faecihominis, Eisenbergiella tayi, Acidaminococcus intestini, Emergencia timonensis, Bifidobacterium pseudocatenulatum, Eubacterium hallii, Anaerofustis stercorihominis, Eubacterium ventriosum, Blautia hydrogenotrophica, and Lachnospiraceae sp. FBI00290, or their functional equivalents, or. b) FBI00001, FBI00002, FBI00010, FBI00013, FBI00029, FBI00032, FBI00033, FBI00034, FBI00043, FBI00044, FBI00048, FBI00050, FBI00051, FBI00057, FBI00059 , FBI00060, FBI00070, FBI00071, FBI00076, FBI00079, FBI00087, FBI00093, FBI00102, FBI00109, FBI00117, FBI00120, FBI00125, FBI00127, FBI00128, FBI00145, The procedure involves administering an effective amount of a microbial consortium or its pharmaceutically acceptable composition containing FBI00162, FBI00174, FBI00184, FBI00190, FBI00191, FBI00194, FBI00198, FBI00199, FBI00200, FBI00201, FBI00205, FBI00206, FBI00211, FBI00220, FBI00221, FBI00236, FBI00245, FBI00248, FBI00251, FBI00254, FBI00267, FBI00278, FBI00288, and FBI00290, or their functional equivalents.

[0020] In certain embodiments, a microbial consortium or its pharmaceutical composition is a) Acutalibacter timonensis, Alistipes onderdonkii, Bacteroides uniformis, Eubacterium rectale, Alistipes timonensis, Bacteroides kribbi, Coprococcus eutactus, Bilophila wadsworthia, Bacteroides caccae, Alistipes shahii, Parasutterella excrementihominis, Paraprevotella clara, Sutterella wadsworthensis, Sutterella massiliensis, Porphyromonas asaccharolytica, Ruminococcus bromii, Monoglobus pectinolyticus, Ruminococcaceae sp.FBI00097, Gordonibacter pamelaeae, Bacteroides uniformis, Gordonibacter pamelaeae, Bacteroides fragilis, Phascolarctobacterium faecium, Monoglobus pectinolyticus, Clostridium aldenense, Ruthenibacterium lactatiformans, Bacteroides ovatus, Bifidobacterium bifidum, Anaerotruncus massiliensis, Clostridium aldenense, Sutterella wadsworthensis, Catabacter hongkongensis, Alistipes senegalensis、Ruminococcaceae sp.FBI00233, Alistipes shahii, Dielma fastidiosa, Eubacterium siraeum, Faecalibacterium prausnitzii, Turicibacter sanguinis, Eubacterium rectale, Bacteroides caccae, Methanobrevibacter smithii, Barnesiella intestinihominis, Alistipes onderdonkii, and Methanobrevibacter smithii, or their functional equivalents. b) Bifidobacterium adolescentis, Bifidobacterium longum, Bifidobacterium pseudocatenulatum, Bacteroides thetaiotaomicron, Coprococcus comes, Fusicatenibacter saccharivorans, Eggerthella lenta, Eubacterium eligens, Bacteroides xylanisolvens, Lactobacillus rogosae, Clostridium citoniae, Collinsella aerofaciens, Blautia obeum, Eggerthella lenta, Blautia wexlerae, Lachnoclostridium pacaense, Bacteroides vulgatus, Parabacteroides merdae, Dorea formicigenerans, Ruminococcus faecis, Roseburia hominis, Anaerostipes hadrus, Bifidobacterium adolescentis, Bifidobacterium pseudocatenulatum, Clostridium bolteae, Eisenbergiella tayi, Dorea longicatena, Eggerthella lenta, Bacteroides stercoris, Hungatella hathawayi, and Bacteroides xylanisolvens, or their functional equivalents, and / or c) Alistipes putredinis, Dialister succinatiphilus, Akkermansia muciniphila, Ruminococcus bromii, Dialister invisus, Bacteroides massiliensis, Bilophila wadsworthia, Holdemanella biformis, Parasutterella excrementihominis, Alistipes sp.FBI00180, Bacteroides coprocola, Alistipes sp.FBI00238, Alistipes putredinis, Eubacterium xylanophilum, and Senegalimassilia anaerobia, or their functional equivalents, further comprising:

[0021] In certain embodiments, a microbial consortium or its pharmaceutical composition is a) FBI00004, FBI00012, FBI00015, FBI00018, FBI00019, FBI00021, FBI00038, FBI00040, FBI00046, FBI00061, FBI00066, FBI00 075, FBI00077, FBI00080, FBI00081, FBI00085, FBI00092, FBI00097, FBI00099, FBI00112, FBI00132, FBI00137, FBI00140, FBI 00149, FBI00151, FBI00176, FBI00189, FBI00197, FBI00208, FBI00212, FBI00224, FBI00226, FBI00229, FBI00233, FBI00235, FBI00237, FBI00243, FBI00244, FBI00258, FBI00260, FBI00263, FBI00270, FBI00273, FBI00277, and FBI00292, or their functional equivalents, b) FBI00009, FBI00011, FBI00016, FBI00020, FBI00025, FBI00027, FBI00030, FBI00047, FB I00052, FBI00053, FBI00056, FBI00062, FBI00078, FBI00096, FBI00104, FBI00110, FBI0011 1, FBI00113, FBI00115, FBI00116, FBI00123, FBI00124, FBI00126, FBI00135, FBI00147, FBI00159, FBI00167, FBI00170, FBI00232, FBI00255, and FBI00271, or their functional equivalents, and / or c) FBI00022, FBI00049, FBI00068, FBI00069, FBI00152, FBI00165, FBI00171, FBI00175, FBI00177, FBI00180, FBI00182, FBI00238, FBI00269, FBI00274, and FBI00281, or their functional equivalents, further included.

[0022] In certain embodiments, the microbial consortium or its pharmaceutical composition further comprises a first strain of Oxalobacter formigenes or FBI00067. In certain embodiments, the microbial consortium or its pharmaceutical composition further comprises a second strain of Oxalobacter formigenes or FBI00133. In certain embodiments, the microbial consortium or its pharmaceutical composition further comprises a third strain of Oxalobacter formigenes or FBI00289.

[0023] In certain embodiments, a microbial consortium or its pharmaceutical composition is a) Clostridium citroniae, Bacteroides salyersiae, Blautia obeum, Parabacteroides merdae, Parabacteroides distasonis, Anaerostipes hadrus, Lachnospiraceae sp.FBI00033, Eubacterium eligens, Bifidobacterium dentium, Blautia wexlerae, Fusicatenibacter saccharivorans, Bacteroides nordii, Dorea formicigenerans, Dorea longicatena, Bacteroides stercorirosoris, Bifidobacterium longum, Bacteroides kribbi, Lachnospiraceae sp.FBI00071, Bacteroides thetaiotaomicron, Clostridium clostridioforme, Clostridium scindens, Roseburia hominis, Clostridium fessum, Coprococcus comes, Blautia faecis, Hungatella hathewayi, Bacteroides stercoris, Collinsella aerofaciens, Hungatella effluvii, Bifidobacterium adolescentis, Bifidobacterium catenulatum, Lactobacillus rogosae, Bacteroides faecis, Bacteroides finegoldii、Clostridiaceae sp.FBI00191, Ruminococcus faecis, Lachnoclostridium pacaense, Clostridium bolteae, Longicatena caecimuris, Eggerthella lenta, Blautia massiliensis, Bacteroides xylanisolvens, Bacteroides vulgatus, Megasphaera massiliensis, Butyricimonas faecihominis, Eisenbergiella tayi, Acidaminococcus intestini, Emergencia timonensis, Bifidobacterium pseudocatenulatum, Eubacterium hallii, Anaerofustis stercorihominis, Eubacterium ventriosum, Blautia hydrogenotrophica, and Lachnospiraceae sp. FBI00290, or their functional equivalents. b) Acutalibacter timonensis, Alistipes onderdonkii, Bacteroides uniformis, Eubacterium rectale, Alistipes timonensis, Bacteroides kribbi, Coprococcus eutactus, Bilophila wadsworthia, Bacteroides caccae, Alistipes shahii, Parasutterella excrementihominis, Paraprevotella clara, Sutterella wadsworthensis, Sutterella massiliensis, Porphyromonas asaccharolytica, Ruminococcus bromii, Monoglobus pectinolyticus, Ruminococcaceae sp.FBI00097, Gordonibacter pamelaeae, Bacteroides uniformis, Gordonibacter pamelaeae, Bacteroides fragilis, Phascolarctobacterium faecium, Monoglobus pectinolyticus, Clostridium aldenense, Ruthenibacterium lactatiformans, Bacteroides ovatus, Bifidobacterium bifidum, Anaerotruncus massiliensis, Clostridium aldenense, Sutterella wadsworthensis, Catabacter hongkongensis, Alistipes senegalensis、Ruminococcaceae sp.FBI00233, Alistipes shahii, Dielma fastidiosa, Eubacterium siraeum, Faecalibacterium prausnitzii, Turicibacter sanguinis, Eubacterium rectale, Bacteroides caccae, Methanobrevibacter smithii, Barnesiella intestinihominis, Alistipes onderdonkii, and Methanobrevibacter smithii, or their functional equivalents. c) Bifidobacterium adolescentis, Bifidobacterium longum, Bifidobacterium pseudocatenulatum, Bacteroides thetaiotaomicron, Coprococcus comes, Fusicatenibacter saccharivorans, Eggerthella lenta, Eubacterium eligens, Bacteroides xylanisolvens, Lactobacillus rogosae, Clostridium citoniae, Collinsella aerofaciens, Blautia obeum, Eggerthella lenta, Blautia wexlerae, Lachnoclostridium pacaense, Bacteroides vulgatus, Parabacteroides merdae, Dorea formicigenerans, Ruminococcus faecis, Roseburia hominis, Anaerostipes hadrus, Bifidobacterium adolescentis, Bifidobacterium pseudocatenulatum, Clostridium bolteae, Eisenbergiella tayi, Dorea longicatena, Eggerthella lenta, Bacteroides stercoris, Hungatella hathawayi, and Bacteroides xylanisolvens, or their functional equivalents, and d) Alistipes putredinis, Dialister succinatiphilus, Akkermansia muciniphila, Ruminococcus bromii, Dialister invisus, Bacteroides massiliensis, Bilophila wadsworthia, Holdemanella biformis, Parasutterella excrementihominis, Alistipes sp.FBI00180, Bacteroides coprocola, Alistipes sp. FBI00238, Alistipes putredinis, Eubacterium xylanophilum, and Senegalimassilia anaerobia, or their functional equivalents.

[0024] In certain embodiments, a microbial consortium or its pharmaceutical composition is a) FBI00001, FBI00002, FBI00010, FBI00013, FBI00029, FBI00032, FBI00033, FBI00034, FBI00043, FBI00044, FBI00048, FBI00050, FBI00051, FBI0005 7, FBI00059, FBI00060, FBI00070, FBI00071, FBI00076, FBI00079, FBI00087, FBI00093, FBI00102, FBI00109, FBI00117, FBI00120, FBI00125, FBI0012 7, FBI00128, FBI00145, FBI00162, FBI00174, FBI00184, FBI00190, FBI00191, FBI00194, FBI00198, FBI00199, FBI00200, FBI00201, FBI00205, FBI00206, FBI00211, FBI00220, FBI00221, FBI00236, FBI00245, FBI00248, FBI00251, FBI00254, FBI00267, FBI00278, FBI00288, and FBI00290, or their functional equivalents, b) FBI00004, FBI00012, FBI00015, FBI00018, FBI00019, FBI00021, FBI00038, FBI00040, FBI00046, FBI00061, FBI00066, FBI00 075, FBI00077, FBI00080, FBI00081, FBI00085, FBI00092, FBI00097, FBI00099, FBI00112, FBI00132, FBI00137, FBI00140, FBI 00149, FBI00151, FBI00176, FBI00189, FBI00197, FBI00208, FBI00212, FBI00224, FBI00226, FBI00229, FBI00233, FBI00235, FBI00237, FBI00243, FBI00244, FBI00258, FBI00260, FBI00263, FBI00270, FBI00273, FBI00277, and FBI00292, or their functional equivalents, c) FBI00009, FBI00011, FBI00016, FBI00020, FBI00025, FBI00027, FBI00030, FBI00047, FBI00052, FBI00053, FBI00056, FBI00062, FBI00078, FBI00096, FBI00104, FBI00110, FBI00 111, FBI00113, FBI00115, FBI00116, FBI00123, FBI00124, FBI00126, FBI00135, FBI00147, FBI00159, FBI00167, FBI00170, FBI00232, FBI00255, and FBI00271, or their functional equivalents, and d) FBI00022, FBI00049, FBI00068, FBI00069, FBI00152, FBI00165, FBI00171, FBI00175, FBI00177, FBI00180, FBI00182, FBI00238, FBI00269, FBI00274, and FBI00281, or their functional equivalents.

[0025] In certain embodiments, the microbial consortium or its pharmaceutical composition further comprises a first strain of Oxalobacter formigenes or FBI00067, a second strain of Oxalobacter formigenes or FBI00133, and a third strain of Oxalobacter formigenes or FBI00289. In certain embodiments, the microbial consortium or its pharmaceutical composition further comprises a first strain of Oxalobacter formigenes or FBI00067, a second strain of Oxalobacter formigenes or FBI00133, and a third strain of Oxalobacter formigenes or FBI00289. In certain embodiments, the microbial consortium or its pharmaceutical composition is FB-001 or its functional equivalent. In certain embodiments, the microbial consortium or its pharmaceutical composition is FB-003 or its functional equivalent.

[0026] In certain embodiments, the microbial consortium or its pharmaceutical composition increases microbial diversity in the gastrointestinal tract. In certain embodiments, the microbial consortium or its pharmaceutical composition increases short-chain fatty acids (SCFAs). In certain embodiments, the microbial consortium or its pharmaceutical composition increases secondary bile acids. In certain embodiments, the microbial consortium or its pharmaceutical composition reduces bacterial pathogens in the target gastrointestinal tract.

[0027] In a particular embodiment, the microbial consortium or its pharmaceutical composition is approximately 5 × 10 9 ~Approx. 5×10 12 Contains several living cells. In certain embodiments, the microbial consortium or its pharmaceutical composition contains about 5 × 10 9 ~Approx. 5×10 10 Contains several living cells. In certain embodiments, the microbial consortium or its pharmaceutical composition contains about 5 × 10 10 ~Approx. 5×10 11Contains several living cells. In certain embodiments, the microbial consortium or its pharmaceutical composition contains about 5 × 10 11 ~Approx. 5×10 12 Contains 10 living cells. In certain embodiments, the microbial consortium or its pharmaceutical composition may contain up to about 10 11 Contains 10 living cells. In certain embodiments, the microbial consortium or its pharmaceutical composition may contain up to about 10 12 Contains 100 surviving cells. In certain embodiments, the method includes administering a loading dose and one or more maintenance doses. In certain embodiments, the loading dose is administered for 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 days. In certain embodiments, the loading dose is administered for 2-3, 3-5, 4-6, or 5-7 days. In certain embodiments, one or more maintenance doses are administered for at least 21 days after the last loading dose.

[0028] In certain embodiments, the method further comprises administering an antibacterial agent, antiviral agent, antifungal agent, anti-inflammatory agent, immunosuppressant, and / or prebiotic. In certain embodiments, the antibacterial agent is selected from the group consisting of ciprofloxacin, levaquin, phloxin, tequin, avelox, norflox, cephalexin, cefuroxime, cefadroxil, cefazolin, cephalothin, cefaclor, cephamandol, cefoxitin, cefprodil, ceftoviprole, amoxicillin, ampicillin, penicillin V, dicloxacillin, carbenicillin, vancomycin, and methicillin, tetracycline, minocycline, oxytetracycline, doxycycline, ertapenem, doripenem, imipenem / cilastatin, and meropenem. In certain embodiments, the antiviral agents include abacavir, acyclovir, adefovir, amprenavir, atazanavir, cidofovir, darunavir, delavirdin, didanosine, docosanol, efavirenz, elvitegravir, emtricitabine, enfuvirtide, etravirine, famciclovir, foscamet, homivirsen, ganciclovir, indinavir, idoxuridine, lamivudine, and ropinavir. The following group is selected: rumaraviroc, mk-2048, nelfinavir, nevirapine, nilmatrelvir, penciclovir, raltegravir, rilpivirine, ritonavir, saquinavir, stabudine, tenofovir trifluridine, valacyclovir, valganciclovir, vidarabine, ivacitabine, amantadine, oseltamivir, rimantidine, tipranavir, zalcitabine, zanamivir, and zidovudine.In certain embodiments, the antifungal agent is selected from the group consisting of miconazole, ketoconazole, clotrimazole, econazole, omoconazole, bifonazole, butoconazole, fenticonazole, isoconazole, oxiconazole, sertaconazole, sulconazole, thioconazole, fluconazole, itraconazole, isabconazole, ravconazole, posaconazole, voriconazole, terconazole, albaconazole, abafandin, terbinafine, naftifine, butenafine, anidurafungin, caspofungin, micafungin, polygodial, benzoic acid, cyclopirox, tolnaphthate, undecylenic acid, flucytosine or 5-fluorocytosine, griseofulvin, and haloprozin. In certain embodiments, the anti-inflammatory and / or immunosuppressant is selected from the group consisting of cyclophosphamide, mycophenolate mofetil, corticosteroids, mesalazine, mesalamine, sulfasalazine, sulfasalazine derivatives, cyclosporine A, mercaptopurine, azathioprine, prednisone, methotrexate, antihistamines, glucocorticoids, epinephrine, theophylline, cromolyn sodium, anti-leukotrienes, anticholinergics, monoclonal anti-IgE, immunomodulatory peptides, immunomodulatory small molecules, immunomodulatory cytokines, immunomodulatory antibodies, and vaccines. In certain embodiments, the prebiotic is selected from the group consisting of amino acids, biotin, fructooligosaccharides, galactooligosaccharides, inulin, lactulose, mannan-oligosaccharides, oligofructose-concentrated inulin, oligofructose, oligodextrose, tagatose, transgalactooligosaccharides, and xylooligosaccharides.

[0029] In certain embodiments, the microbial consortium or its pharmaceutical composition is present in the food product.

[0030] Furthermore, this disclosure provides a method for treating a disease in a subject. In a particular embodiment, the method is a) Clostridium citroniae, Bacteroides salyersiae, Blautia obeum, Parabacteroides merdae, Parabacteroides distasonis, Anaerostipes hadrus, Lachnospiraceae sp.FBI00033, Eubacterium eligens, Bifidobacterium dentium, Blautia wexlerae, Fusicatenibacter saccharivorans, Bacteroides nordii, Dorea formicigenerans, Dorea longicatena, Bacteroides stercorirosoris, Bifidobacterium longum, Bacteroides kribbi, Lachnospiraceae sp.FBI00071, Bacteroides thetaiotaomicron, Clostridium clostridioforme, Clostridium scindens, Roseburia hominis, Clostridium fessum, Coprococcus comes, Blautia faecis, Hungatella hathewayi, Bacteroides stercoris, Collinsella aerofaciens, Hungatella effluvii, Bifidobacterium adolescentis, Bifidobacterium catenulatum, Lactobacillus rogosae, Bacteroides faecis, Bacteroides finegoldii、Clostridiaceae sp.FBI00191, Ruminococcus faecis, Lachnoclostridium pacaense, Clostridium bolteae, Longicatena caecimuris, Eggerthella lenta, Blautia massiliensis, Bacteroides xylanisolvens, Bacteroides vulgatus, Megasphaera massiliensis, Butyricimonas faecihominis, Eisenbergiella tayi, Acidaminococcus intestini, Emergencia timonensis, Bifidobacterium pseudocatenulatum, Eubacterium hallii, Anaerofustis stercorihominis, Eubacterium ventriosum, Blautia hydrogenotrophica, and Lachnospiraceae sp. FBI00290, or their functional equivalents, or. b) FBI00001, FBI00002, FBI00010, FBI00013, FBI00029, FBI00032, FBI00033, FBI00034, FBI00043, FBI00044, FBI00048, FBI00050, FBI00051, FBI00057, FBI00059 , FBI00060, FBI00070, FBI00071, FBI00076, FBI00079, FBI00087, FBI00093, FBI00102, FBI00109, FBI00117, FBI00120, FBI00125, FBI00127, FBI00128, FBI00145, The procedure involves administering an effective amount of a microbial consortium or its pharmaceutically acceptable composition containing FBI00162, FBI00174, FBI00184, FBI00190, FBI00191, FBI00194, FBI00198, FBI00199, FBI00200, FBI00201, FBI00205, FBI00206, FBI00211, FBI00220, FBI00221, FBI00236, FBI00245, FBI00248, FBI00251, FBI00254, FBI00267, FBI00278, FBI00288, and FBI00290, or their functional equivalents.

[0031] In certain embodiments, the disease is irritable bowel syndrome, diarrhea, constipation, celiac disease, and leaky gut syndrome, colitis, ulcerative colitis, or Crohn's disease.

[0032] In certain embodiments, a microbial consortium or its pharmaceutical composition is a) Acutalibacter timonensis, Alistipes onderdonkii, Bacteroides uniformis, Eubacterium rectale, Alistipes timonensis, Bacteroides kribbi, Coprococcus eutactus, Bilophila wadsworthia, Bacteroides caccae, Alistipes shahii, Parasutterella excrementihominis, Paraprevotella clara, Sutterella wadsworthensis, Sutterella massiliensis, Porphyromonas asaccharolytica, Ruminococcus bromii, Monoglobus pectinolyticus, Ruminococcaceae sp.FBI00097, Gordonibacter pamelaeae, Bacteroides uniformis, Gordonibacter pamelaeae, Bacteroides fragilis, Phascolarctobacterium faecium, Monoglobus pectinolyticus, Clostridium aldenense, Ruthenibacterium lactatiformans, Bacteroides ovatus, Bifidobacterium bifidum, Anaerotruncus massiliensis, Clostridium aldenense, Sutterella wadsworthensis, Catabacter hongkongensis, Alistipes senegalensis、Ruminococcaceae sp.FBI00233, Alistipes shahii, Dielma fastidiosa, Eubacterium siraeum, Faecalibacterium prausnitzii, Turicibacter sanguinis, Eubacterium rectale, Bacteroides caccae, Methanobrevibacter smithii, Barnesiella intestinihominis, Alistipes onderdonkii, and Methanobrevibacter smithii, or their functional equivalents. b) Bifidobacterium adolescentis, Bifidobacterium longum, Bifidobacterium pseudocatenulatum, Bacteroides thetaiotaomicron, Coprococcus comes, Fusicatenibacter saccharivorans, Eggerthella lenta, Eubacterium eligens, Bacteroides xylanisolvens, Lactobacillus rogosae, Clostridium citoniae, Collinsella aerofaciens, Blautia obeum, Eggerthella lenta, Blautia wexlerae, Lachnoclostridium pacaense, Bacteroides vulgatus, Parabacteroides merdae, Dorea formicigenerans, Ruminococcus faecis, Roseburia hominis, Anaerostipes hadrus, Bifidobacterium adolescentis, Bifidobacterium pseudocatenulatum, Clostridium bolteae, Eisenbergiella tayi, Dorea longicatena, Eggerthella lenta, Bacteroides stercoris, Hungatella hathawayi, and Bacteroides xylanisolvens, or their functional equivalents, and / or c) Alistipes putredinis, Dialister succinatiphilus, Akkermansia muciniphila, Ruminococcus bromii, Dialister invisus, Bacteroides massiliensis, Bilophila wadsworthia, Holdemanella biformis, Parasutterella excrementihominis, Alistipes sp.FBI00180, Bacteroides coprocola, Alistipes sp.FBI00238, Alistipes putredinis, Eubacterium xylanophilum, and Senegalimassilia anaerobia, or their functional equivalents, further comprising:

[0033] In certain embodiments, a microbial consortium or its pharmaceutical composition is a) FBI00004, FBI00012, FBI00015, FBI00018, FBI00019, FBI00021, FBI00038, FBI00040, FBI00046, FBI00061, FBI00066, FBI00 075, FBI00077, FBI00080, FBI00081, FBI00085, FBI00092, FBI00097, FBI00099, FBI00112, FBI00132, FBI00137, FBI00140, FBI 00149, FBI00151, FBI00176, FBI00189, FBI00197, FBI00208, FBI00212, FBI00224, FBI00226, FBI00229, FBI00233, FBI00235, FBI00237, FBI00243, FBI00244, FBI00258, FBI00260, FBI00263, FBI00270, FBI00273, FBI00277, and FBI00292, or their functional equivalents, b) FBI00009, FBI00011, FBI00016, FBI00020, FBI00025, FBI00027, FBI00030, FBI00047, FB I00052, FBI00053, FBI00056, FBI00062, FBI00078, FBI00096, FBI00104, FBI00110, FBI0011 1, FBI00113, FBI00115, FBI00116, FBI00123, FBI00124, FBI00126, FBI00135, FBI00147, FBI00159, FBI00167, FBI00170, FBI00232, FBI00255, and FBI00271, or their functional equivalents, and / or c) FBI00022, FBI00049, FBI00068, FBI00069, FBI00152, FBI00165, FBI00171, FBI00175, FBI00177, FBI00180, FBI00182, FBI00238, FBI00269, FBI00274, and FBI00281, or their functional equivalents, further included.

[0034] In certain embodiments, the microbial consortium or its pharmaceutical composition further comprises a first strain of Oxalobacter formigenes or FBI00067.

[0035] In certain embodiments, the microbial consortium or its pharmaceutical composition further comprises a second strain of Oxalobacter formigenes or FBI00133.

[0036] In certain embodiments, the microbial consortium or its pharmaceutical composition further comprises a third strain of Oxalobacter formigenes or FBI00289.

[0037] In certain embodiments, a microbial consortium or its pharmaceutical composition is a) Clostridium citroniae, Bacteroides salyersiae, Blautia obeum, Parabacteroides merdae, Parabacteroides distasonis, Anaerostipes hadrus, Lachnospiraceae sp.FBI00033, Eubacterium eligens, Bifidobacterium dentium, Blautia wexlerae, Fusicatenibacter saccharivorans, Bacteroides nordii, Dorea formicigenerans, Dorea longicatena, Bacteroides stercorirosoris, Bifidobacterium longum, Bacteroides kribbi, Lachnospiraceae sp.FBI00071, Bacteroides thetaiotaomicron, Clostridium clostridioforme, Clostridium scindens, Roseburia hominis, Clostridium fessum, Coprococcus comes, Blautia faecis, Hungatella hathewayi, Bacteroides stercoris, Collinsella aerofaciens, Hungatella effluvii, Bifidobacterium adolescentis, Bifidobacterium catenulatum, Lactobacillus rogosae, Bacteroides faecis, Bacteroides finegoldii、Clostridiaceae sp.FBI00191, Ruminococcus faecis, Lachnoclostridium pacaense, Clostridium bolteae, Longicatena caecimuris, Eggerthella lenta, Blautia massiliensis, Bacteroides xylanisolvens, Bacteroides vulgatus, Megasphaera massiliensis, Butyricimonas faecihominis, Eisenbergiella tayi, Acidaminococcus intestini, Emergencia timonensis, Bifidobacterium pseudocatenulatum, Eubacterium hallii, Anaerofustis stercorihominis, Eubacterium ventriosum, Blautia hydrogenotrophica, and Lachnospiraceae sp. FBI00290, or their functional equivalents. b) Acutalibacter timonensis, Alistipes onderdonkii, Bacteroides uniformis, Eubacterium rectale, Alistipes timonensis, Bacteroides kribbi, Coprococcus eutactus, Bilophila wadsworthia, Bacteroides caccae, Alistipes shahii, Parasutterella excrementihominis, Paraprevotella clara, Sutterella wadsworthensis, Sutterella massiliensis, Porphyromonas asaccharolytica, Ruminococcus bromii, Monoglobus pectinolyticus, Ruminococcaceae sp.FBI00097, Gordonibacter pamelaeae, Bacteroides uniformis, Gordonibacter pamelaeae, Bacteroides fragilis, Phascolarctobacterium faecium, Monoglobus pectinolyticus, Clostridium aldenense, Ruthenibacterium lactatiformans, Bacteroides ovatus, Bifidobacterium bifidum, Anaerotruncus massiliensis, Clostridium aldenense, Sutterella wadsworthensis, Catabacter hongkongensis, Alistipes senegalensis、Ruminococcaceae sp.FBI00233, Alistipes shahii, Dielma fastidiosa, Eubacterium siraeum, Faecalibacterium prausnitzii, Turicibacter sanguinis, Eubacterium rectale, Bacteroides caccae, Methanobrevibacter smithii, Barnesiella intestinihominis, Alistipes onderdonkii, and Methanobrevibacter smithii, or their functional equivalents. c) Bifidobacterium adolescentis, Bifidobacterium longum, Bifidobacterium pseudocatenulatum, Bacteroides thetaiotaomicron, Coprococcus comes, Fusicatenibacter saccharivorans, Eggerthella lenta, Eubacterium eligens, Bacteroides xylanisolvens, Lactobacillus rogosae, Clostridium citoniae, Collinsella aerofaciens, Blautia obeum, Eggerthella lenta, Blautia wexlerae, Lachnoclostridium pacaense, Bacteroides vulgatus, Parabacteroides merdae, Dorea formicigenerans, Ruminococcus faecis, Roseburia hominis, Anaerostipes hadrus, Bifidobacterium adolescentis, Bifidobacterium pseudocatenulatum, Clostridium bolteae, Eisenbergiella tayi, Dorea longicatena, Eggerthella lenta, Bacteroides stercoris, Hungatella hathawayi, and Bacteroides xylanisolvens, or their functional equivalents, and d) Alistipes putredinis, Dialister succinatiphilus, Akkermansia muciniphila, Ruminococcus bromii, Dialister invisus, Bacteroides massiliensis, Bilophila wadsworthia, Holdemanella biformis, Parasutterella excrementihominis, Alistipes sp.FBI00180, Bacteroides coprocola, Alistipes sp. FBI00238, Alistipes putredinis, Eubacterium xylanophilum, and Senegalimassilia anaerobia, or their functional equivalents.

[0038] In certain embodiments, a microbial consortium or its pharmaceutical composition is a) FBI00001, FBI00002, FBI00010, FBI00013, FBI00029, FBI00032, FBI00033, FBI00034, FBI00043, FBI00044, FBI00048, FBI00050, FBI00051, FBI0005 7, FBI00059, FBI00060, FBI00070, FBI00071, FBI00076, FBI00079, FBI00087, FBI00093, FBI00102, FBI00109, FBI00117, FBI00120, FBI00125, FBI0012 7, FBI00128, FBI00145, FBI00162, FBI00174, FBI00184, FBI00190, FBI00191, FBI00194, FBI00198, FBI00199, FBI00200, FBI00201, FBI00205, FBI00206, FBI00211, FBI00220, FBI00221, FBI00236, FBI00245, FBI00248, FBI00251, FBI00254, FBI00267, FBI00278, FBI00288, and FBI00290, or their functional equivalents, b) FBI00004, FBI00012, FBI00015, FBI00018, FBI00019, FBI00021, FBI00038, FBI00040, FBI00046, FBI00061, FBI00066, FBI00 075, FBI00077, FBI00080, FBI00081, FBI00085, FBI00092, FBI00097, FBI00099, FBI00112, FBI00132, FBI00137, FBI00140, FBI 00149, FBI00151, FBI00176, FBI00189, FBI00197, FBI00208, FBI00212, FBI00224, FBI00226, FBI00229, FBI00233, FBI00235, FBI00237, FBI00243, FBI00244, FBI00258, FBI00260, FBI00263, FBI00270, FBI00273, FBI00277, and FBI00292, or their functional equivalents, c) FBI00009, FBI00011, FBI00016, FBI00020, FBI00025, FBI00027, FBI00030, FBI00047, FBI00052, FBI00053, FBI00056, FBI00062, FBI00078, FBI00096, FBI00104, FBI00110, FBI00 111, FBI00113, FBI00115, FBI00116, FBI00123, FBI00124, FBI00126, FBI00135, FBI00147, FBI00159, FBI00167, FBI00170, FBI00232, FBI00255, and FBI00271, or their functional equivalents, and d) FBI00022, FBI00049, FBI00068, FBI00069, FBI00152, FBI00165, FBI00171, FBI00175, FBI00177, FBI00180, FBI00182, FBI00238, FBI00269, FBI00274, and FBI00281, or their functional equivalents.

[0039] In certain embodiments, the microbial consortium or its pharmaceutical composition further comprises a first strain of Oxalobacter formigenes or FBI00067, a second strain of Oxalobacter formigenes or FBI00133, and a third strain of Oxalobacter formigenes or FBI00289. In certain embodiments, the microbial consortium or its pharmaceutical composition further comprises a first strain of Oxalobacter formigenes or FBI00067, a second strain of Oxalobacter formigenes or FBI00133, and a third strain of Oxalobacter formigenes or FBI00289. In certain embodiments, the microbial consortium or its pharmaceutical composition is FB-001 or its functional equivalent. In certain embodiments, the microbial consortium or its pharmaceutical composition is FB-003 or its functional equivalent. In certain embodiments, the microbial consortium or its pharmaceutical composition increases microbial diversity in the gastrointestinal tract. In certain embodiments, the microbial consortium or its pharmaceutical composition increases short-chain fatty acids (SCFAs). In certain embodiments, the microbial consortium or its pharmaceutical composition increases secondary bile acids. In certain embodiments, the microbial consortium or its pharmaceutical composition reduces bacterial pathogens in the target gastrointestinal tract.

[0040] In a particular embodiment, the microbial consortium or its pharmaceutical composition is approximately 5 × 10 9 ~Approx. 5×10 12 Contains several living cells. In certain embodiments, the microbial consortium or its pharmaceutical composition contains about 5 × 10 9 ~Approx. 5×10 10 Contains several living cells. In certain embodiments, the microbial consortium or its pharmaceutical composition contains about 5 × 10 10 ~Approx. 5×10 11 Contains several living cells. In certain embodiments, the microbial consortium or its pharmaceutical composition contains about 5 × 10 11 ~Approx. 5×10 12Contains 10 living cells. In certain embodiments, the microbial consortium or its pharmaceutical composition may contain up to about 10 11 Contains 10 living cells. In certain embodiments, the microbial consortium or its pharmaceutical composition may contain up to about 10 12 Contains 100 surviving cells. In certain embodiments, the method includes administering a loading dose and one or more maintenance doses. In certain embodiments, the loading dose is administered for 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 days. In certain embodiments, the loading dose is administered for 2-3, 3-5, 4-6, or 5-7 days. In certain embodiments, one or more maintenance doses are administered for at least 21 days after the last loading dose.

[0041] In certain embodiments, the method further comprises administering an antibacterial agent, antiviral agent, antifungal agent, anti-inflammatory agent, immunosuppressant, and / or prebiotic. In certain embodiments, the antibacterial agent is selected from the group consisting of ciprofloxacin, levaquin, phloxin, tequin, avelox, norflox, cephalexin, cefuroxime, cefadroxil, cefazolin, cephalothin, cefaclor, cephamandol, cefoxitin, cefprodil, ceftoviprole, amoxicillin, ampicillin, penicillin V, dicloxacillin, carbenicillin, vancomycin, and methicillin, tetracycline, minocycline, oxytetracycline, doxycycline, ertapenem, doripenem, imipenem / cilastatin, and meropenem. In certain embodiments, the antiviral agents include abacavir, acyclovir, adefovir, amprenavir, atazanavir, cidofovir, darunavir, delavirdin, didanosine, docosanol, efavirenz, elvitegravir, emtricitabine, enfuvirtide, etravirine, famciclovir, foscamet, homivirsen, ganciclovir, indinavir, idoxuridine, lamivudine, and ropinavir. The following group is selected: rumaraviroc, mk-2048, nelfinavir, nevirapine, nilmatrelvir, penciclovir, raltegravir, rilpivirine, ritonavir, saquinavir, stabudine, tenofovir trifluridine, valacyclovir, valganciclovir, vidarabine, ivacitabine, amantadine, oseltamivir, rimantidine, tipranavir, zalcitabine, zanamivir, and zidovudine.In certain embodiments, the antifungal agent is selected from the group consisting of miconazole, ketoconazole, clotrimazole, econazole, omoconazole, bifonazole, butoconazole, fenticonazole, isoconazole, oxiconazole, sertaconazole, sulconazole, thioconazole, fluconazole, itraconazole, isabconazole, ravconazole, posaconazole, voriconazole, terconazole, albaconazole, abafandin, terbinafine, naftifine, butenafine, anidurafungin, caspofungin, micafungin, polygodial, benzoic acid, cyclopirox, tolnaphthate, undecylenic acid, flucytosine or 5-fluorocytosine, griseofulvin, and haloprozin. In certain embodiments, the anti-inflammatory and / or immunosuppressant is selected from the group consisting of cyclophosphamide, mycophenolate mofetil, corticosteroids, mesalazine, mesalamine, sulfasalazine, sulfasalazine derivatives, cyclosporine A, mercaptopurine, azathioprine, prednisone, methotrexate, antihistamines, glucocorticoids, epinephrine, theophylline, cromolyn sodium, anti-leukotrienes, anticholinergics, monoclonal anti-IgE, immunomodulatory peptides, immunomodulatory small molecules, immunomodulatory cytokines, immunomodulatory antibodies, and vaccines. In certain embodiments, the prebiotic is selected from the group consisting of amino acids, biotin, fructooligosaccharides, galactooligosaccharides, inulin, lactulose, mannan-oligosaccharides, oligofructose-concentrated inulin, oligofructose, oligodextrose, tagatose, transgalactooligosaccharides, and xylooligosaccharides.

[0042] In certain embodiments, the microbial consortium or its pharmaceutical composition is present in a food product. In certain embodiments, the method disclosed herein further comprises diagnosing IBD in a subject before administering the microbial consortium or its pharmaceutical composition.

[0043] This disclosure provides a method for reducing dysbiosis in a subject, further comprising administering to a patient a therapeutically effective amount of a pharmaceutical composition containing a consortium to reduce gastrointestinal dysbiosis in the patient. In certain embodiments, reducing dysbiosis includes microbial engraftment of the consortium, increased microbial diversity in the gastrointestinal tract, increased short-chain fatty acids (SCFAs), increased secondary bile acids, and / or a reduction in bacterial pathogens. In certain embodiments, the consortium is FB-001 or a functional equivalent thereof. In certain embodiments, the consortium is FB-003 or a functional equivalent thereof.

[0044] In addition, the present disclosure provides a method for restoring the microbiome in a patient, comprising administering to the patient a therapeutically effective amount of a pharmaceutical composition containing a consortium. In certain embodiments, restoring the microbiome includes the engraftment of microorganisms of the consortium, an increase in microbial diversity of the gastrointestinal tract, an increase in short-chain fatty acids (SCFAs), an increase in secondary bile acids, and / or a decrease in bacterial pathogens. In certain embodiments, the consortium is FB-001 or a functional equivalent thereof. In certain embodiments, the consortium is FB-003 or a functional equivalent thereof.

[0045] This disclosure provides a method for increasing the recovery of a healthy microbiome in a patient after a dysbiosis-inducing event, comprising administering a therapeutically effective amount of a pharmaceutical composition comprising a consortium to the target. In certain embodiments, the recovery of a healthy microbiome includes the engraftment of the consortium's microorganisms, an increase in microbial diversity of the gastrointestinal tract, an increase in short-chain fatty acids (SCFAs), an increase in secondary bile acids, and / or a decrease in bacterial pathogens. In certain embodiments, the consortium is FB-001 or a functional equivalent thereof. In certain embodiments, the consortium is FB-003 or a functional equivalent thereof. In certain embodiments, the dysbiosis-inducing event is treatment with one or more antibiotics, an infectious disease, or an underlying disease. In certain embodiments, the underlying disease is IBD, colitis, ulcerative colitis, or Crohn's disease.

[0046] This disclosure provides compositions for treating or reducing the severity of at least one symptom of a gastrointestinal disease, disorder, or condition associated with dysbiosis in a patient, comprising a consortium in an amount effective to aggregate and optionally engraft in the gastrointestinal tract of the patient. In certain embodiments, the gastrointestinal disease is selected from the group consisting of IBD, colitis, ulcerative colitis, and Crohn's disease. In certain embodiments, the dysbiosis is associated with a decrease in microbial diversity in the gastrointestinal tract, a decrease in short-chain fatty acids (SCFAs), a decrease in secondary bile acids, and / or an increase in bacterial pathogens. In certain embodiments, the consortium is FB-001 or a functional equivalent thereof. In certain embodiments, the consortium is FB-003 or a functional equivalent thereof.

[0047] The disclosure also provides a method for treating or reducing the severity of at least one symptom of a gastrointestinal disorder associated with dysbiosis, comprising administering an effective amount of a pharmaceutical composition comprising a consortium. In certain embodiments, the consortium is FB-001 or a functional equivalent thereof. In certain embodiments, the consortium is FB-003 or a functional equivalent thereof.

[0048] This disclosure provides compositions comprising FB-003 or its functional equivalent. This disclosure also provides methods for producing FB-003 or its functional equivalent.

[0049] This disclosure provides a method for treating IBD, colitis, ulcerative colitis, or Crohn's disease by administering a consortium. In certain embodiments, the consortium is FB-003 or FB-001. This disclosure provides a method for reducing symptoms associated with IBD, colitis, ulcerative colitis, or Crohn's disease by administering a consortium. In certain embodiments, the consortium is FB-003 or FB-001. This disclosure provides any method or composition described herein. [Brief explanation of the drawing]

[0050] [Figure 1A] Figure 1A shows an exemplary co-culture experiment, and Figure 1B shows an exemplary co-culture experiment modified to result in 100% strain detection after co-culture. [Figure 1B] Same as above. [Figure 2A] Figure 2A shows the design of the DS bucket for the consortium, and Figure 2B shows the yield of co-cultured strains depending on the inoculation species. [Figure 2B] Same as above. [Figure 3A] Figures 3A and 3B show examples of different freeze-drying excipients. [Figure 3B] Same as above. [Figure 4A] Figures 4A and 4B show examples of different freeze-drying excipients and reducing agents. [Figure 4B] Same as above. [Figure 5A] Figures 5A and 5B show examples of different freeze-drying excipients. [Figure 5B] Same as above. [Figure 6A]Figure 6A is a Venn diagram showing the overlapping microorganisms of the five representative consortia designed and disclosed herein. Figure 6B shows the breakdown of microbial types in each of the five representative consortia. [Figure 6B] Same as above. [Figure 7A] Figures 7A and 7B show schematic diagrams of the experimental design for the study described in Example 5. [Figure 7B] Same as above. [Figure 8] This shows that YCFAC + GalNAc cannot support the growth of Akkermansia. [Figure 9] This study shows that threonine supports the growth of Akkermansia in the absence of GalNAc. [Figure 10] A diagram illustrating the co-culture method for the production of FB-001 and FB-003 is shown. [Figure 11] This document outlines the strain isolation and purification process, RCB banking, and RCB identity / purity testing. [Figure 12] This document describes a method for generating a master cell bank (MCB). [Figure 13] A phylogenetic tree is shown that illustrates the taxonomic composition of certain consortia disclosed herein, including the FB-001 and FB-003 consortia. [Figure 14A] Figures 14A–14C show tables summarizing the strains and species of the microbial consortia disclosed herein. [Figure 14B] Same as above. [Figure 14C] Same as above. [Figure 15A]Figure 15A shows the effect of FB-001 in reducing intestinal permeability, and Figure 15B shows FB-001's ability to produce short-chain fatty acids (SCFAs) at levels comparable to those of a normal, healthy gut. Butyrate, an SCFA, is important because it supports the health of gastrointestinal epithelial cells, energy metabolism, and cellular signaling, thereby improving barrier function. In this experiment, O. formigenes did not show activity and / or viability; therefore, the drug product used in these experiments is the research version of FB-003 (i.e., a strain of FB-001 without O. formigenes). [Figure 15B] Same as above. [Figure 16] This specification shows the manufacturing process used for O. formigenes in the production of the consortium described herein. Furthermore, DS5-DS7 of FB-001 (i.e., the three O. formigenes active pharmaceutical ingredients) used this manufacturing process for both GMP and non-GMP manufacturing. [Figure 17] This specification shows the manufacturing process used for DS1 in the production of the consortium described herein. Furthermore, DS1 of FB-001 used this manufacturing process for both GMP and non-GMP manufacturing. [Figure 18] This specification shows the manufacturing process used for DS2 in the production of the consortium described herein. Furthermore, DS2 of FB-001 used this manufacturing process for both GMP and non-GMP manufacturing. [Figure 19] This specification shows the manufacturing process used for DS3 in the production of the consortium described herein. Furthermore, DS3 of FB-001 used this manufacturing process for both GMP and non-GMP manufacturing. [Figure 20] This specification shows the manufacturing process used for DS4 in the production of the consortium described herein. Furthermore, DS4 of FB-001 used this manufacturing process for both GMP and non-GMP manufacturing. [Figure 21A]Figure 21A shows the experimental design for in vivo evaluation of FB-003 engraftment and metabolic function after antibiotic treatment in mice. Figure 21B shows that FB-003 exhibits stable engraftment for more than 60 days in SPF mice. The vehicle used in this experiment, "veh," was plain culture medium (the term "culture medium" is used for simplification in Figure 21A; "abx" represents antibiotics). The antibiotics used in this experiment ("antibiotics" in Figure 21A and "abx" in Figure 21B) were 0.575 mg / mL enrofloxacin and 1 mg / mL ampicillin supplied in drinking water for 11 days. Figure 21C shows the diverse colony formation of FB-003 based on genus-level engraftment. Figure 21D shows the diverse colony formation of FB-003 based on strain-level engraftment. The engraftment of FB-003 shown in Figures 21C and 21D is from day 1 to day 60 after administration of FB-003 to SPF mice, indicating that engraftment stabilizes approximately one week after administration. [Figure 21B] Same as above. [Figure 21C] Same as above. [Figure 21D] Same as above. [Figure 22A]Figures 22A–22C demonstrate that FB-004 treatment can rapidly generate a modified SCFA profile in mice. Specifically, total SCFA recovery after antibiotic treatment that clears the microbiome (0.575 mg / mL enrofloxacin and 1 mg / mL ampicillin) is faster with FB-003 than with the vehicle control, and FB-003 can control the SCFA profile of SPF mice, and mice treated with its vehicle (i.e., culture medium) develop abnormal dysbiotic communities dominated by butyrate-producing strains. Figure 22A shows total SCFA (excluding acetate) concentrations after antibiotic treatment in mice treated with + / -FB-003. Figure 22B shows SCFA levels after antibiotic and FB-003 treatment. Figure 22C shows SCFA levels after antibiotic and vehicle (i.e., culture medium control) treatment. Comparing Figures 22B and 22C, the SCFA ratio differed between the FB-003 treatment group and the control group. As a result, butyrate was dominant over propionate in the control group, which is an indication of dysbiosis. [Figure 22B] Same as above. [Figure 22C] Same as above. [Figure 23A] Figure 23A shows that antibiotics dramatically disrupt the bile acid pool in the intestines. Figure 23B shows that FB-003 rapidly restores balance to the bile acid pool after antibiotic treatment induces dysbiosis. [Figure 23B] Same as above. [Figure 24A]Figures 24A–24F show the design and results of the DSS colitis mouse model experiment. Figure 24A shows a schematic diagram of the DSS colitis experimental design for the DSS colitis model. Figure 24B shows the experimental design for sample collection and analysis. Figure 24C shows the body weight results for 5% DSS+ / - FB-003 in the presence of prior antibiotic treatment. Figure 24D shows the body weight results for 5% DSS+ / - FB-003 in the absence of prior antibiotic treatment. Figure 24E shows that antibiotics are required to replace the natural mouse microbiome, that antibiotic treatment increases the severity of DSS colitis, and that FB-003 treatment dramatically improves the clinical score of mice (and the experiment also showed reduced body weight loss). Figure 24F shows that FB-003 still shows improvement in clinical score in the antibiotic-free setting (reduced body weight loss was also observed). For Figures 24E and 24F, the total clinical score was calculated as the area under the curve (AUC). Data are presented as mean ± SEM (n=2 or naive, n=10 per treatment group). The data were analyzed using standard one-way ANOVA followed by Sidaq's multiple comparison test, comparing the mean of the Abx+FB-003 group to the Abx+vehicle group, and comparing the FB-003 treatment group to the vehicle group. Figure 24G shows the stool consistency score after 5% DSS-induced ulcerative colitis. Specifically, the stool consistency score was calculated as the area under the curve (AUC). Data are presented as mean ± SEM (n=2 or naive, n=10 per treatment group). The data were analyzed using standard one-way ANOVA followed by Sidaq's multiple comparison test, comparing the mean of the Abx+FB-003 group to the Abx+vehicle group, and comparing the FB-003 treatment group to the vehicle group. [Figure 24B] Same as above. [Figure 24C] Same as above. [Figure 24D] Same as above. [Figure 24E] Same as above. [Figure 24F] Same as above. [Figure 24G] Same as above. [Figure 25] This study demonstrates that FB-003 improves survival in a DSS colitis model. [Figure 26-1] This document provides a chart that provides references disclosing certain types of functions within the consortia disclosed herein, including FB-003, Consortia A, and Consortia B. [Figure 26-2] Same as above. [Figure 26-3] Same as above. [Figure 26-4] Same as above. [Figure 27A] Figure 27A shows the clinical score of the mouse colon in the DSS test described in the examples. Figures 27B and 27C show images of the colon of mice treated with FB-003 in contrast to the vehicle control. [Figure 27B] Same as above. [Figure 27C] Same as above. [Modes for carrying out the invention]

[0051] This disclosure relates to compositions and methods for engrafting the microbial consortia disclosed herein. This disclosure is based in part on the discovery that the microbial consortia disclosed herein can effectively engraft in a subject, reduce dysbiosis in the subject, restore the microbiome, and recover the microbiome. Furthermore, this disclosure relates to methods for treating IBD, colitis, ulcerative colitis, and Crohn's disease, including administering the microbial consortia disclosed herein. Not for limitation, but for clarity of explanation, this section is divided into the subsections outlined below.

[0052] definition Unless otherwise specified, all technical and scientific terms used herein have the meanings generally understood by those skilled in the art. The following references provide general definitions of many of the terms used in the subject matter disclosed herein: Singleton et al., Dictionary of Microbiology and Molecular Biology (2nd ed. 1994), The Cambridge Dictionary of Science and Technology (Walker ed., 1988), The Glossary of Genetics, 5th Ed., R. Rieger et al. (eds.), Springer Verlag (1991), and Hale & Marham, The Harper Collins Dictionary of Biology (1991). Where used herein, unless otherwise specified, the following terms have the meanings attributed to them below.

[0053] The aspects and embodiments of the Disclosure described herein are understood to include "comprises," "consist of," and "essentially consist of." The terms "comprises" and "comprising" are intended to have the broader meanings attributed to them under U.S. patent law and may mean "includes," "including," etc. For the purposes of facilitating understanding of this Disclosure, several terms and phrases are defined below.

[0054] As used herein, the terms "a" and "an" mean "one or more" and include the plural form unless otherwise specified.

[0055] As used herein, the terms “microorganism” or “microbiota” refer to microbial organisms, including but not limited to bacteria, archaea, protists, and unicellular fungi.

[0056] As used herein, the term “active microorganism” refers to a microorganism that expresses one or more metabolic enzymes in sufficient quantities to metabolize a substrate that causes or contributes to disease in an animal.

[0057] As used herein, the term “supportive community” refers to one or more microbial strains that, when administered with the active microorganism, enhance one or more characteristics of the active microorganism, selected from the group consisting of gastrointestinal engraftment, biomass, metabolic substrate metabolism, and long-term stability.

[0058] As used herein, the term “synthetic microorganism” refers to a microorganism that expresses one or more enzymes in sufficient quantities to catalyze a combination of one or more metabolites produced by active microorganisms and one or more fermentation products produced by fermenting microorganisms in the gastrointestinal niche.

[0059] As used herein, the term “fermenting microorganism” refers to a microorganism that expresses one or more enzymes in sufficient quantities to catalyze a fermentation reaction in the gastrointestinal niche.

[0060] As used herein, the term “long-term stability” refers to the ability of one or more microorganisms, or a microbial consortium, to colonize one of two or more niches in the gastrointestinal tract and maintain metabolic activity despite transient or long-term environmental changes to the gastrointestinal niche.

[0061] As used herein, the terms “metabolism,” “metabolizing,” and “metabolization,” or variations thereof, refer to the biochemical conversion of a metabolic substrate into a metabolite. In certain embodiments, metabolism includes isomerization.

[0062] As used herein, the term “biomass” refers to the total mass of one or more microorganisms or consortia in a given area or volume.

[0063] As used herein, the terms “microbial consortium” and “microbial consortium” are interchangeable and refer to a mixture of two or more isolated microbial strains that are expanded in culture, where one microbial strain in the mixture has a beneficial or desired effect on another microbial strain in the mixture.

[0064] As used herein, the term “Consortium” is used as a capital letter term to refer to one or more of the microbial consortia described herein.

[0065] As used herein, “dysbiosis” refers to an imbalance of microbiome homeostasis within the internal organs and tissues of a subject (e.g., the intestines) or on the external organs, tissues, and surfaces of a subject (e.g., the skin).

[0066] As used herein, the terms “gastrointestinal engraftment,” “engraft,” or “engraft” refer to the establishment of one or more microorganisms or a microbial consortium in one or more niches of the gastrointestinal tract that lack one or more microorganisms or a microbial consortium prior to the administration of the microbial consortium. For clarity, engraftment refers to the engraftment of one or more microorganisms administered to a subject. In certain embodiments, gastrointestinal engraftment may be transient. In certain embodiments, gastrointestinal engraftment may be permanent.

[0067] As used herein, the term “pharmaceutical composition” refers to a combination of an active agent with an inactive or active carrier that makes the composition particularly suitable for therapeutic use in vivo or ex vivo.

[0068] As used herein, the term “pharmaceutically acceptable carrier” refers to any of the standard pharmaceutically acceptable carriers, such as phosphate-buffered saline, water, emulsions (e.g., oil / water or water / oil emulsions), and various types of wetting agents. The composition may also contain stabilizers and preservatives. For examples of carriers, stabilizers, and adjuvants, see, for example, Martin, Remington's Pharmaceutical Sciences, 15 th See Ed. Mack Publ. Co., Easton, PA

[1975] .

[0069] As used herein, the term “effective amount” means an amount sufficient to achieve a beneficial or desired result. In certain non-limiting embodiments, the effective amount may be an amount that results in improved gastrointestinal engraftment (e.g., engraftment of one or more of several active microorganisms), increased biomass (e.g., one or more of several active microorganisms), increased metabolism, or improved long-term stability.

[0070] As used herein, “significantly” or “significant” refers to a change or modification of a measurable parameter to a degree that is statistically significant, as determined by a statistically relevant test of appropriate significance. For example, in certain non-limiting embodiments, a change or modification is significant if it is statistically significant, for example, according to Student's t-test, chi-squared, or Mann-Whitney test.

[0071] As used herein, the term “standardized substrate metabolism assay” refers to an experimental assay known to those skilled in the art, used to quantify the amount of substrate converted to metabolites.

[0072] As used herein, the term “Subject” refers to an organism treated by the microbial consortiums and compositions described herein. Such organisms preferably include, but are not limited to, mammals (e.g., mice, monkeys, horses, cattle, pigs, dogs, cats, etc.), and more preferably humans.

[0073] The terms "identity" or "percent sequence identity" in the context of two or more nucleic acid or polypeptide sequences refer to the percentage of identical nucleotide or amino acid residues that two or more sequences or subsequences have when compared and aligned with each other, using one of the sequence comparison algorithms described below (e.g., BLASTP and BLASTN available to those skilled in the art or other algorithms) or by visual inspection, to the maximum correspondence. Depending on the application, the "identity" percentage can be present over the region of the sequences being compared, e.g., over a functional domain, or alternatively, over the entire length of the two sequences being compared.

[0074] For sequence comparison, typically, one sequence functions as a reference sequence to which a test sequence is compared. When using a sequence comparison algorithm, the test sequence and the reference sequence are input into a computer, and optionally, subsequence coordinates are specified and sequence algorithm program parameters are specified. Then, the sequence comparison algorithm calculates the percent sequence identity for the test sequence(s) relative to the reference sequence based on the specified program parameters.

[0075] Optimal alignment of arrays for comparison can be carried out by the local homology algorithm of Smith & Waterman, Adv. Appl. Math. 2:482 (1981), by the homology alignment algorithm of Needleman & Wunsch, J. Mol. Biol. 48:443 (1970), by the search for the similarity method of Pearson & Lipman, Proc. Nat’l. Acad. Sci. USA 85:2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or by visual inspection (generally, see Ausubel et al.).

[0076] An example of an algorithm suitable for determining percent sequence identity and sequence similarity is the BLAST algorithm described in Altschul et al., J. Mol. Biol. 215:403 - 410 (1990). Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (www.ncbi.nlm.nih.gov / ).

[0077] When used with 16S rRNA sequences, at least 97% "sequence identity" indicates that two microbial strains are likely to belong to the same species, but 16S rRNA sequences with less than 97% sequence identity indicate that the two microbial strains are likely to belong to different species, and 16S rRNA sequences with less than 95% sequence identity indicate that the two microbial strains are likely to belong to separate genera (Stackebrandt E., and Goebel, B.M., Int J Syst Bact, 44(1994)846 - 849.).

[0078] As used herein, the terms “functional equivalent” or “functionally equivalent” refer to microorganisms, microbial consortia, and compositions that share similar or identical roles (e.g., oxalate metabolism). For example, two different microbial consortia capable of catalyzing high concentrations of oxalate are functional equivalents of each other, without any limitation. In certain non-limiting embodiments, functionally equivalent microorganisms, microbial consortia, and compositions may be based on the characteristics outlined in Table 3 (see the Examples section).

[0079] Throughout this specification, where a composition is described as having, including, or comprising, certain components, or where a process and method is described as having, including, or comprising, certain steps, it is intended that there exist additional compositions of the disclosure that are essentially composed of or consist of the listed components, and processes and methods of the disclosure that are essentially composed of or consist of the listed processing steps.

[0080] As a general rule, percentages for compositions are given by weight unless otherwise specified. Furthermore, if a variable is not defined, its previous definition takes precedence.

[0081] Dysbiosis The microbiome exists within multiple species (e.g., mammals) and includes bacteria, archaea, protists, fungi, and viruses. Traditionally, the microbiome (e.g., the human microbiome) has contained trillions of microorganisms (e.g., bacteria) from thousands of species, performing functions that can benefit the host organism (e.g., a human subject). For example, species present in the microbiome benefit the host (e.g., a human subject) by performing useful or necessary functions such as assisting in the digestion of food in the subject's intestinal tract, protecting the body from infiltration by pathogenic microorganisms, and promoting immunological development. In certain embodiments, organisms that perform these functions may be called symbiotic or commensal organisms because they exist without harming the host (e.g., a human subject) and, in some cases, actually benefit the host. In certain embodiments, in dysbiosis, the physiological / normal microbiome of the host (e.g., a human subject) is perturbed or damaged, which can lead to various diseases and / or disorders. In certain embodiments, dysbiosis may result from, for example, the loss of beneficial species, loss of microbial diversity, an increase in pathogenic organisms, and / or changes in metabolic capacity. In certain embodiments, species that normally dominate the microbiome become underexpressed (e.g., commensal or symbiotic species), and species that are normally underexpressed (e.g., opportunistic species) become overexpressed. See Petersen et al., “Defining dysbiosis and its influence on host immunity and disease.” Cell Microbiol 2014, July 16(7), 1024-1033.

[0082] In certain embodiments, the compositions and methods described herein reduce dysbiosis. In certain embodiments, the compositions and methods result in an increase in the abundance of beneficial bacterial species in the microbiome. In certain embodiments, the compositions and methods result in a decrease in the abundance of pathogenic bacterial species. In certain embodiments, the compositions and methods described herein do not reduce all characteristics of dysbiosis. In certain embodiments, the compositions and methods result in an increase in the abundance of beneficial bacterial species in the microbiome. In certain embodiments, the compositions and methods result in an increase in the abundance of beneficial bacterial species in the microbiome, but do not increase the diversity of the microbiome. In certain embodiments, the term “reduce dysbiosis” refers to restoring the composition and homeostasis of the microbiota community. In certain embodiments, disruption of the microbiome may allow pathogens from within the microbiome or other sources to colonize, overpopulate, and / or cause disease in the target. In certain embodiments, dysbiosis is associated with many diseases and / or disorders, including inflammatory bowel disease (IBD), colitis, ulcerative colitis, and Crohn's disease.

[0083] In certain embodiments, dysbiosis may be detected and / or monitored by a number of methods, including stool tests (e.g., identification and / or quantification of microbial populations, enzyme assays, metabolite assays, immune function), and / or hydrogen / methane breath tests. Additional methods for detecting dysbiosis, as incorporated herein, can be found in Wei et al., Applied and Environmental Microbiology 87, no.11(2021):e00395-21, the contents of which are incorporated in their entirety by reference.

[0084] In certain embodiments, reducing dysbiosis involves a change (e.g., increase or decrease) in the abundance of one or more bacterial populations. In certain embodiments, bacterial abundance, including the abundance of a particular species or bacterial strain and the abundance of bacterial populations (e.g., bacteria belonging to a particular phylum), can be assessed using any method known to those skilled in the art. In certain embodiments, bacterial abundance can be assessed directly or indirectly. In certain embodiments, a method for directly assessing bacterial abundance in a sample (e.g., a microbiome or a sample thereof) includes identifying and quantifying bacterial strains in a fecal sample from a subject. In certain embodiments, a method for indirectly assessing bacterial abundance in a sample (e.g., a microbiome or a sample thereof) includes sequencing of nucleic acid samples (e.g., 16S rRNA genes for a given bacterial species or other bacterial genes) obtained from a fecal or biopsy sample, and detection and quantification of metabolites (e.g., phospholipid fatty acid metabolism, microbial biomass carbon analysis) associated with a particular bacterium in a fecal sample from a subject.

[0085] In certain embodiments, the abundance of one or more bacterial populations in a sample from a subject may be compared to the abundance of bacterial populations in a sample from the same subject obtained at a different time (e.g., previously or later). In certain embodiments, the abundance of one or more bacterial populations in a sample from a subject may be compared to the abundance of bacterial populations in a sample from a different subject (e.g., a reference subject).

[0086] In certain embodiments, dysbiosis is characterized by an increased abundance of inflammation and / or disease-related microorganisms. In certain embodiments, dysbiosis is characterized by an increased abundance of Proteobacteria. In certain embodiments, the increased abundance of inflammation and / or disease-related microorganisms is relative to the abundance of inflammation-related microorganisms prior to exposure to an event referred to as a dysbiosis-inducing event.

[0087] In some embodiments, the dysbiosis of the subject is characterized by a decrease in the abundance of microorganisms that are thought to provide one or more beneficial effects to the subject. In certain embodiments, the dysbiosis is characterized by a decrease in the abundance of bacteria of the phylum Bacteroidetes. In certain embodiments, the dysbiosis of the subject's microbiota is characterized by a decrease in the abundance of bacteria of the phylum Firmicutes. In certain embodiments, the dysbiosis is characterized by a decrease in the abundance of bacteria belonging to Clostridium cluster IV and / or Clostridium cluster XIVa. In certain embodiments, the dysbiosis is characterized by a decrease in the abundance of bacteria belonging to Clostridium cluster XVII. In certain embodiments, the decrease in the abundance of beneficial microorganisms is relative to the abundance of microorganisms associated with inflammation prior to exposure to an event referred to as a dysbiosis-inducing event, as described herein.

[0088] In certain embodiments, dysbiosis is dysbiosis of the gastrointestinal microbiota. In certain embodiments, dysbiosis of the gastrointestinal microbiota is characterized by an increase in the abundance of inflammatory and / or disease-related microorganisms. In certain embodiments, dysbiosis of the gastrointestinal microbiota is characterized by an increase in the abundance of Proteobacteria. In certain embodiments, the increase in the abundance of inflammatory and / or disease-related microorganisms is relative to the abundance of inflammatory microorganisms prior to exposure to an event (e.g., a dysbiosis-inducing event).

[0089] In certain embodiments, dysbiosis of the gastrointestinal microbiota is characterized by a decrease in the abundance of microorganisms that are thought to provide one or more beneficial effects to the subject. In certain embodiments, dysbiosis of the gastrointestinal microbiota is characterized by a decrease in the abundance of bacteria of the phylum Bacteroidetes. In certain embodiments, dysbiosis of the gastrointestinal microbiota is characterized by a decrease in the abundance of bacteria of the phylum Firmicutes. In certain embodiments, dysbiosis of the gastrointestinal microbiota is characterized by a decrease in the abundance of bacteria belonging to Clostridium cluster IV and / or Clostridium cluster XIVa. In certain embodiments, dysbiosis of the gastrointestinal microbiota is characterized by a decrease in the abundance of bacteria belonging to Clostridium cluster XVII. In certain embodiments, the decrease in the abundance of beneficial microorganisms is relative to the abundance of microorganisms associated with inflammation prior to exposure to an event (e.g., a dysbiosis-inducing event).

[0090] In certain embodiments, reducing dysbiosis results in an increase in the abundance of bacteria of the phylum Bacteroidetes (e.g., bacteria of the genus Bacteroides) compared to the abundance of Bacteroides in the host (e.g., human subject) (or its microbiome) before administration of the pharmaceutical composition. In certain embodiments, reducing dysbiosis results in an increase in the abundance of bacteria of the phylum Bacteroidetes (e.g., bacteria of the genus Bacteroides) compared to the abundance of Bacteroides in a reference host (e.g., human subject, e.g., reference subject) (or its microbiome) that did not receive the pharmaceutical composition. In certain embodiments, reducing dysbiosis results in an increase in the abundance of one or more bacterial species belonging to the genus Bacteroides. In certain embodiments, reducing dysbiosis results in an overall increase in the abundance of bacterial species belonging to the genus Bacteroides.

[0091] Biological niche Disclosed herein are microbial consortia for administration to animals (e.g., human subjects) comprising multiple active microorganisms that metabolize a first metabolite. In certain embodiments, the first metabolite causes or contributes to disease in the animal. The microbial consortia disclosed herein further comprises an effective amount of supporting microbial communities that metabolize one or more metabolites produced by the multiple active microorganisms, one or more of which inhibit the metabolism of the multiple active microorganisms. These microbial consortia are advantageous in that they have enhanced characteristics when administered to animals compared to the administration of the multiple active microorganisms alone. Enhanced characteristics of the microbial consortia include, without any limitation, improved gastrointestinal engraftment, increased biomass, increased metabolism of the first metabolite, and improved long-term stability.

[0092] This disclosure provides a microbial consortium capable of colonizing one or more niches in the gastrointestinal tract. In certain embodiments, the colonized microbial consortium is capable of metabolizing substrates that cause or contribute to disease in animals. These niches include a specific microbial community whose composition varies according to several environmental factors, including, but not limited to, a particular physical compartment of the gastrointestinal tract inhabited by the microbial community, the chemical and physicochemical properties of the habitat, the metabolic substrate composition of the habitat, and other coexisting microbial species.

[0093] consortium This disclosure provides a consortium comprising multiple active microorganisms and supporting communities of effective amounts of microorganisms.

[0094] In a particular embodiment, the consortium includes a plurality of microorganisms designated as "Consortium I" (e.g., active microorganisms and supporting community microorganisms). In certain embodiments, Consortia I provides Acidaminococcus intestini, Bacteroides stercoris, Blautia hydrogenotrophica, Coprococcus eutactus, Holdemanella biformis, Akkermansia muciniphila, Bacteroides stercoris, Blautia luti, Coprococcus eutactus, Holdemanella biformis, Alistipes finegoldii, Bacteroides thetaiotaomicron, Blautia luti, Desulfovibrio desulfuricans, Hungatella hathewayi, Alistipes onderdonkii, Bacteroides thetaiotaomicron, Blautia luti, Desulfovibrio desulfuricans, Hungatella hathewayi, Alistipes onderdonkii, Bacteroides thetaiotaomicron, Blautia obeum, Dialister invisus, Neglecta timonensis, Alistipes onderdonkii, Bacteroides uniformis, Blautia obeum, Dorea formicigenerans, Oxalobacter formigenes, Alistipes putredinis, Bacteroides uniformis, Blautia obeum, Dorea formicigenerans, Oxalobacter formigenes, Alistipes putredinis, Bacteroides uniformis, Blautia obeum, Dorea formicigenerans, Oxalobacter formigenes, Alistipes senegalensis, Bacteroides uniformis, Blautiawexlerae, Dorea longicatena, Parabacteroides distasonis, Alistipes senegalensis, Bacteroides vulgatus, Blautia wexlerae, Dorea longicatena, Parabacteroides distasonis, Alistipes shahii, Bacteroides vulgatus, Blautia wexlerae, Dorea longicatena, Parabacteroides distasonis, Alistipes shahii, Bacteroides vulgatus, Clostridium aldenense, Eggerthella lenta, Parabacteroides merdae, Alistipes shahii, Bacteroides vulgatus, Clostridium aldenense, Eggerthella lenta, Parabacteroides merdae, Alistipes timonensis, Bacteroides xylanisolvens, Clostridium amygdalinum, Eggerthella lenta, Parabacteroides merdae, Anaerofustis stercorihominis, Bacteroides xylanisolvens, Clostridium bolteae, Eggerthella lenta, Paraprevotella clara, Anaerostipes hadrus, Bacteroides xylanisolvens, Clostridium bolteae, Eubacterium eligens, Parasutterella excrementihominis, Anaerostipes hadrus, Bifidobacterium adolescentis, Clostridium citoniae, Eubacterium eligens, Parasutterella excrementihominis, Anaerotruncus colihominis, Bifidobacterium adolescentis, Clostridiumcitroniae, Eubacterium eligens, Roseburia hominis, Bacteroides caccae, Bifidobacterium catenulatum, Clostridium scindens, Eubacterium eligens, Roseburia hominis, Bacteroides caccae, Bifidobacterium dentium, Clostridium symbiosum, Eubacterium hallii, Roseburia hominis, Bacteroides cellulosilyticus, Bifidobacterium longum, Clostridium symbiosum, Eubacterium rectale, Roseburia hominis, Bacteroides coprocola, Bifidobacterium longum, Clostridium symbiosum, Eubacterium rectale, Ruminococcus bromii, Bacteroides finegoldii, Bifidobacterium longum, Collinsella aerofaciens, Eubacterium rectale, Ruminococcus bromii, Bacteroides fragilis, Bifidobacterium longum, Collinsella aerofaciens, Eubacterium rectale, Ruminococcus bromii, Bacteroides massiliensis, Bifidobacterium pseudocatenulatum, Collinsella aerofaciens, Eubacterium siraeum, Ruminococcus bromii, Bacteroides massiliensis, Bifidobacterium pseudocatenulatum, Collinsella aerofaciens, Eubacterium ventriosum, Ruminococcus faecis, Bacteroides nordii, Bifidobacteriumpseudocatenulatum, Coprococcus comes, Eubacterium xylanophilum, Ruminococcus faecis, Bacteroides oleiciplenus, Blautia faecis, Coprococcus comes, Faecalibacterium prausnitzii, Turicibacter sanguinis, Bacteroides ovatus, Blautia faecis, Coprococcus comes, Faecalibacterium prausnitzii, Bacteroides salyersiae, Blautia faecis, Coprococcus comes, Gordonibacter pamelaeae, Bacteroides stercoris, Blautia faecis, Coprococcus eutactus, and Gordonibacter pamelaeae.

[0095] In a particular embodiment, the consortium includes a plurality of microorganisms designated as "Consortium II" (e.g., active microorganisms and supporting community microorganisms). In certain embodiments, Consortia II provides Akkermansia muciniphila, Bacteroides vulgatus, Clostridium amygdalinum, Eggerthella lenta, Oxalobacter formigenes, Alistipes onderdonkii, Bifidobacterium dentium, Clostridium citroniae, Eubacterium eligens, Parabacteroides distasonis, Alistipes putredinis, Bifidobacterium faecale, Clostridium citroniae, Eubacterium eligens, Parabacteroides distasonis, Alistipes shahii, Bifidobacterium longum, Clostridium scindens, Eubacterium rectale, Parabacteroides merdae, Alistipes timonensis, Bifidobacterium longum, Clostridium symbiosum, Eubacterium rectale, Paraprevotella clara, Bacteroides caccae, Bifidobacterium pseudocatenulatum, Collinsella aerofaciens, Faecalibacterium prausnitzii, Parasutterella excrementihominis, Bacteroides koreensis, Bifidobacterium pseudocatenulatum, Coprococcus comes, Fusicatenibacter saccharivorans, Phascolarctobacterium faecium, Bacteroides kribbi, Bifidobacterium pseudocatenulatum, Coprococcuseutactus, Fusicatenibacter saccharivorans, Phascolarctobacterium faecium, Bacteroides kribbi, Blautia faecis, Desulfovibrio desulfuricans, Gordonibacter pamelaeae, Phascolarctobacterium faecium, Bacteroides nordii, Blautia faecis, Dialister succinatiphilus, Lachnoclostridium pacaense, Roseburia hominis, Bacteroides ovatus, Blautia obeum, Dorea formicigenerans, Lachnospira pectinoschiza, Ruminococcus bromii, Bacteroides salyersiae, Blautia obeum, Dorea longicatena, Monoglobus pectinolyticus, Ruminococcus bromii, Bacteroides thetaiotaomicron, Blautia obeum, Eggerthella lenta, Neglecta timonensis, Ruminococcus faecis, Bacteroides thetaiotaomicron, Blautia wexlerae, Eggerthella lenta, Oxalobacter formigenes, Sutterella massiliensis, Bacteroides uniformis, Blautia wexlerae, Eggerthella lenta, Oxalobacter formigenes, and Sutterella wadsworthensis.

[0096] In a particular embodiment, the consortium includes a plurality of microorganisms designated as “Consortium III” (e.g., active microorganisms and supporting community microorganisms). In certain embodiments, Consortia III provides Akkermansia muciniphila, Bacteroides vulgatus, Clostridium scindens, Eubacterium rectale, Parabacteroides merdae, Anaerotruncus colihominis, Bacteroides vulgatus, Clostridium symbiosum, Eubacterium rectale, Ruminococcus bromii, Bacteroides caccae, Bacteroides vulgatus, Clostridium symbiosum, Eubacterium rectale, Ruminococcus bromii, Bacteroides caccae, Bifidobacterium adolescentis, Clostridium symbiosum, Eubacterium rectale, Ruminococcus bromii, Bacteroides cellulosilyticus, Bifidobacterium adolescentis, Collinsella aerofaciens, Eubacterium siraeum, Ruminococcus bromii, Bacteroides fragilis, Bifidobacterium bifidum, Collinsella aerofaciens, Faecalibacterium prausnitzii, Sutterella wadsworthensis, Bacteroides massiliensis, Bifidobacterium bifidum, Collinsella aerofaciens, Gordonibacter pamelaeae, Sutterella wadsworthensis, Bacteroides massiliensis, Bifidobacterium catenulatum, Collinsella aerofaciens, Gordonibacterpamelaeae, Sutterella wadsworthensis, Bacteroides salyersiae, Bifidobacterium dentium, Coprococcus comes, Hydrogenoanaerobacterium saccharovorans, Bacteroides vulgatus, Bacteroides stercoris, Bifidobacterium longum, Coprococcus comes, Lachnospiraceae sp., Clostridium citroniae, Bacteroides stercoris, Bifidobacterium longum, Coprococcus comes, Lactonifactor longoviformis, Eggerthella lenta, Bacteroides stercoris, Bifidobacterium longum, Desulfovibrio desulfuricans, Neglecta timonensis, Parabacteroides merdae, Bacteroides thetaiotaomicron, Bifidobacterium longum, Desulfovibrio desulfuricans, Oxalobacter formigenes, Parabacteroides merdae, Bacteroides thetaiotaomicron, Bifidobacterium pseudocatenulatum, Dorea longicatena, Oxalobacter formigenes, Eggerthella lenta, Bacteroides thetaiotaomicron, Bifidobacterium pseudocatenulatum, Dorea longicatena, Oxalobacter formigenes, Clostridium citroniae, Bacteroides uniformis, Bifidobacterium pseudocatenulatum, Dorea longicatena, Parabacteroides distasonis, Bacteroides uniformis, Bacteroidesincluding uniformis, Citrobacter freundii, Eggerthella lenta, Parabacteroides distasonis, Bacteroides uniformis, Clostridium amygdalinum, Eggerthella lenta, and Parabacteroides distasonis.

[0097] In a particular embodiment, the consortium includes a plurality of microorganisms designated as "Consortium IV" (e.g., active microorganisms and supporting community microorganisms). In certain embodiments, Consortia IV includes Alistipes finegoldii, Bacteroides vulgatus, Clostridium bolteae, Dorea longicatena, Oxalobacter formigenes, Alistipes putredinis, Bacteroides vulgatus, Clostridium bolteae, Eggerthella lenta, Parabacteroides merdae Alistipes putredinis, Bacteroides xylanisolvens, Clostridium citroniae, Eggerthella lenta, Parabacteroides merdae, Anaerotruncus colihominis, Bacteroides xylanisolvens, Clostridium citroniae, Eggerthella lenta, Parabacteroides merdae, Bacteroides caccae, Bacteroides xylanisolvens, Clostridium scindens, Eggerthella lenta, Ruminococcus bromii, Bacteroides cellulosilyticus, Bifidobacterium bifidum, Clostridium symbiosum, Eubacterium eligens, Ruminococcus bromii, Bacteroides coprocola, Bifidobacterium bifidum, Clostridium symbiosum, Eubacterium eligens, Ruminococcus bromii, Bacteroides fragilis, Bifidobacterium catenulatum, Clostridium symbiosum, Eubacterium eligens, Ruminococcus bromii, Bacteroides ovatus, Bifidobacteriumdentium, Collinsella aerofaciens, Eubacterium eligens, Sutterella wadsworthensis, Bacteroides salyersiae, Bifidobacterium longum, Collinsella aerofaciens, Eubacterium hallii, Bacteroides stercoris, Bifidobacterium longum, Collinsella aerofaciens, Eubacterium rectale, Bacteroides stercoris, Bifidobacterium longum, Collinsella aerofaciens, Eubacterium siraeum, Bacteroides stercoris, Bifidobacterium longum, Coprococcus comes, Eubacterium ventriosum, Bacteroides thetaiotaomicron, Bifidobacterium pseudocatenulatum, Coprococcus eutactus, Faecalibacterium prausnitzii, Bacteroides thetaiotaomicron, Bifidobacterium pseudocatenulatum, Coprococcus eutactus, Faecalibacterium prausnitzii, Bacteroides thetaiotaomicron, Bifidobacterium pseudocatenulatum, Coprococcus eutactus, Hungatella hathewayi, Bacteroides uniformis, Blautia hydrogenotrophica, Desulfovibrio desulfuricans, Hungatella hathawayi, Bacteroides uniformis, Blautia obeum, Desulfovibrio desulfuricans, Neglecta timonensis, Bacteroides vulgatus, Blautia obeum, Doreaformicigenerans, Oxalobacter formigenes, Bacteroides vulgatus, Clostridium amygdalinum, Dorea longicatena, and Oxalobacter formigenes.

[0098] In a particular embodiment, the consortium includes a plurality of microorganisms designated as "Consortium V" (e.g., active microorganisms and supporting community microorganisms). In certain embodiments, Consortia V contains Acidaminococcus intestini, Bacteroides uniformis, Clostridium citroniae, Eubacterium ventriosum, Phascolarctobacterium faecium, Akkermansia muciniphila, Bacteroides vulgatus, Clostridium clostridioforme, Eubacterium siraeum, Phascolarctobacterium faecium, Alistipes finegoldii, Bacteroides vulgatus, Clostridium scindens, Eubacterium xylanophilum, Phocea massiliensis, Alistipes onderdonkii, Bacteroides xylanisolvens, Clostridium swellfunianum, Faecalibacterium prausnitzii, Phocea massiliensis, Alistipes onderdonkii, Bacteroides xylanisolvens, Clostridium symbiosum, Faecalibacterium prausnitzii, Porphyromonas asaccharolytica, Alistipes putredinis, Barnesiella intestinihominis, Clostridium symbiosum, Faecalicatena contorta, Porphyromonas asaccharolytica, Alistipes putredinis, Bifidobacterium adolescentis, Collinsella aerofaciens, Fusicatenibacter saccharivorans, Roseburia hominis, Alistipes senegalensis, Bifidobacteriumadolescentis, Collinsella aerofaciens, Fusicatenibacter saccharivorans, Roseburia hominis, Alistipes senegalensis, Bifidobacterium bifidum, Coprococcus comes, Gordonibacter pamelaeae, Ruminococcus bromii, Alistipes shahii, Bifidobacterium bifidum, Coprococcus comes, Gordonibacter pamelaeae, Ruminococcus bromii, Alistipes timonensis, Bifidobacterium catenulatum, Coprococcus eutactus, Holdemanella biformis, Ruminococcus faecis, Anaerofustis stercorihominis, Bifidobacterium dentium, Coprococcus eutactus, Holdemanella biformis, Ruminococcus faecis, Anaerostipes hadrus, Bifidobacterium faecale, Desulfovibrio desulfuricans, Hungatella effluvii, Ruthenibacterium lactatiformans, Anaerostipes hadrus, Bifidobacterium longum, Desulfovibrio desulfuricans, Hungatella hathewayi, Senegalimassilia anaerobia, Anaerotruncus colihominis, Bifidobacterium longum, Dialister invisus, Hungatella hathewayi, Sutterella massiliensis, Bacteroides caccae, Bifidobacterium pseudocatenulatum, Dialister succinatiphilus, Hydrogenoanaerobacteriumsaccharovorans, Sutterella wadsworthensis, Bacteroides caccae, Bifidobacterium pseudocatenulatum, Dielma fastidiosa, Lachnoclostridium pacaense, Sutterella wadsworthensis, Bacteroides coprocola, Bifidobacterium pseudocatenulatum, Dorea formicigenerans, Lachnoclostridium pacaense, Turicibacter sanguinis, Bacteroides faecis, Blautia faecis, Dorea formicigenerans, Lachnospira pectinoschiza, Bacteroides finegoldii, Blautia faecis, Dorea longicatena, Lachnospira pectinoschiza, Bacteroides fragilis, Blautia hydrogenotrophica, Dorea longicatena, Lactonifactor longoviformis, Bacteroides koreensis, Blautia luti, Eggerthella lenta, Longicatena caecimuris, Bacteroides koreensis, Blautia obeum, Eggerthella lenta, Megasphaera massiliensis, Bacteroides kribbi, Blautia obeum, Eggerthella lenta, Monoglobus pectinolyticus, Bacteroides kribbi, Blautia wexlerae, Eggerthella lenta, Monoglobus pectinolyticus, Bacteroides massiliensis, Blautia wexlerae, Eisenbergiella tayi, Neglecta timonensis, Bacteroides nordii, Butyricimonasfaecihominis, Eisenbergiella tayi, Oxalobacter formigenes, Bacteroides oleiciplenus, Catabacter hongkongensis, Emergencia timonensis, Oxalobacter formigenes, Bacteroides ovatus, Citrobacter freundii, Eubacterium eligens, Oxalobacter formigenes, Bacteroides salyersiae, Clostridium aldenense, Eubacterium eligens, Parabacteroides distasonis, Bacteroides stercoris, Clostridium aldenense, Eubacterium hallii, Parabacteroides merdae, Bacteroides stercoris, Clostridium amygdalinum, Eubacterium oxidoreducens, Parabacteroides merdae, Bacteroides thetaiotaomicron, Clostridium bolteae, Eubacterium rectale, Paraprevotella clara, Bacteroides thetaiotaomicron, Clostridium bolteae, Eubacterium rectale, Parasutterella excrementihominis, Bacteroides uniformis, Clostridium citroniae, Eubacterium ruminantium, and Parasutterella excrementihominis.

[0099] In a particular embodiment, the consortium includes a plurality of microorganisms designated as “Consortium VI” (e.g., active microorganisms and supporting community microorganisms). In certain embodiments, Consortia VI provides the following: Acidaminococcus intestini, Bacteroides stercorirosoris, Butyricimonas sp. casseliflavus, Megasphaera massiliensis, Acutalibacter timonensis, Bacteroides stercoris, Citrobacter portucalensis, Enterococcus durans, Methanobrevibacter smithii, Akkermansia muciniphila, Bacteroides thetaiotaomicron, Clostridiaceae sp.FBI00191, Enterococcus durans, Monoglobus pectinilyticus, Alistipes onderdonkii, Bacteroides thetaiotaomicron, Clostridium aldenense, Enterococcus durans, Monoglobus pectinilyticus, Alistipes onderdonkii, Bacteroides uniformis, Clostridium aldenense, Enterococcus faecalis, Oxalobacter formigenes, Alistipes putredinis, Bacteroides uniformis, Clostridium bolteae, Enterococcus faecium, Oxalobacter formigenes, Alistipes putredinis, Bacteroides vulgatus, Clostridium bolteae, Escherichiaflexneri, Oxalobacter formigenes, Alistipes senegalensis, Bacteroides vulgatus, Clostridium citroniae, Eubacterium eligens, Parabacteroides distasonis, Alistipes shahii, Bacteroides xylanisolvens, Clostridium citroniae, Eubacterium eligens, Parabacteroides distasonis, Alistipes shahii, Bacteroides xylanisolvens, Clostridium clostridioforme, Eubacterium hallii, Parabacteroides merdae, Alistipes sp.FBI00180, Bacteroides xylanisolvens, Clostridium fessum, Eubacterium rectale, Parabacteroides merdae, Alistipes sp.FBI00238, Barnesiella intestinihominis, Clostridium fessum, Eubacterium rectale, Paraprevotella clara, Alistipes timonensis, Bifidobacterium adolescentis, Clostridium scindens, Eubacterium siraeum, Parasutterella excrementihominis, Anaerofustis stercorihominis, Bifidobacterium adolescentis, Collinsella aerofaciens, Eubacterium ventriosum, Parasutterella excrementihominis, Anaerostipes hadrus, Bifidobacterium adolescentis, Collinsella aerofaciens, Eubacterium xylanophilum, Phascolarctobacterium faecium, Anaerostipeshadrus, Bifidobacterium adolescentis, Coprococcus comes, Faecalibacterium prausnitzii, Phascolarctobacterium faecium, Anaerotruncus massiliensis, Bifidobacterium bifidum, Coprococcus comes, Faecalibacterium prausnitzii, Porphyromonas asaccharolytica, Bacteroides caccae, Bifidobacterium bifidum, Coprococcus eutactus, Faecalicatena contorta, Porphyromonas asaccharolytica, Bacteroides caccae, Bifidobacterium catenulatum, Dialister invisus, Fusicatenibacter saccharivorans, Roseburia hominis, Bacteroides cellulosilyticus, Bifidobacterium dentium, Coprococcus eutactus, Fusicatenibacter saccharivorans, Roseburia hominis, Bacteroides cellulosilyticus, Bifidobacterium longum, Dialister succinatiphilus, Gordonibacter pamelaeae, Ruminococcaceae sp.FBI00097, Bacteroides coprocola, Bifidobacterium longum, Dialister succinatiphilus, Gordonibacter pamelaeae, Ruminococcaceae sp.FBI00097, Bacteroides dorei, Bifidobacterium pseudocatenulatum, Dielma fastidiosa, Holdemanella biformis, Ruminococcaceae sp.FBI00233, Bacteroidesdorei, Bifidobacterium pseudocatenulatum, Dorea formicigenerans, Holdemanella biformis, Ruminococcus bromii, Bacteroides faecis, Bilophila wadsworthia, Dorea formicigenerans, Hungatella effluvii, Ruminococcus bromii, Bacteroides finegoldii, Bilophila wadsworthia, Dorea longicatena, Hungatella effluvii, Ruminococcus faecis, Bacteroides fragilis, Blautia faecis, Dorea longicatena, Hungatella effluvii, Ruminococcus faecis, Bacteroides kribbi / Bacteroides koreensis species cluster, Blautia faecis, Eggerthella lenta, Lachnoclostridium pacaense, Ruthenibacterium lactatiformans, Bacteroides kribbi / Bacteroides koreensis species cluster, Blautia hydrogenotrophica, Eggerthella lenta, Lachnoclostridium pacaense, Senegalimassilia anaerobia, Bacteroides kribbi / Bacteroides koreensis species cluster, Blautia luti, Eisenbergiella tayi, Lachnospiraceae sp.FBI00033, Sutterella massiliensis, Bacteroides massiliensis, Blautia massiliensis, Emergencia timonensis, Lachnospiraceae sp.FBI00071, Sutterella wadsworthensis, Bacteroidesmassiliensis, Blautia obeum, Eisenbergiella tayi, Lachnospiraceae sp. FBI00150, Sutterella wadsworthensis, Bacteroides nordii, Blautia obeum, Enterobacter himalayensis, Lachnospiraceae sp. FBI00290, Turicibacter sanguinis, Bacteroides ovatus, Blautia wexlerae, Enterobacter hormaechei, Lactobacillus rogosae, Bacteroides salyersiae, Blautia wexlerae, Enterococcus casseliflavus, Lactobacillus rogosae, Bacteroides salyersiae, Butyricimonas faecihominis, Enterococcus casseliflavus, and Lactonifactor longoviformis.

[0100] In certain embodiments, the consortium includes several microorganisms designated as “Consortium VII” (e.g., active microorganisms and supporting community microorganisms). In certain embodiments, Consortium VII includes Acidaminococcus intestini, Bacteroides thetaiotaomicron, Citrobacter portucalensis, Eubacterium eligens, Oxalobacter formigenes, Acutalibacter timonensis, Bacteroides uniformis, and Clostridiaceae sp.FBI00191, Eubacterium hallii, Parabacteroides distasonis, Akkermansia muciniphila, Bacteroides uniformis, Clostridium aldenense, Eubacterium rectale, Parabacteroides merdae, Alistipes onderdonkii, Bacteroides vulgatus, Clostridium aldenense, Eubacterium rectale, Parabacteroides merdae, Alistipes onderdonkii, Bacteroides vulgatus, Clostridium bolteae, Eubacterium siraeum, Paraprevotella clara, Alistipes putredinis, Bacteroides xylanisolvens, Clostridium bolteae, Eubacterium ventriosum, Parasutterella excrementihominis, Alistipes putredinis, Bacteroides xylanisolvens, Clostridium citroniae, Faecalibacterium prausnitzii, Parasutterella excrementihominis, Alistipes senegalensis, Bacteroides xylanisolvens, Clostridium citroniae, Eubacterium xylanophilum, Phascolarctobacterium faecium, Alistipes shahii, Barnesiella human intestine、Clostridium clostridioforme、Faecalibacterium prausnitzii、Phascolarctobacterium faecium、Alistipes sp.FBI00180, Bifidobacterium adolescentis, Clostridium fessum, Faecalicatena contorta, Porphyromonas asaccharolytica, Alistipes sp.FBI00238, Bifidobacterium adolescentis, Clostridium fessum, Fusicatenibacter saccharivorans, Porphyromonas asaccharolytica, Alistipes timonensis, Bifidobacterium adolescentis, Clostridium scindens, Fusicatenibacter saccharivorans, Roseburia hominis, Anaerofustis stercorihominis, Bifidobacterium bifidum, Collinsella aerofaciens, Gordonibacter pamelaeae, Roseburia hominis, Anaerostipes hadrus, Bifidobacterium bifidum, Collinsella aerofaciens, Gordonibacter pamelaeae, Ruminococcaceae sp.FBI00097, Anaerostipes hadrus, Bifidobacterium catenulatum, Coprococcus comes, Holdemanella biformis, Ruminococcaceae sp.FBI00097, Anaerotruncus massiliensis, Bifidobacterium dentium, Coprococcus comes, Holdemanella biformis, Ruminococcaceae sp.FBI00233, Bacteroides caccae, Bifidobacterium longum, Coprococcus eutactus, Hungatella effluvii, Ruminococcus bromii, Bacteroides caccae, Bifidobacterium longum, Coprococcus eutactus, Hungatella effluvii, Ruminococcus bromii, Bacteroides coprocola, Bifidobacterium pseudocatenulatum, Dialister invisus, Hungatella effluvii, Ruminococcus faecis, Bacteroides faecis, Bifidobacterium pseudocatenulatum, Dialister succinatiphilus, Lachnoclostridium pacaense, Ruminococcus faecis, Bacteroides finegoldii, Bifidobacterium pseudocatenulatum, Dielma fastidiosa, Lachnoclostridium pacaense, Ruthenibacterium lactatiformans, Bacteroides fragilis, Bilophila wadsworthia, Dorea formicigenerans, Lachnospiraceae sp.FBI00033, Senegalimassilia anaerobia, Bacteroides kribbi / Bacteroides koreensis species cluster, Bilophila wadsworthia, Dorea formicigenerans, Lachnospiraceae sp.FBI00071, Sutterella massiliensis, Bacteroides kribbi / Bacteroides koreensis species cluster, Blautia faecis, Dorea longicatena, Lachnospiraceae sp.FBI00290, Sutterella wadsworthensis, Bacteroides kribbi / Bacteroides koreensis species cluster, Blautia faecis, Dorea longicatena, Lactobacillus rogosae, Sutterella wadsworthensis, Bacteroides massiliensis, Blautia hydrogenotrophica, Eggerthella lenta, Lactobacillus rogosae, Turicibacter sanguinis, Bacteroides nordii, Blautia massiliensis, Eggerthella lenta, Lactonifactor longoviformis, Bacteroides ovatus, Blautia obeum, Eggerthella lenta, Longicatena caecimuris, Bacteroides salyersiae, Blautia obeum, Eggerthella lenta, Megasphaera massiliensis, Bacteroides stercorirosoris, Blautia wexlerae, Eisenbergiella tayi, Monoglobus pectinolyticus, Bacteroides stercoris, Blautia wexlerae, Eisenbergiella tayi, Monoglobus pectinolyticus, Bacteroides stercoris, Butyricimonas faecihominis, Emergencia timonensis, Oxalobacter formigenes, Bacteroides thetaiotaomicron, Catabacter hongkongensis, Eubacterium eligens, and Oxalobacter formigenes.

[0101] In certain embodiments, the consortium includes several microorganisms designated as “Consortium VIII” (e.g., active microorganisms and supporting community microorganisms). In certain embodiments, Consortium VIII includes Acidaminococcus intestini, Bacteroides thetaiotaomicron, Butyricimonas faecihominis, Eisenbergiella tayi, Monoglobus pectinilyticus, Acutalibacter timonensis, Bacteroides thetaiotaomicron, Catabacter hongkongensis, Emergencia timonensis, Monoglobus pectinilyticus, Akkermansia muciniphila, Bacteroides uniformis, Citrobacter portucalensis, Eubacterium eligens, Oxalobacter formigenes, Alistipes onderdonkii, Bacteroides uniformis, Clostridiaceae sp.FBI00191, Eubacterium eligens, Oxalobacter formigenes, Alistipes onderdonkii, Bacteroides vulgatus, Clostridium aldenense, Eubacterium hallii, Oxalobacter formigenes, Alistipes putredinis, Bacteroides vulgatus, Clostridium aldenense, Eubacterium rectale, Parabacteroides distasonis, Alistipes putredinis, Bacteroides xylanisolvens, Clostridium bolteae, Eubacterium rectale, Parabacteroides merdae, Alistipes senegalensis, Bacteroides xylanisolvens, Clostridium bolteae, Eubacterium siraeum, Parabacteroides merdae, Alistipes shahii, Bacteroides xylanisolvens, Clostridium citroniae, Eubacterium ventriosum, Paraprevotella clara, Alistipes sp.FBI00180, Barnesiella intestinihominis, Clostridium citroniae, Faecalibacterium prausnitzii, Parasutterella excrementihominis, Alistipes sp.FBI00238, Bifidobacterium adolescentis, Clostridium clostridioforme, Eubacterium xylanophilum, Parasutterella excrementihominis, Alistipes timonensis, Bifidobacterium adolescentis, Clostridium fessum, Faecalibacterium prausnitzii, Phascolarctobacterium faecium, Anaerofustis stercorihominis, Bifidobacterium adolescentis, Clostridium fessum, Faecalicatena contorta, Phascolarctobacterium faecium, Anaerostipes hadrus, Bifidobacterium bifidum, Clostridium scindens, Fusicatenibacter saccharivorans, Porphyromonas asaccharolytica, Anaerostipes hadrus, Bifidobacterium bifidum, Collinsella aerofaciens, Fusicatenibacter saccharivorans, Porphyromonas asaccharolytica, Anaerotruncus massiliensis, Bifidobacterium catenulatum, Collinsella aerofaciens, Gordonibacter pamelaeae, Roseburia hominis, Bacteroides caccae, Bifidobacterium dentium, Coprococcus comes, Gordonibacter pamelaeae, Roseburia hominis, Bacteroides caccae, Bifidobacterium longum, Coprococcus comes, Holdemanella biformis, Ruminococcaceae sp.FBI00097, Bacteroides coprocola, Bifidobacterium longum, Coprococcus eutactus, Holdemanella biformis, Ruminococcaceae sp.FBI00097, Bacteroides faecis, Bifidobacterium pseudocatenulatum, Coprococcus eutactus, Hungatella effluvii, Ruminococcaceae sp.FBI00233, Bacteroides finegoldii, Bifidobacterium pseudocatenulatum, Dialister invisus, Hungatella effluvii, Ruminococcus bromii, Bacteroides fragilis, Bifidobacterium pseudocatenulatum, Dialister succinatiphilus, Hungatella effluvii, Ruminococcus bromii, Bacteroides kribbi / Bacteroides koreensis species cluster, Bilophila wadsworthia, Dielma fastidiosa, Lachnoclostridium pacaense, Ruminococcus faecis, Bacteroides kribbi / Bacteroides koreensis species cluster, Bilophila wadsworthia, Dorea formicigenerans, Lachnoclostridium pacaense, Ruminococcus faecis, Bacteroides kribbi / Bacteroides koreensis species cluster, Blautia faecis, Dorea formicigenerans, Lachnospiraceae sp.FBI00033, Ruthenibacterium lactatiformans, Bacteroides massiliensis, Blautia faecis, Dorea longicatena, Lachnospiraceae sp.FBI00071, Senegalimassilia anaerobia, Bacteroides nordii, Blautia hydrogenotrophica, Dorea longicatena, Lachnospiraceae sp.FBI00290, Sutterella massiliensis, Bacteroides ovatus, Blautia massiliensis, Eggerthella lenta, Lactobacillus rogosae, Sutterella wadsworthensis, Bacteroides salyersiae, Blautia obeum, Eggerthella lenta, Lactobacillus rogosae, Sutterella wadsworthensis, Bacteroides stercorirosoris, Blautia obeum, Eggerthella lenta, Lactonifactor longoviformis, Turicibacter sanguinis, Bacteroides stercoris, Blautia wexlerae, Eggerthella lenta, Longicatena caecimuris, Bacteroides stercoris, Blautia wexlerae, Eisenbergiella tayi, and Megasphaera including Massiliensis.

[0102] In a particular embodiment, the consortium includes a plurality of microorganisms designated as “Consortium IX” (e.g., active microorganisms and supporting community microorganisms). In certain embodiments, Consortia formigenes, Alistipes onderdonkii, Bacteroides uniformis, Clostridiaceae sp.FBI00191, Eubacterium hallii, Oxalobacter formigenes, Alistipes onderdonkii, Bacteroides uniformis, Clostridiales sp.FBI00377, Eubacterium rectale, Oxalobacter formigenes, Alistipes putredinis, Bacteroides vulgatus, Clostridium aldenense, Eubacterium rectale, Parabacteroides distasonis, Alistipes putredinis, Bacteroides vulgatus, Clostridium aldenense, Eubacterium siraeum, Parabacteroides distasonis, Alistipes senegalensis, Bacteroides xylanisolvens, Clostridium bolteae, Eubacterium ventriosum, Parabacteroides merdae, Alistipes shahii, Bacteroides xylanisolvens, Clostridium bolteae, Eubacterium xylanophilum, Parabacteroidesmerdae, Alistipes shahii, Bacteroides xylanisolvens, Clostridium citroniae, Faecalibacterium prausnitzii, Paraprevotella clara, Alistipes sp.FBI00180, Barnesiella intestinihominis, Clostridium citroniae, Fusicatenibacter saccharivorans, Parasutterella excrementihominis, Alistipes sp.FBI00238, Bifidobacterium adolescentis, Clostridium clostridioforme, Fusicatenibacter saccharivorans, Parasutterella excrementihominis, Alistipes timonensis, Bifidobacterium adolescentis, Clostridium fessum, Gordonibacter pamelaeae, Phascolarctobacterium faecium, Anaerofustis stercorihominis, Bifidobacterium adolescentis, Clostridium scindens, Gordonibacter pamelaeae, Porphyromonas asaccharolytica, Anaerostipes hadrus, Bifidobacterium bifidum, Collinsella aerofaciens, Holdemanella biformis, Porphyromonas asaccharolytica, Anaerostipes hadrus, Bifidobacterium catenulatum, Collinsella aerofaciens, Hungatella effluvii, Roseburia hominis, Anaerotruncus massiliensis, Bifidobacterium dentium, Coprococcus comes, Hungatella effluvii, Roseburiahominis, Bacteroides caccae, Bifidobacterium longum, Coprococcus comes, Hungatella effluvii, Ruminococcaceae sp.FBI00082, FBI00097, Bacteroides caccae, Bifidobacterium longum, Coprococcus eutactus, Lachnoclostridium pacaense, Ruminococcaceae sp.FBI00233, Bacteroides coprocola, Bifidobacterium pseudocatenulatum, Dialister invisus, Lachnoclostridium pacaense, Ruminococcus bromii, Bacteroides faecis, Bifidobacterium pseudocatenulatum, Dialister succinatiphilus, Lachnospiraceae sp.FBI00033, Ruminococcus bromii, Bacteroides finegoldii, Bifidobacterium pseudocatenulatum, Dielma fastidiosa, Lachnospiraceae sp.FBI00071, Ruminococcus faecis, Bacteroides fragilis, Bilophila wadsworthia, Dorea formicigenerans, Lachnospiraceae sp.FBI00290, Ruminococcus faecis, Bacteroides kribbi / Bacteroides koreensis species cluster, Bilophila wadsworthia, Dorea formicigenerans, Lactobacillus rogosae, Ruthenibacterium lactatiformans, Bacteroides kribbi / Bacteroides koreensis species cluster, Blautia faecis, Dorea longicatena, Lactobacillusrogosae, Senegalimassilia anaerobia, Bacteroides massiliensis, Blautia faecis, Dorea longicatena, Longicatena caecimuris, Sutterella massiliensis, Bacteroides nordii, Blautia hydrogenotrophica, Eggerthella lenta, Megasphaera massiliensis, Sutterella wadsworthensis, Bacteroides ovatus, Blautia massiliensis, Eggerthella lenta, Methanobrevibacter smithii, Sutterella wadsworthensis, Bacteroides salyersiae, Blautia obeum, Eggerthella lenta, Methanobrevibacter smithii, Turicibacter sanguinis, Bacteroides stercorirosoris, Blautia obeum, Eggerthella lenta, Monoglobus pectinolyticus, Bacteroides stercoris, Blautia wexlerae, Eisenbergiella tayi, Monoglobus pectinolyticus, Bacteroides stercoris, Blautia wexlerae, Eisenbergiella tayi, and Neglecta timonensis.

[0103] In a particular embodiment, the consortium includes multiple microorganisms designated as "Consortium X" (e.g., active microorganisms and supporting community microorganisms). In certain embodiments, Consortia timonensis, Alistipes onderdonkii, Bacteroides uniformis, Clostridiaceae sp.FBI00191, Eubacterium hallii, Neglecta timonensis, Alistipes onderdonkii, Bacteroides uniformis, Clostridiales sp.FBI00377, Eubacterium rectale, Oxalobacter formigenes, Alistipes putredinis, Bacteroides vulgatus, Clostridium aldenense, Eubacterium rectale, Oxalobacter formigenes, Alistipes putredinis, Bacteroides vulgatus, Clostridium aldenense, Eubacterium siraeum, Oxalobacter formigenes, Alistipes senegalensis, Bacteroides xylanisolvens, Clostridium bolteae, Eubacterium ventriosum, Parabacteroides distasonis, Alistipes shahii, Bacteroides xylanisolvens, Clostridium bolteae, Eubacterium xylanophilum, Parabacteroidesdistasonis, Alistipes shahii, Bacteroides xylanisolvens, Clostridium citroniae, Faecalibacterium prausnitzii, Parabacteroides merdae, Alistipes sp.FBI00180, Barnesiella intestinihominis, Clostridium citroniae, Faecalibacterium prausnitzii, Parabacteroides merdae, Alistipes sp.FBI00238, Bifidobacterium adolescentis, Clostridium clostridioforme, Fusicatenibacter saccharivorans, Paraprevotella clara, Alistipes timonensis, Bifidobacterium adolescentis, Clostridium fessum, Fusicatenibacter saccharivorans, Parasutterella excrementihominis, Anaerofustis stercorihominis, Bifidobacterium adolescentis, Clostridium scindens, Gordonibacter pamelaeae, Parasutterella excrementihominis, Anaerostipes hadrus, Bifidobacterium bifidum, Collinsella aerofaciens, Gordonibacter pamelaeae, Phascolarctobacterium faecium, Anaerostipes hadrus, Bifidobacterium catenulatum, Collinsella aerofaciens, Holdemanella biformis, Porphyromonas asaccharolytica, Anaerotruncus massiliensis, Bifidobacterium dentium, Coprococcus comes, Holdemanellabiformis, Porphyromonas asaccharolytica, Bacteroides caccae, Bifidobacterium longum, Coprococcus comes, Hungatella effluvii, Roseburia hominis, Bacteroides caccae, Bifidobacterium longum, Coprococcus eutactus, Hungatella effluvii, Roseburia hominis, Bacteroides coprocola, Bifidobacterium pseudocatenulatum, Dialister invisus, Hungatella effluvii, Ruminococcaceae sp.FBI00082 FBI00097, Bacteroides faecis, Bifidobacterium pseudocatenulatum, Dialister succinatiphilus, Lachnoclostridium pacaense, Ruminococcaceae sp.FBI00233, Bacteroides finegoldii, Bifidobacterium pseudocatenulatum, Dielma fastidiosa, Lachnoclostridium pacaense, Ruminococcus bromii, Bacteroides fragilis, Bilophila wadsworthia, Dorea formicigenerans, Lachnospiraceae sp.FBI00033, Ruminococcus bromii, Bacteroides kribbi / Bacteroides koreensis species cluster, Bilophila wadsworthia, Dorea formicigenerans, Lachnospiraceae sp.FBI00071, Ruminococcus faecis, Bacteroides kribbi / Bacteroides koreensis species cluster, Blautia faecis, Dorea longicatena, Lachnospiraceaesp.FBI00290, Ruminococcus faecis, Bacteroides massiliensis, Blautia faecis, Dorea longicatena, Lactobacillus rogosae, Ruthenibacterium lactatiformans, Bacteroides nordii, Blautia hydrogenotrophica, Eggerthella lenta, Lactobacillus rogosae, Senegalimassilia anaerobia, Bacteroides ovatus, Blautia massiliensis, Eggerthella lenta, Longicatena caecimuris, Sutterella massiliensis, Bacteroides salyersiae, Blautia obeum, Eggerthella lenta, Megasphaera massiliensis, Sutterella wadsworthensis, Bacteroides stercorirosoris, Blautia obeum, Eggerthella lenta, Methanobrevibacter smithii, Sutterella wadsworthensis, Bacteroides stercoris, Blautia wexlerae, Eisenbergiella tayi, Methanobrevibacter smithii, Turicibacter sanguinis, Bacteroides stercoris, Blautia wexlerae, Eisenbergiella tayi, and Monoglobus including pectinolyticus

[0104] In a particular embodiment, the consortium includes a plurality of microorganisms designated as “Consortium XI” (e.g., active microorganisms and supporting community microorganisms). In certain embodiments, Consortia aerofaciens, Alistipes onderdonkii, Blautia hydrogenotrophica, Hungatella effluvii, Bifidobacterium adolescentis, Coprococcus comes, Alistipes putredinis, Blautia massiliensis, Lachnoclostridium pacaense, Bifidobacterium pseudocatenulatum, Dorea formicigenerans, Alistipes senegalensis, Blautia obeum, Lachnospiraceae sp.FBI00033, Blautia faecis, Dorea longicatena, Alistipes shahii, Blautia wexlerae, Lachnospiraceae sp.FBI00071, Clostridium citroniae, Eggerthella lenta, Alistipes sp.FBI00180, Butyricimonas faecihominis, Lachnospiraceae sp.FBI00290, Faecalibacterium prausnitzii, Eggerthella lenta, Alistipes sp.FBI00238, Catabacter hongkongensis, Lactobacillus rogosae, Holdemanella biformis, Eggerthellalenta, Alistipes timonensis, Clostridiaceae sp.FBI00191, Longicatena caecimuris, Bacteroides xylanisolvens, Eisenbergiella tayi, Anaerofustis stercorihominis, Clostridiales sp.FBI00377, Megasphaera massiliensis, Bifidobacterium adolescentis, Eubacterium eligens, Anaerostipes hadrus, Clostridium aldenense, Methanobrevibacter smithii, Bifidobacterium pseudocatenulatum, Eubacterium rectale, Anaerotruncus massiliensis, Clostridium bolteae, Monoglobus pectinolyticus, Blautia faecis, Fusicatenibacter saccharivorans, Bacteroides caccae, Clostridium clostridioforme, Neglecta timonensis, Alistipes onderdonkii, Gordonibacter pamelaeae, Bacteroides coprocola, Clostridium fessum, Oxalobacter formigenes, Clostridium citroniae, Hungatella effluvia, Bacteroides faecis, Clostridium scindens, Oxalobacter formigenes, Alistipes putredinis, Hungatella effluvia, Bacteroides finegoldii, Collinsella aerofaciens, Oxalobacter formigenes, Alistipes shahii, Lachnoclostridium pacaense, Bacteroides fragilis, Coprococcus comes, Parabacteroidesdistasonis, Anaerostipes hadrus, Lactobacillus rogosae, Bacteroides kribbi / Bacteroides koreensis species cluster, Coprococcus eutactus, Parabacteroides merdae, Bacteroides caccae, Methanobrevibacter smithii, Bacteroides massiliensis, Dialister invisus, Paraprevotella clara, Bacteroides kribbi / Bacteroides koreensis species cluster, Monoglobus pectinolyticus, Bacteroides nordii, Dialister succinatiphilus, Parasutterella excrementihominis, Bacteroides stercoris, Neglecta timonensis, Bacteroides ovatus, Dielma fastidiosa, Phascolarctobacterium faecium, Bacteroides thetaiotaomicron, Parabacteroides distasonis, Bacteroides salyersiae, Dorea formicigenerans, Porphyromonas asaccharolytica, Bacteroides uniformis, Parabacteroides merdae, Bacteroides stercorirosoris, Dorea longicatena, Roseburia hominis, Bacteroides vulgatus, Parasutterella excrementihominis, Bacteroides stercoris, Eggerthella lenta, Ruminococcaceae sp. FBI00082 FBI00097, Bacteroides xylanisolvens, Porphyromonas asaccharolytica, Bacteroidesthetaiotaomicron, Eisenbergiella tayi, Ruminococcaceae sp. FBI00233, Bifidobacterium adolescentis, Roseburia hominis, Bacteroides uniformis, Eubacterium eligens, Ruminococcus bromii, Bifidobacterium longum, Ruminococcus bromii, Bacteroides vulgatus, Eubacterium hallii, Ruminococcus faecis, Bifidobacterium pseudocatenulatum, Ruminococcus faecis, Barnesiella intestinihominis, Eubacterium rectale, Ruthenibacterium lactatiformans, Bilophila wadsworthia, Sutterella wadsworthensis, Bifidobacterium bifidum, Eubacterium siraeum, Senegalimassilia anaerobia, Blautia obeum, Bifidobacterium catenulatum, Eubacterium ventriosum, Sutterella massiliensis, Blautia wexlerae, Bifidobacterium dentium, Eubacterium xylanophilum, Sutterella wadsworthensis, and Clostridium aldenense.

[0105] In a particular embodiment, the consortium includes a plurality of microorganisms designated as “Consortium XII” (e.g., active microorganisms and supporting community microorganisms). In certain embodiments, Consortia faecium, Alistipes onderdonkii, Bacteroides vulgatus, Clostridium citroniae, Fusicatenibacter saccharivorans, Phascolarctobacterium faecium, Alistipes onderdonkii, Bacteroides xylanisolvens, Clostridium citroniae, Fusicatenibacter saccharivorans, Porphyromonas asaccharolytica, Alistipes putredinis, Bacteroides xylanisolvens, Clostridium clostridioforme, Gordonibacter pamelaeae, Porphyromonas asaccharolytica, Alistipes putredinis, Bacteroides xylanisolvens, Clostridium fessum, Gordonibacter pamelaeae, Roseburia hominis, Alistipes senegalensis, Barnesiella intestinihominis, Clostridium fessum, Holdemanella biformis, Roseburia hominis, Alistipes shahii, Bifidobacteriumadolescentis, Clostridium scindens, Holdemanella biformis, Ruminococcaceae sp.FBI00082 FBI00097, Alistipes shahii, Bifidobacterium adolescentis, Collinsella aerofaciens, Hungatella effluvii, Ruminococcaceae sp.FBI00082 FBI00097, Alistipes sp.FBI00180, Bifidobacterium adolescentis, Collinsella aerofaciens, Hungatella effluvii, Ruminococcaceae sp.FBI00233, Alistipes sp.FBI00238, Bifidobacterium bifidum, Coprococcus comes, Hungatella effluvii, Ruminococcus bromii, Alistipes timonensis, Bifidobacterium bifidum, Coprococcus comes, Lachnoclostridium pacaense, Ruminococcus bromii, Anaerofustis stercorihominis, Bifidobacterium catenulatum, Coprococcus eutactus, Lachnoclostridium pacaense, Ruminococcus faecis, Anaerostipes hadrus, Bifidobacterium dentium, Coprococcus eutactus, Lachnospiraceae sp.FBI00033, Ruminococcus faecis, Anaerostipes hadrus, Bifidobacterium longum, Dialister invisus, Lachnospiraceae sp.FBI00071, Ruthenibacterium lactatiformans, Anaerotruncus massiliensis, Bifidobacterium longum, Dialistersuccinatiphilus, Lachnospiraceae sp.FBI00290, Senegalimassilia anaerobia, Bacteroides caccae, Bifidobacterium pseudocatenulatum, Dielma fastidiosa, Lactobacillus rogosae, Sutterella massiliensis, Bacteroides caccae, Bifidobacterium pseudocatenulatum, Dorea formicigenerans, Lactobacillus rogosae, Sutterella wadsworthensis, Bacteroides coprocola, Bifidobacterium pseudocatenulatum, Dorea formicigenerans, Longicatena caecimuris, Sutterella wadsworthensis, Bacteroides faecis, Bilophila wadsworthia, Dorea longicatena, Megasphaera massiliensis, Turicibacter sanguinis, Bacteroides finegoldii, Bilophila wadsworthia, Dorea longicatena, Methanobrevibacter smithii, Bacteroides thetaiotaomicron, Bacteroides fragilis, Blautia faecis, Eggerthella lenta, Methanobrevibacter smithii, Bacteroides uniformis, Bacteroides kribbi / Bacteroides koreensis species cluster、Blautia faecis、Eggerthella lenta、Monoglobus pectinilyticus、Clostridium aldenense、Bacteroides kribbi / Bacteroides koreensis species cluster、Blautia hydrogenotrophica、Eggerthellalenta, Monoglobus pectinolyticus, Clostridium aldenense, Bacteroides kribbi / Bacteroides koreensis species cluster, Blautia massiliensis, Eggerthella lenta, Neglecta timonensis, Eubacterium ventriosum, Bacteroides massiliensis, Blautia obeum, Eisenbergiella tayi, Neglecta timonensis, Eubacterium xylanophilum, Bacteroides nordii, Blautia obeum, Eisenbergiella tayi, Oxalobacter formigenes, Paraprevotella clara, Bacteroides ovatus, Blautia wexlerae, Eubacterium eligens, Oxalobacter formigenes, Parasutterella excrementihominis, Bacteroides salyersiae, Blautia wexlerae, Eubacterium eligens, Oxalobacter formigenes, Bacteroides thetaiotaomicron, Bacteroides stercorirosoris, Butyricimonas faecihominis, Eubacterium hallii, Parabacteroides distasonis, Clostridiales sp.FBI00377, Bacteroides stercoris, Catabacter hongkongensis, Eubacterium rectale, Parabacteroides distasonis, Eubacterium siraeum, Bacteroides stercoris, Clostridiaceae sp. FBI00191, Eubacterium rectale, Parabacteroides merdae, and Parabacteroides merdae.

[0106] In a particular embodiment, the consortium includes a plurality of microorganisms designated as “Consortium XIII” (e.g., active microorganisms and supporting community microorganisms). In certain embodiments, Consortia timonensis, Alistipes onderdonkii, Bacteroides uniformis, Clostridiaceae sp.FBI00191, Eubacterium hallii, Neglecta timonensis, Alistipes onderdonkii, Bacteroides uniformis, Clostridiales sp.FBI00377, Eubacterium rectale, Oxalobacter formigenes, Alistipes putredinis, Bacteroides vulgatus, Clostridium aldenense, Eubacterium rectale, Oxalobacter formigenes, Alistipes putredinis, Bacteroides vulgatus, Clostridium aldenense, Eubacterium siraeum, Oxalobacter formigenes, Alistipes senegalensis, Bacteroides xylanisolvens, Clostridium bolteae, Eubacterium ventriosum, Parabacteroides distasonis, Alistipes shahii, Bacteroides xylanisolvens, Clostridium bolteae, Eubacterium xylanophilum, Parabacteroidesdistasonis, Alistipes shahii, Bacteroides xylanisolvens, Clostridium citroniae, Faecalibacterium prausnitzii, Parabacteroides merdae, Alistipes sp.FBI00180, Barnesiella intestinihominis, Clostridium citroniae, Faecalibacterium prausnitzii, Parabacteroides merdae, Alistipes sp.FBI00238, Bifidobacterium adolescentis, Clostridium clostridioforme, Fusicatenibacter saccharivorans, Paraprevotella clara, Alistipes timonensis, Bifidobacterium adolescentis, Clostridium fessum, Fusicatenibacter saccharivorans, Parasutterella excrementihominis, Anaerofustis stercorihominis, Bifidobacterium adolescentis, Clostridium scindens, Gordonibacter pamelaeae, Parasutterella excrementihominis, Anaerostipes hadrus, Bifidobacterium bifidum, Collinsella aerofaciens, Gordonibacter pamelaeae, Phascolarctobacterium faecium, Anaerostipes hadrus, Bifidobacterium catenulatum, Collinsella aerofaciens, Holdemanella biformis, Porphyromonas asaccharolytica, Anaerotruncus massiliensis, Bifidobacterium dentium, Coprococcus comes, Holdemanellabiformis, Porphyromonas asaccharolytica, Bacteroides caccae, Bifidobacterium longum, Coprococcus comes, Hungatella effluvii, Roseburia hominis, Bacteroides caccae, Bifidobacterium longum, Coprococcus eutactus, Hungatella effluvii, Roseburia hominis, Bacteroides coprocola, Bifidobacterium pseudocatenulatum, Dialister invisus, Hungatella effluvii, Ruminococcaceae sp.FBI00082 FBI00097, Bacteroides faecis, Bifidobacterium pseudocatenulatum, Dialister succinatiphilus, Lachnoclostridium pacaense, Ruminococcaceae sp.FBI00233, Bacteroides finegoldii, Bifidobacterium pseudocatenulatum, Dielma fastidiosa, Lachnoclostridium pacaense, Ruminococcus bromii, Bacteroides fragilis, Bilophila wadsworthia, Dorea formicigenerans, Lachnospiraceae sp.FBI00033, Ruminococcus bromii, Bacteroides kribbi / Bacteroides koreensis species cluster, Bilophila wadsworthia, Dorea formicigenerans, Lachnospiraceae sp.FBI00071, Ruminococcus faecis, Bacteroides kribbi / Bacteroides koreensis species cluster, Blautia faecis, Dorea longicatena, Lachnospiraceaesp.FBI00290, Ruminococcus faecis, Bacteroides massiliensis, Blautia faecis, Dorea longicatena, Lactobacillus rogosae, Ruthenibacterium lactatiformans, Bacteroides nordii, Blautia hydrogenotrophica, Eggerthella lenta, Lactobacillus rogosae, Senegalimassilia anaerobia, Bacteroides ovatus, Blautia massiliensis, Eggerthella lenta, Longicatena caecimuris, Sutterella massiliensis, Bacteroides salyersiae, Blautia obeum, Eggerthella lenta, Megasphaera massiliensis, Sutterella wadsworthensis, Bacteroides stercorirosoris, Blautia obeum, Eggerthella lenta, Methanobrevibacter smithii, Sutterella wadsworthensis, Bacteroides stercoris, Blautia wexlerae, Eisenbergiella tayi, Methanobrevibacter smithii, Turicibacter sanguinis, Bacteroides stercoris, Blautia wexlerae, Eisenbergiella tayi, and Monoglobus including pectinolyticus

[0107] In a particular embodiment, the consortium includes multiple microorganisms designated as “Consortium XIV” (e.g., active microorganisms and supporting community microorganisms). In certain embodiments, Consortia excrementihominis, Alistipes finegoldii, Bacteroides vulgatus, Clostridium clostridioforme, Eubacterium ventriosum, Phascolarctobacterium faecium, Alistipes onderdonkii, Bacteroides vulgatus, Clostridium scindens, Eubacterium xylanophilum, Phascolarctobacterium faecium, Alistipes onderdonkii, Bacteroides xylanisolvens, Clostridium swellfunianum, Faecalibacterium prausnitzii, Phocea massiliensis, Alistipes putredinis, Bacteroides xylanisolvens, Clostridium symbiosum, Faecalibacterium prausnitzii, Phocea massiliensis, Alistipes putredinis, Barnesiella intestinihominis, Clostridium symbiosum, Fusicatenibacter saccharivorans, Porphyromonas asaccharolytica, Alistipes senegalensis, Bifidobacteriumadolescentis, Collinsella aerofaciens, Fusicatenibacter saccharivorans, Porphyromonas asaccharolytica, Alistipes senegalensis, Bifidobacterium adolescentis, Collinsella aerofaciens, Gordonibacter pamelaeae, Roseburia hominis, Alistipes shahii, Bifidobacterium bifidum, Coprococcus comes, Gordonibacter pamelaeae, Roseburia hominis, Alistipes shahii, Bifidobacterium bifidum, Coprococcus comes, Holdemanella biformis, Ruminococcus bromii, Alistipes timonensis, Bifidobacterium catenulatum, Coprococcus eutactus, Holdemanella biformis, Ruminococcus bromii, Anaerofustis stercorihominis, Bifidobacterium dentium, Coprococcus eutactus, Hungatella effluvii, Ruminococcus faecis, Anaerostipes hadrus, Bifidobacterium faecale, Desulfovibrio desulfuricans, Hungatella hathawayi, Ruminococcus faecis, Anaerostipes hadrus, Bifidobacterium longum, Desulfovibrio desulfuricans, Hungatella hathawayi, Ruthenibacterium lactatiformans, Anaerotruncus colihominis, Bifidobacterium longum, Dialister invisus, Hydrogenoanaerobacteriumsaccharovorans, Senegalimassilia anaerobia, Bacteroides caccae, Bifidobacterium pseudocatenulatum, Dialister succinatiphilus, Lachnoclostridium pacaense, Sutterella massiliensis, Bacteroides caccae, Bifidobacterium pseudocatenulatum, Dielma fastidiosa, Lachnoclostridium pacaense, Sutterella wadsworthensis, Bacteroides coprocola, Bifidobacterium pseudocatenulatum, Dorea formicigenerans, Lachnospira pectinoschiza, Sutterella wadsworthensis, Bacteroides faecis, Blautia faecis, Dorea formicigenerans, Lachnospira pectinoschiza, Turicibacter sanguinis, Bacteroides finegoldii, Blautia faecis, Dorea longicatena, Longicatena caecimuris, Bacteroides stercoris, Bacteroides fragilis, Blautia hydrogenotrophica, Dorea longicatena, Megasphaera massiliensis, Bacteroides stercoris, Bacteroides koreensis, Blautia luti, Eggerthella lenta, Methanobrevibacter smithii、Bacteroides thetaiotaomicron、Bacteroides koreensis、Blautia obeum、Eggerthella lenta、Methanobrevibacter smithii、Bacteroides thetaiotaomicron、Bacteroides kribbi、Blautiaobeum, Eggerthella lenta, Monoglobus pectinolyticus, Clostridium aldenense, Bacteroides kribbi, Blautia wexlerae, Eggerthella lenta, Monoglobus pectinolyticus, Clostridium aldenense, Bacteroides massiliensis, Blautia wexlerae, Eisenbergiella tayi, Neglecta timonensis, Clostridium bolteae, Bacteroides nordii, Butyricimonas faecihominis, Eisenbergiella tayi, Oxalobacter formigenes, Clostridium bolteae, Bacteroides oleiciplenus, Catabacter hongkongensis, Emergencia timonensis, Oxalobacter formigenes, Parabacteroides merdae, Bacteroides ovatus, Citrobacter freundii, Eubacterium eligens, Oxalobacter formigenes, Parabacteroides merdae, Bacteroides salyersiae, Clostridiaceae sp., Eubacterium eligens, Parabacteroides distasonis, Paraprevotella clara, Eubacterium rectale, Eubacterium rectale, Eubacterium hallii, Parabacteroides including distasones, and Eubacterium oxidoreducens.

[0108] In a particular embodiment, the consortium includes a plurality of microorganisms designated as "Consortium XV" (e.g., active microorganisms and supporting community microorganisms). In certain embodiments, Consortia timonensis, Alistipes onderdonkii, Bacteroides uniformis, Clostridiaceae sp.FBI00191, Eubacterium hallii, Neglecta timonensis, Alistipes onderdonkii, Bacteroides uniformis, Clostridiales sp.FBI00377, Eubacterium rectale, Oxalobacter formigenes, Alistipes putredinis, Bacteroides vulgatus, Clostridium aldenense, Eubacterium rectale, Oxalobacter formigenes, Alistipes putredinis, Bacteroides vulgatus, Clostridium aldenense, Eubacterium siraeum, Oxalobacter formigenes, Alistipes senegalensis, Bacteroides xylanisolvens, Clostridium bolteae, Eubacterium ventriosum, Parabacteroides distasonis, Alistipes shahii, Bacteroides xylanisolvens, Clostridium bolteae, Eubacterium xylanophilum, Parabacteroidesdistasonis, Alistipes shahii, Bacteroides xylanisolvens, Clostridium citroniae, Faecalibacterium prausnitzii, Parabacteroides merdae, Alistipes sp.FBI00180, Barnesiella intestinihominis, Clostridium citroniae, Faecalibacterium prausnitzii, Parabacteroides merdae, Alistipes sp.FBI00238, Bifidobacterium adolescentis, Clostridium clostridioforme, Fusicatenibacter saccharivorans, Paraprevotella clara, Alistipes timonensis, Bifidobacterium adolescentis, Clostridium fessum, Fusicatenibacter saccharivorans, Parasutterella excrementihominis, Anaerofustis stercorihominis, Bifidobacterium adolescentis, Clostridium scindens, Gordonibacter pamelaeae, Parasutterella excrementihominis, Anaerostipes hadrus, Bifidobacterium bifidum, Collinsella aerofaciens, Gordonibacter pamelaeae, Phascolarctobacterium faecium, Anaerostipes hadrus, Bifidobacterium catenulatum, Collinsella aerofaciens, Holdemanella biformis, Porphyromonas asaccharolytica, Anaerotruncus massiliensis, Bifidobacterium dentium, Coprococcus comes, Holdemanellabiformis, Porphyromonas asaccharolytica, Bacteroides caccae, Bifidobacterium longum, Coprococcus comes, Hungatella effluvii, Roseburia hominis, Bacteroides caccae, Bifidobacterium longum, Coprococcus eutactus, Hungatella effluvii, Roseburia hominis, Bacteroides coprocola, Bifidobacterium pseudocatenulatum, Dialister invisus, Hungatella effluvii, Ruminococcaceae sp.FBI00082 FBI00097, Bacteroides faecis, Bifidobacterium pseudocatenulatum, Dialister succinatiphilus, Lachnoclostridium pacaense, Ruminococcaceae sp.FBI00233, Bacteroides finegoldii, Bifidobacterium pseudocatenulatum, Dielma fastidiosa, Lachnoclostridium pacaense, Ruminococcus bromii, Bacteroides fragilis, Bilophila wadsworthia, Dorea formicigenerans, Lachnospiraceae sp.FBI00033, Ruminococcus bromii, Bacteroides kribbi / Bacteroides koreensis species cluster, Bilophila wadsworthia, Dorea formicigenerans, Lachnospiraceae sp.FBI00071, Ruminococcus faecis, Bacteroides kribbi / Bacteroides koreensis species cluster, Blautia faecis, Dorea longicatena, Lachnospiraceaesp.FBI00290, Ruminococcus faecis, Bacteroides massiliensis, Blautia faecis, Dorea longicatena, Lactobacillus rogosae, Ruthenibacterium lactatiformans, Bacteroides nordii, Blautia hydrogenotrophica, Eggerthella lenta, Lactobacillus rogosae, Senegalimassilia anaerobia, Bacteroides ovatus, Blautia massiliensis, Eggerthella lenta, Longicatena caecimuris, Sutterella massiliensis, Bacteroides salyersiae, Blautia obeum, Eggerthella lenta, Megasphaera massiliensis, Sutterella wadsworthensis, Bacteroides stercorirosoris, Blautia obeum, Eggerthella lenta, Methanobrevibacter smithii, Sutterella wadsworthensis, Bacteroides stercoris, Blautia wexlerae, Eisenbergiella tayi, Methanobrevibacter smithii, Turicibacter sanguinis, Bacteroides stercoris, Blautia wexlerae, Eisenbergiella tayi, and Monoglobus including pectinolyticus

[0109] In a particular embodiment, the consortium includes a group of microorganisms designated as “Consortium XVI” (e.g., active microorganisms and supporting community microorganisms). In certain embodiments, Consortia faecium, Alistipes finegoldii, Bacteroides vulgatus, Clostridium scindens, Eubacterium xylanophilum, Phascolarctobacterium faecium, Alistipes onderdonkii, Bacteroides vulgatus, Clostridium swellfunianum, Faecalibacterium prausnitzii, Phocea massiliensis, Alistipes onderdonkii, Bacteroides xylanisolvens, Clostridium symbiosum, Faecalibacterium prausnitzii, Phocea massiliensis, Alistipes putredinis, Bacteroides xylanisolvens, Clostridium symbiosum, Fusicatenibacter saccharivorans, Porphyromonas asaccharolytica, Alistipes putredinis, Barnesiella intestinihominis, Collinsella aerofaciens, Fusicatenibacter saccharivorans, Porphyromonas asaccharolytica, Alistipessenegalensis, Bifidobacterium adolescentis, Collinsella aerofaciens, Gordonibacter pamelaeae, Roseburia hominis, Alistipes senegalensis, Bifidobacterium adolescentis, Coprococcus comes, Gordonibacter pamelaeae, Roseburia hominis, Alistipes shahii, Bifidobacterium bifidum, Coprococcus comes, Holdemanella biformis, Ruminococcus bromii, Alistipes shahii, Bifidobacterium bifidum, Coprococcus eutactus, Holdemanella biformis, Ruminococcus bromii, Alistipes timonensis, Bifidobacterium catenulatum, Coprococcus eutactus, Hungatella effluvii, Ruminococcus faecis, Anaerofustis stercorihominis, Bifidobacterium dentium, Desulfovibrio desulfuricans, Hungatella hathawayi, Ruminococcus faecis, Anaerostipes hadrus, Bifidobacterium faecale, Desulfovibrio desulfuricans, Hungatella hathawayi, Ruthenibacterium lactatiformans, Anaerostipes hadrus, Bifidobacterium longum, Dialister invisus, Hydrogenoanaerobacterium saccharovorans, Senegalimassilia anaerobia, Anaerotruncus colihominis, Bifidobacterium longum, Dialistersuccinatiphilus, Lachnoclostridium pacaense, Sutterella massiliensis, Bacteroides caccae, Bifidobacterium pseudocatenulatum, Dielma fastidiosa, Lachnoclostridium pacaense, Sutterella wadsworthensis, Bacteroides caccae, Bifidobacterium pseudocatenulatum, Dorea formicigenerans, Lachnospira pectinoschiza, Sutterella wadsworthensis, Bacteroides coprocola, Bifidobacterium pseudocatenulatum, Dorea formicigenerans, Lachnospira pectinoschiza, Turicibacter sanguinis, Bacteroides faecis, Blautia faecis, Dorea longicatena, Longicatena caecimuris, Bacteroides stercoris, Bacteroides finegoldii, Blautia faecis, Dorea longicatena, Megasphaera massiliensis, Bacteroides stercoris, Bacteroides fragilis, Blautia hydrogenotrophica, Eggerthella lenta, Methanobrevibacter smithii, Bacteroides thetaiotaomicron, Bacteroides koreensis, Blautia luti、Eggerthella lenta、Methanobrevibacter smithii、Bacteroides thetaiotaomicron、Bacteroides koreensis、Blautia obeum、Eggerthella lenta、Monoglobus pectinilyticus、Clostridium aldenense、Bacteroideskribbi, Blautia obeum, Eggerthella lenta, Monoglobus pectinolyticus, Clostridium bolteae, Bacteroides kribbi, Blautia wexlerae, Eisenbergiella tayi, Neglecta timonensis, Clostridium bolteae, Bacteroides massiliensis, Blautia wexlerae, Eisenbergiella tayi, Oxalobacter formigenes, Clostridium citroniae, Bacteroides nordii, Butyricimonas faecihominis, Emergencia timonensis, Oxalobacter formigenes, Eubacterium oxidoreducens, Bacteroides oleiciplenus, Catabacter hongkongensis, Eubacterium eligens, Oxalobacter formigenes, Eubacterium rectale, Bacteroides ovatus, Clostridiaceae sp., Eubacterium eligens, Parabacteroides distasonis, Eubacterium rectale, Bacteroides salyersiae, Clostridium aldenense, Eubacterium hallii, Parabacteroides distasonis, Eubacterium ruminantium, Parasutterella excrementihominis, Paraprevotella clara, Parabacteroides including feces, and Parabacteroids feces.

[0110] In a particular embodiment, the consortium includes a plurality of microorganisms designated as “Consortium XVII” (e.g., active microorganisms and supporting community microorganisms). In certain embodiments, Consortia muciniphila, Bacteroides vulgatus, Clostridium citroniae, Fusicatenibacter saccharivorans, Ruminococcaceae sp.FBI00097, Alistipes onderdonkii, Bacteroides xylanisolvens, Clostridium clostridioforme, Gordonibacter pamelaeae, Ruminococcaceae sp.FBI0009, Alistipes onderdonkii, Bacteroides xylanisolvens, Clostridium fessum, Gordonibacter pamelaeae, Ruminococcaceae sp.FBI00233, Alistipes putredinis, Bacteroides xylanisolvens, Clostridium fessum, Holdemanella biformis, Ruminococcus bromii, Alistipes putredinis, Barnesiella intestinihominis, Clostridium scindens, Holdemanella biformis, Ruminococcus bromii, Alistipes senegalensis, Bifidobacterium adolescentis, Collinsellaaerofaciens, Hungatella effluvii, Ruminococcus faecis, Alistipes shahii, Bifidobacterium adolescentis, Collinsella aerofaciens, Hungatella effluvii, Ruminococcus faecis, Alistipes sp.FBI00180, Bifidobacterium adolescentis, Coprococcus comes, Hungatella effluvii, Ruthenibacterium lactatiformans, Alistipes sp.FBI00238, Bifidobacterium bifidum, Coprococcus comes, Lachnoclostridium pacaense, Senegalimassilia anaerobia, Alistipes timonensis, Bifidobacterium bifidum, Coprococcus eutactus, Lachnoclostridium pacaense, Sutterella massiliensis, Anaerofustis stercorihominis, Bifidobacterium catenulatum, Coprococcus eutactus, Lachnospiraceae sp.FBI00033, Sutterella wadsworthensis, Anaerostipes hadrus, Bifidobacterium dentium, Dialister invisus, Lachnospiraceae sp.FBI00071, Sutterella wadsworthensis, Anaerostipes hadrus, Bifidobacterium longum, Dialister succinatiphilus, Lachnospiraceae sp.FBI00290, Turicibacter sanguinis, Anaerotruncus massiliensis, Bifidobacterium longum, Dielma fastidiosa, Lactobacillus rogosae, Bacteroidesstercoris, Bacteroides caccae, Bifidobacterium pseudocatenulatum, Dorea formicigenerans, Lactobacillus rogosae, Bacteroides stercoris, Bacteroides caccae, Bifidobacterium pseudocatenulatum, Dorea formicigenerans, Lactonifactor longoviformis, Bacteroides thetaiotaomicron, Bacteroides coprocola, Bilophila wadsworthia, Dorea longicatena, Longicatena caecimuris, Bacteroides thetaiotaomicron, Bacteroides faecis, Bilophila wadsworthia, Dorea longicatena, Megasphaera massiliensis, Bacteroides uniformis, Bacteroides finegoldii, Blautia faecis, Eggerthella lenta, Monoglobus pectinolyticus, Citrobacter portucalensis, Bacteroides fragilis, Blautia faecis, Eggerthella lenta, Monoglobus pectinolyticus, Clostridiaceae sp.FBI00191, Bacteroides kribbi / Bacteroides koreensis species cluster, Blautia hydrogenotrophica、Eisenbergiella tayi、Oxalobacter formigenes、Clostridium aldenense、Bacteroides kribbi / Bacteroides koreensis species cluster、Blautia massiliensis、Eisenbergiella tayi、Oxalobacter formigenes、Clostridium aldenense、Bacteroideskribbi / Bacteroides koreensis species cluster, Blautia obeum, Emergencia timonensis, Oxalobacter formigenes, Clostridium bolteae, Bacteroides massiliensis, Blautia obeum, Eubacterium eligens, Parabacteroides distasonis, Eubacterium siraeum, Bacteroides nordii, Blautia wexlerae, Eubacterium eligens, Parabacteroides merdae, Eubacterium ventriosum, Bacteroides ovatus, Blautia wexlerae, Eubacterium hallii, Parabacteroides merdae, Eubacterium xylanophilum, Bacteroides salyersiae, Butyricimonas faecihominis, Eubacterium rectale, Paraprevotella clara, Faecalibacterium prausnitzii, Bacteroides stercorirosoris, Catabacter hongkongensis, Eubacterium rectale, Parasutterella excrementihominis, Faecalibacterium prausnitzii, Phascolarctobacterium faecium, Phascolarctobacterium faecium, Porphyromonas asaccharolytica, Parasutterella excrementihominis, and Porphyromonas including asaccharolytic

[0111] In a particular embodiment, the consortium includes a group of microorganisms designated as “Consortium XVIII” (e.g., active microorganisms and supporting community microorganisms). In certain embodiments, Consortia thetaiotaomicron, Bifidobacterium pseudocatenulatum, Collinsella aerofaciens, Faecalibacterium prausnitzii, Ruminococcus bromii, Bacteroides thetaiotaomicron, Bifidobacterium pseudocatenulatum, Desulfovibrio desulfuricans, Neglecta timonensis, Bacteroides vulgatus, Clostridium amygdalinum, Dorea Including Bifidobacterium longicatena, Oxalobacter formigenes, Bifidobacterium dentium, Clostridium citroniae, Eggerthella lenta, Oxalobacter formigenes, Bifidobacterium longum, Clostridium citroniae, Eggerthella lenta, and Oxalobacter formigenes.

[0112] In a particular embodiment, the consortium includes a group of microorganisms designated as “Consortium XIX” (e.g., active microorganisms and supporting community microorganisms). In certain embodiments, Consortia pectinilyticus, Akkermansia muciniphila, Bacteroides thetaiotaomicron, Butyricimonas faecihominis, Emergencia timonensis, Parabacteroides distasonis, Alistipes onderdonkii, Bacteroides thetaiotaomicron, Catabacter hongkongensis, Eubacterium eligens, Oxalobacter formigenes, Alistipes onderdonkii, Bacteroides uniformis, Clostridiaceae sp.FBI00191, Eubacterium eligens, Oxalobacter formigenes, Alistipes putredinis, Bacteroides uniformis, Clostridium aldenense, Eubacterium hallii, Oxalobacter formigenes, Alistipes putredinis, Bacteroides vulgatus, Clostridium aldenense, Eubacterium rectale, Parabacteroides distasonis, Alistipes senegalensis, Bacteroides vulgatus, Clostridium bolteae, Eubacterium rectale, Parabacteroides merdae, Alistipes shahii, Bacteroides xylanisolvens, Clostridium bolteae, Eubacterium siraeum, Parabacteroides merdae, Alistipes shahii, Bacteroides xylanisolvens, Clostridium citroniae, Eubacterium ventriosum, Paraprevotella clara, Alistipes sp.FBI00180, Bacteroides xylanisolvens, Clostridium citroniae, Eubacterium xylanophilum, Parasutterella excrementihominis, Alistipes sp.FBI00238, Barnesiella intestinihominis, Clostridium clostridioforme, Faecalibacterium prausnitzii, Parasutterella excrementihominis, Alistipes timonensis, Bifidobacterium adolescentis, Clostridium fessum, Fusicatenibacter saccharivorans, Phascolarctobacterium faecium, Anaerofustis stercorihominis, Bifidobacterium adolescentis, Clostridium scindens, Fusicatenibacter saccharivorans, Porphyromonas asaccharolytica, Anaerostipes hadrus, Bifidobacterium bifidum, Collinsella aerofaciens, Gordonibacter pamelaeae, Roseburia hominis, Anaerostipes hadrus, Bifidobacterium catenulatum, Collinsella aerofaciens, Gordonibacter pamelaeae, Roseburia hominis, Anaerotruncus massiliensis, Bifidobacterium dentium, Coprococcus comes, Holdemanella biformis, Ruminococcaceae sp. FBI00097, Bacteroides caccae, Bifidobacterium longum, Coprococcus comes、Hungatella effluvii、Ruminococcaceae sp.FBI00233, Bacteroides caccae, Bifidobacterium longum, Coprococcus eutactus, Hungatella effluvii, Ruminococcus bromii, Bacteroides coprocola, Bifidobacterium pseudocatenulatum, Dialister invisus, Hungatella hathewayi, Ruminococcus bromii, Bacteroides faecis, Bifidobacterium pseudocatenulatum, Dialister succinatiphilus, Lachnoclostridium pacaense, Ruminococcus faecis, Bacteroides finegoldii, Bifidobacterium pseudocatenulatum, Dielma fastidiosa, Lachnoclostridium pacaense, Ruminococcus faecis, Bacteroides fragilis, Bifidobacterium adolescentis, Dorea formicigenerans, Lachnospiraceae sp.FBI00033, Ruthenibacterium lactatiformans, Bacteroides kribbi, Bilophila wadsworthia, Dorea formicigenerans, Lachnospiraceae sp.FBI00071, Senegalimassilia anaerobia, Bacteroides kribbi, Bilophila wadsworthia、Dorea longicatena、Lachnospiraceae sp.FBI00290, Sutterella massiliensis, Bacteroides massiliensis, Blautia faecis, Dorea longicatena, Lactobacillus rogosae, Sutterella wadsworthensis, Bacteroides nordii, Blautia hydrogenotrophica, Eggerthella lenta, Lactobacillus rogosae, Sutterella wadsworthensis, Bacteroides ovatus, Blautia massiliensis, Eggerthella lenta, Longicatena caecimuris, Turicibacter sanguinis, Bacteroides salyersiae, Blautia obeum, Eggerthella lenta, Megasphaera massiliensis, Bacteroides stercorirosoris, Blautia obeum, Eggerthella lenta, and Methanobrevibacter smithii.

[0113] In a particular embodiment, the consortium includes microbiota included in consortium I. In a particular embodiment, the consortium includes microbiota included in consortium II. In a particular embodiment, the consortium includes microbiota included in consortium III. In a particular embodiment, the consortium includes microbiota included in consortium IV. In a particular embodiment, the consortium includes microbiota included in consortium V. In a particular embodiment, the consortium includes microbiota included in consortium VI. In a particular embodiment, the consortium includes microbiota included in consortium VII. In a particular embodiment, the consortium includes microbiota included in consortium VIII. In a particular embodiment, the consortium includes microbiota included in consortium IX. In a particular embodiment, the consortium includes microbiota included in consortium X. In a particular embodiment, the consortium includes microbiota included in consortium XI. In a particular embodiment, the consortium includes microbiota included in consortium XII. In a particular embodiment, the consortium includes microbiota included in consortium XIII. In a particular embodiment, the consortium includes microbiota included in consortium XIV. In a particular embodiment, the consortium includes microbiota included in consortium XV. In a particular embodiment, the consortium includes microbiota included in consortium XVI. In a particular embodiment, the consortium includes microbiota included in consortium XVII. In a particular embodiment, the consortium includes microbiota included in consortium XVIII. In a particular embodiment, the consortium includes microbiota included in consortium XIX.

[0114] In certain embodiments, the consortium includes microbiota that is at least 97% or at least 98% identical to those listed in Consortium I. In certain embodiments, the consortium includes microbiota that is at least 97% or at least 98% identical to those listed in Consortium II. In certain embodiments, the consortium includes microbiota that is at least 97% or at least 98% identical to those listed in Consortium III. In certain embodiments, the consortium includes microbiota that is at least 97% or at least 98% identical to those listed in Consortium IV. In certain embodiments, the consortium includes microbiota that is at least 97% or at least 98% identical to those listed in Consortium V. In certain embodiments, the consortium includes microbiota that is at least 97% or at least 98% identical to those listed in Consortium VI. In certain embodiments, the consortium includes microbiota that is at least 97% or at least 98% identical to those listed in Consortium VII. In certain embodiments, the consortium includes microbiota that is at least 97% or at least 98% identical to those listed in Consortium VIII. In certain embodiments, the consortium includes microbiota that is at least 97% or at least 98% identical to those listed in Consortium IX. In certain embodiments, the consortium includes microbiota that is at least 97% or at least 98% identical to those listed in Consortium X. In certain embodiments, the consortium includes microbiota that is at least 97% or at least 98% identical to those listed in Consortium XI. In certain embodiments, the consortium includes microbiota that is at least 97% or at least 98% identical to those listed in Consortium XII.In certain embodiments, the consortium includes microbiota that is at least 97% or at least 98% identical to those listed in Consortium XIII. In certain embodiments, the consortium includes microbiota that is at least 97% or at least 98% identical to those listed in Consortium XIV. In certain embodiments, the consortium includes microbiota that is at least 97% or at least 98% identical to those listed in Consortium XV. In certain embodiments, the consortium includes microbiota that is at least 97% or at least 98% identical to those listed in Consortium XVI. In certain embodiments, the consortium includes microbiota that is at least 97% or at least 98% identical to those listed in Consortium XVII. In certain embodiments, the consortium includes microbiota that is at least 97% or at least 98% identical to those listed in Consortium XVIII. In a particular embodiment, the consortium includes a microbiota that is at least 97% or at least 98% identical to those listed in Consortium XIX.

[0115] In a particular embodiment, the consortium includes at least 146, at least 147, or at least 148 microorganisms from Consortium I. In a particular embodiment, the consortium includes at least 72, at least 73, or at least 74 microorganisms from Consortium II. In a particular embodiment, the consortium includes at least 85, at least 86, or at least 87 microorganisms from Consortium III. In a particular embodiment, the consortium includes at least 84, at least 85, or at least 86 microorganisms from Consortium IV. In a particular embodiment, the consortium includes at least 153, at least 154, or at least 155 microorganisms from Consortium V. In a particular embodiment, the consortium includes at least 176, at least 177, or at least 178 microorganisms from Consortium VI. In a particular embodiment, the consortium includes at least 153, at least 154, or at least 155 microorganisms from Consortium VII. In a particular embodiment, the consortium includes at least 153, at least 154, or at least 155 microorganisms from Consortium VIII. In a particular embodiment, the consortium includes at least 148, at least 149, or at least 150 microorganisms from Consortium IX. In a particular embodiment, the consortium includes at least 149, at least 150, or at least 151 microorganisms from Consortium X. In a particular embodiment, the consortium includes at least 147, at least 148, or at least 149 microorganisms from Consortium XI. In a particular embodiment, the consortium includes at least 155, at least 156, or at least 157 microorganisms from Consortium XII. In a particular embodiment, the consortium includes at least 149 microorganisms, at least 150 microorganisms, or at least 151 microorganisms of Consortium XIII.In a particular embodiment, the consortium includes at least 155, at least 156, or at least 157 microorganisms from consortium XIV. In a particular embodiment, the consortium includes at least 149, at least 150, or at least 151 microorganisms from consortium XV. In a particular embodiment, the consortium includes at least 153, at least 154, or at least 155 microorganisms from consortium XVI. In a particular embodiment, the consortium includes at least 150, at least 151, or at least 152 microorganisms from consortium XVII. In a particular embodiment, the consortium includes at least 29, or at least 30 microorganisms from consortium XVIII. In a particular embodiment, the consortium includes at least 143, at least 144, or at least 145 microorganisms from consortium XIX.

[0116] In certain embodiments, the microbial consortium described herein includes microbial strains having a relative abundance of approximately 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, 5%, 1%, 0.1%, 0.01%, 0.001%, 0.0001%, 0.00001%, or 0.000001% of the entire microbial consortium. In certain embodiments, the relative abundance of a microbial strain is determined by metagenomic sequencing and calculated as the percentage of reads classified as a specific microbial strain, divided by the genome size. In certain embodiments, the relative abundance of microbial strains in this disclosure is determined by metagenomic shotgun sequencing.

[0117] In certain embodiments, the consortium includes the microbiota described in Table 1. In certain embodiments, the consortium includes microbiota that is at least 97% or at least 98% identical to those listed in Table 1. In certain embodiments, the consortium includes a plurality of microorganisms designated as "FB-001" (e.g., active microorganisms and supportive community microorganisms). In certain embodiments, the consortium includes a plurality of microorganisms listed in Table 1. In certain embodiments, the consortium includes at least 143 microorganisms, at least 144 microorganisms, or at least 145 microorganisms of FB-001. Table 1 is provided below. [Table 1-1] [Table 1-2] [Table 1-3] [Table 1-4]

[0118] In certain embodiments, the consortium is FB-003 as described in Table 2. In certain embodiments, the consortium comprises a microbiota that is at least 97% or at least 98% identical to those listed in Table 2. In certain embodiments, the consortium comprises a plurality of microorganisms designated as "FB-003" (e.g., active microorganisms and supporting community microorganisms). In certain embodiments, the consortium comprises a plurality of microorganisms listed in Table 2. In certain embodiments, the consortium comprises at least 140 microorganisms, at least 141 microorganisms, or at least 142 microorganisms of FB-001. Table 2 is provided below. [Table 2]

[0119] In a particular embodiment, the consortium includes a microbiota that is at least 97% or at least 98% identical to consortia I-XIX or any of those listed in Table 1 or 2.

[0120] In a particular embodiment, the consortium includes a plurality of microorganisms designated as "Consortium A" (e.g., active microorganisms and supporting community microorganisms). In certain embodiments, consortia A comprises the species Anaerofustis stercorihominis, Anaerostipes hadrus, Bacteroides kribbi, Bacteroides stercoris, Bacteroides thetaiotaomicron, Bacteroides vulgatus, Bacteroides xylanisolvens, Bifidobacterium adolescentis, Bifidobacterium catenulatum, Bifidobacterium dentinum, Bifidobacterium longum, Bifidobacterium pseudocatenulatum, Blautia obeum, Blautia wexlerae, Butyricimonas faecihominis, Clostridium bolteae, Clostridium citroniae, Clostridium scindens, Collinsella aerofaciens, Coprococcus comes, Dorea formicigenerans, Dorea longicatena, Eggerthella lenta, Emergencia timonensis, Eubacterium eligens, Eubacterium hallii, Eubacterium ventriosum, Hungatella hathewayi, Parabacteroides distasonis, Parabacteroides merdae, Roseburia hominis, Ruminococcus faecis, Alistipes onderdonkii, Alistipes senegalensis, Alistipes shahii, Alistipes timonensis, Anaerotruncus massiliensis, Bacteroides caccae, Bacteroides fragilis, Bacteroides ovatus, Bacteroidesuniformis, Bifidobacterium bifidum, Bilophila wadsworthia, Catabacter hongkongensis, Clostridium aldenense, Coprococcus eutactus, Dielma fastidiosa, Eubacterium rectale, Eubacterium siraeum, Faecalibacterium prausnitzii, Gordonibacter pamelaeae, Methanobrevibacter smithii, Monoglobus pectinolyticus, Paraprevotella clara, Ruminococcus bromii, Ruthenibacterium lactatiformans, Sutterella wadsworthensis, Akkermansia muciniphila, Bacteroides massiliensis, Dialister succinatiphilus, Eubacterium xylanophilum, Acidaminococcus intestine, Bacteroides faecis, Blautia faecis, Blautia hydrogenotrophica, Blautia massiliensis, Eisenbergiella tayi, Fusicatenibacter saccharivorans, Megasphaera massiliensis, Parasutterella excrementihominis, Phascolarctobacterium faecium, Ruminococcaceae sp.FBI00097, Ruminococcaceae sp.FBI00233, Sutterella massiliensis, Alistipes putredinis, Holdemanella biformis, Bifidobacterium dentium, Bacteroides finegoldii, Bacteroides nordii, Bacteroides salyersiae, Bacteroides stercorirosoris, Clostridiaceaesp.FBI00191 Clostridium clostridioforme Clostridium fessum Hungatella effluvia Lachnoclostridium pacaense Lachnospiraceae sp.FBI00033 Lachnospiraceae sp.FBI00071 Lachnospiraceae sp.FBI00290、Lactobacillus rogosae、Longicatena caecimuris、Barnesiella intestinhominis、Porphyromonas asaccharolytica、Acutalibacter timonensis、Turicibacter sanguinis、Alistipes sp.FBI00238、Bacteroids Coprocola 1. A strain of Dialister invisus.

[0121] In a particular embodiment, the consortium includes a plurality of microorganisms designated as "Consortium B" (e.g., active microorganisms and supporting community microorganisms). In certain embodiments, Consortia B comprises the species Anaerofustis stercorihominis, Anaerostipes hadrus, Bacteroides kribbi, Bacteroides stercoris, Bacteroides thetaiotaomicron, Bacteroides vulgatus, Bacteroides xylanisolvens, Bifidobacterium adolescentis, Bifidobacterium catenulatum, Bifidobacterium dentinum, Bifidobacterium longum, Bifidobacterium pseudocatenulatum, Blautia obeum, Blautia wexlerae, Butyricimonas faecihominis, Clostridium bolteae, Clostridium citroniae, Clostridium scindens, Collinsella aerofaciens, Coprococcus comes, Dorea formicigenerans, Dorea longicatena, Eggerthella lenta, Emergencia timonensis, Eubacterium eligens, Eubacterium hallii, Eubacterium ventriosum, Hungatella hathewayi, Parabacteroides distasonis, Parabacteroides merdae, Roseburia hominis, Ruminococcus faecis, Alistipes onderdonkii, Alistipes senegalensis, Alistipes shahii, Alistipes timonensis, Anaerotruncus massiliensis, Bacteroides caccae, Bacteroides fragilis, Bacteroides ovatus, Bacteroidesuniformis, Bifidobacterium bifidum, Bilophila wadsworthia, Catabacter hongkongensis, Clostridium aldenense, Coprococcus eutactus, Dielma fastidiosa, Eubacterium rectale, Eubacterium siraeum, Faecalibacterium prausnitzii, Gordonibacter pamelaeae, Methanobrevibacter smithii, Monoglobus pectinolyticus, Paraprevotella clara, Ruminococcus bromii, Ruthenibacterium lactatiformans, Sutterella wadsworthensis, Akkermansia muciniphila, Bacteroides massiliensis, Dialister succinatiphilus, Eubacterium xylanophilum, Acidaminococcus intestine, Bacteroides faecis, Blautia faecis, Blautia hydrogenotrophica, Blautia massiliensis, Eisenbergiella tayi, Fusicatenibacter saccharivorans, Megasphaera massiliensis, Parasutterella excrementihominis, Phascolarctobacterium faecium, Ruminococcaceae, Sutterella massiliensis, Alistipes putredinis, Holdemanella biformis, Bifidobacterium dentium, Bacteroides finegoldii, Bacteroides nordii, Bacteroides salyersiae, Bacteroides stercorirosoris, Clostridiaceae, Clostridium clostridioforme, ClostridiumIncludes one or more strains of each of the following: fessum, Hungatella effluvia, Lachnoclostridium pacaense, Lachnospiraceae, Lactobacillus rogosae, Longicatena caecimuris, Barnesiella intestinihominis, Porphyromonas asaccharolytica, Acutalibacter timonensis, Turicibacter sanguinis, Alistipes sp., Bacteroides coprocola, and Dialister invisus.

[0122] In a particular embodiment, Consortia A and Consortia B include strains having various functions as shown in Figure 26.

[0123] In certain embodiments, Consortia A and Consortia B further comprise one or more O. formigenes strains. In certain embodiments, Consortia A and Consortia B comprise strains having various functions as shown in Figure 26, and one or more O. formigenes strains.

[0124] In certain embodiments, the consortium includes microbial strains having a relative abundance of approximately 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, 5%, 1%, 0.1%, 0.01%, 0.001%, 0.0001%, 0.00001%, or 0.000001% of the entire microbial consortium. In certain embodiments, the relative abundance of a microbial strain is determined by metagenomic sequencing and calculated as the percentage of reads classified as a specific microbial strain, divided by the genome size. In certain embodiments, the relative abundance of microbial strains in this disclosure is determined by metagenomic shotgun sequencing.

[0125] Microbial activity and supporting communities The consortia described herein comprises multiple active microorganisms.

[0126] Furthermore, the consortium of this disclosure further includes a microbial support community that enhances one or more characteristics of a plurality of active microorganisms. For example, in a certain non-limiting embodiment, the microbial support community enhances the gastrointestinal engraftment of the plurality of active microorganisms. In another embodiment, the microbial support community enhances the biomass of the plurality of active microorganisms. In another embodiment, the microbial support community enhances the metabolism of a first metabolic substrate by the plurality of active microorganisms. In another embodiment, the microbial support community enhances the long-term stability of the plurality of active microorganisms.

[0127] The microbial support communities disclosed herein metabolize one or more metabolites produced by multiple active microorganisms, and one or more metabolites inhibit the metabolism of multiple active microorganisms. For example, in certain non-limiting embodiments, the microbial support community metabolizes formate produced by multiple active microorganisms, and the presence of formate inhibits the metabolism of oxalate by multiple active microorganisms. In certain embodiments, the microbial support community of this disclosure catalyzes the fermentation of polysaccharides to one or more of the group consisting of acetate, acetoin, 2-oxoglutarate, propionate, 1,3-propanediol, succinate, ethanol, lactate, butyrate, 2,3-butanediol, acetone, butanol, formate, H2, and CO2. In certain embodiments, the supporting community of microorganisms catalyzes the fermentation of amino acids to one or more of the group consisting of acetate, propionate, butanoate, butyrate, isobutyrate, 2-methylbutyrate, isovalerate, isocaproate, 3-phenylpropanoate, phloretinate, 3-(1H-indole-3-yl)propanoate, 5-aminopentanoate, H2, H2S, and CO2. In certain embodiments, the supporting community catalyzes the synthesis of one or more of the group consisting of methane from H2 and CO2, formate and methane from H2, acetate from H2 and CO2, formate and acetate from H2, acetate and sulfide from H2, CO2, and sulfate, propionate and CO2 from succinate, succinate from H2 and fumarate, succinate from formate and fumarate, and butyrate from lactate, acetate, H2, and CO2. In certain embodiments, a supporting community of the microorganisms of the Disclosure catalyzes the deconjugation of conjugated bile acids to produce primary bile acids, converting cholic acid (CA) to 7-oxocholic acid, 7-oxocholic acid to 7-betacholic acid (7-betaCA), chenodeoxycholic acid (CDCA) to 7-oxochenodeoxycholic acid, and / or 7-oxochenodeoxycholic acid to ursodeoxycholic acid (UDCA).

[0128] Consortium Design In certain embodiments, the microbial consortium disclosed herein is designed to meet one or more of the following criteria: (i) the ability to eliminate or reduce the level of a first metabolic substrate that causes or contributes to disease in animals. (ii) the ability to metabolize or transform one or more metabolites produced by the metabolism of the first metabolic substrate, (iii) The ability to metabolize one or more nutrients typically found in the human diet, (iv) The ability to fulfill unique and potentially beneficial biological functions in the gastrointestinal (GI) tract (e.g., bile salt hydrolase activity or butyrate production), (v) The ability to engraft in various biological niches and physical and metabolic compartments of animal GI tubes, (vi) Ability to increase biomass when planted on GI tubes, (vii) Ability to have long-term stability in the GI tube of animals, (viii) the ability to increase the flux of the first metabolite to the precursor in the biochemical pathway that converts the precursor to a metabolite that is not the first metabolite, (ix) Diversity of microbial species of constituent components across one or more taxonomic phyla, and (x) Spontaneous prevalence of microbial species of constituents in the GI tube of healthy adults.

[0129] In certain embodiments, the microbial consortium of the present disclosure is designed to comprise a plurality of active microorganisms capable of metabolizing a first metabolite that causes or contributes to disease in animals. In certain embodiments, the first metabolite may be selected from, but is not limited to, oxalates and bile acids (e.g., litcholic acid (LCA), deoxycholic acid (DCA)). In certain embodiments, the microbial consortium is designed to be capable of metabolizing the first metabolite over a range of pH found in the GI tube (e.g., pH 4–8). In certain embodiments, the microbial consortium is designed to be capable of metabolizing the first metabolite in the presence of varying concentrations of the first metabolite because they are present in different regions of the GI tube.

[0130] In certain embodiments, the consortium is FB-001 (for example, disclosed in Table 1) or its functional equivalent. In certain embodiments, FB-001 is defined by its function. In certain embodiments, FB-001 is defined by its function as described in Tables 3 and / or 4. In certain embodiments, FB-001 is defined by its function as described in Tables 3 and 4. In certain embodiments, FB-001 is defined by its function as described in Table 3 or 4. In certain embodiments, FB-001 is defined by its function as described in Tables 14, 15, and 16. In certain embodiments, FB-001 is defined by its function as described in one or more of Tables 14, 15, and 16. In certain embodiments, FB-001 is defined by its function as described in Tables 3, 4, 14, 15, and 16. In certain embodiments, FB-001 is defined by its functions as described in one or more of Tables 3, 4, 14, 15, and 16. In certain embodiments, methods for determining the functions of FB-001 are provided in Examples 5 and 6.

[0131] In certain embodiments, the consortium is FB-003 (for example, disclosed in Table 2) or its functional equivalent. In certain embodiments, FB-003 is defined by its function. In certain embodiments, FB-003 is defined by its function as described in Tables 3 and / or 4. In certain embodiments, FB-003 is defined by its function as described in Tables 3 and 4. In certain embodiments, FB-003 is defined by its function as described in Table 3 or 4. In certain embodiments, FB-003 is defined by its function as described in Tables 14, 15, and 16. In certain embodiments, FB-003 is defined by its function as described in one or more of Tables 14, 15, and 16. In certain embodiments, FB-003 is defined by its function as described in Tables 3, 4, 14, 15, and 16. In a particular embodiment, FB-003 is defined by its function as described in one or more of Tables 3, 4, 14, 15, and 16.

[0132] In certain embodiments, the consortium is consortium A or B, or a functional equivalent thereof. In certain embodiments, consortia A and B are defined by their function. In certain embodiments, FB-003 is a consortium of consortium A or consortium B. In certain embodiments, consortia A and B are defined by their function as described in Tables 3 and / or 4. In certain embodiments, consortia A and B are defined by their function as described in Tables 3 and 4. In certain embodiments, consortia A and B are defined by their function as described in Table 3 or 4. In certain embodiments, consortia A and B are defined by their function as described in Tables 14, 15, and 16. In certain embodiments, consortia A and B are defined by their function as described in one or more of Tables 14, 15, and 16. In certain embodiments, consortia A and B are defined by their function as described in Tables 3, 4, 14, 15, and 16. In a particular embodiment, consortia A and B are defined by their functions as described in one or more of Tables 3, 4, 14, 15, and 16.

[0133] Preparation method This disclosure also provides methods for preparing and / or producing the microbial consortia described herein. Figures 10–12 illustrate certain methods for preparing and producing the microbial consortia described herein.

[0134] In certain embodiments, the method includes obtaining donor stool and preparing a stool dilution. In certain embodiments, the stool dilution is plated onto an agar plate. In certain embodiments, the agar plate contains an anaerobic medium. In certain embodiments, the agar plate contains colonies. These colonies can be characterized and quality-analyzed. For example, without any limitations, 16s RNA and / or MALDI mass spectrometry can be performed. In certain embodiments, the characterized colonies can be further expanded in a broth culture. After growth and expansion, the microorganisms can be stored in vials for further use.

[0135] In certain embodiments, microorganisms can be further grown in a bioreactor containing cell culture medium. In certain embodiments, the cell culture medium may include: a) soytone, D-cellobiose, yeast extract, dextrose (glucose), maltose monohydrate, magnesium sulfate heptahydrate, calcium chloride dihydrate, potassium dihydrogen phosphate, dipotassium hydrogen phosphate, sodium chloride, sodium bicarbonate, volatile fatty acid solution, L-cysteine ​​HCl monohydrate, hemin solution, vitamin solution, or a combination thereof, b) Soytone, D-cellobiose, yeast extract, dextrose (glucose), maltose monohydrate, magnesium sulfate heptahydrate, calcium chloride dihydrate, potassium dihydrogen phosphate, dipotassium hydrogen phosphate, sodium chloride, ammonium sulfate, sodium bicarbonate, volatile fatty acid solution, L-cysteine ​​HCl monohydrate, hemin solution, vitamin solution, or a combination thereof.

[0136] In certain embodiments, the cell culture medium is YCFAC. In certain embodiments, the cell culture medium further comprises threonine.

[0137] In certain embodiments, microorganisms can be grown in a bioreactor under anaerobic conditions. In certain embodiments, microorganisms can be grown in a bioreactor in the presence of a gas overlay. In certain embodiments, microorganisms can be grown in a bioreactor in the absence of gas sparing.

[0138] In certain embodiments, the method includes expanding microorganisms in a mixed culture.

[0139] In a particular embodiment, this method a) Clostridium citroniae, Bacteroides salyersiae, Blautia obeum, Parabacteroides merdae, Parabacteroides distasonis, Anaerostipes hadrus, Lachnospiraceae sp.FBI00033, Eubacterium eligens, Bifidobacterium dentium, Blautia wexlerae, Fusicatenibacter saccharivorans, Bacteroides nordii, Dorea formicigenerans, Dorea longicatena, Bacteroides stercorirosoris, Bifidobacterium longum, Bacteroides kribbi, Lachnospiraceae sp.FBI00071, Bacteroides thetaiotaomicron, Clostridium clostridioforme, Clostridium scindens, Roseburia hominis, Clostridium fessum, Coprococcus comes, Blautia faecis, Hungatella hathewayi, Bacteroides stercoris, Collinsella aerofaciens, Hungatella effluvii, Bifidobacterium adolescentis, Bifidobacterium catenulatum, Lactobacillus rogosae, Bacteroides faecis, Bacteroides finegoldii、Clostridiaceae sp.FBI00191, Ruminococcus faecis, Lachnoclostridium pacaense, Clostridium bolteae, Longicatena caecimuris, Eggerthella lenta, Blautia massiliensis, Bacteroides xylanisolvens, Bacteroides vulgatus, Megasphaera massiliensis, Butyricimonas faecihominis, Eisenbergiella tayi, Acidaminococcus intestini, Emergencia timonensis, Bifidobacterium pseudocatenulatum, Eubacterium hallii, Anaerofustis stercorihominis, Eubacterium ventriosum, Blautia hydrogenotrophica, and Lachnospiraceae sp. FBI00290, or their functional equivalents, or. b) FBI00001, FBI00002, FBI00010, FBI00013, FBI00029, FBI00032, FBI00033, FBI00034, FBI00043, FBI00044, FBI00048, FBI00050, FBI00051, FBI00057, FBI000 59, FBI00060, FBI00070, FBI00071, FBI00076, FBI00079, FBI00087, FBI00093, FBI00102, FBI00109, FBI00117, FBI00120, FBI00125, FBI00127, FBI00128, FBI001 The method comprises expanding a microorganism in a first mixed culture or composition containing 45, FBI00162, FBI00174, FBI00184, FBI00190, FBI00191, FBI00194, FBI00198, FBI00199, FBI00200, FBI00201, FBI00205, FBI00206, FBI00211, FBI00220, FBI00221, FBI00236, FBI00245, FBI00248, FBI00251, FBI00254, FBI00267, FBI00278, FBI00288, and FBI00290, or their functional equivalents.

[0140] In a particular embodiment, this method a) Acutalibacter timonensis, Alistipes onderdonkii, Bacteroides uniformis, Eubacterium rectale, Alistipes timonensis, Bacteroides kribbi, Coprococcus eutactus, Bilophila wadsworthia, Bacteroides caccae, Alistipes shahii, Parasutterella excrementihominis, Paraprevotella clara, Sutterella wadsworthensis, Sutterella massiliensis, Porphyromonas asaccharolytica, Ruminococcus bromii, Monoglobus pectinolyticus, Ruminococcaceae sp.FBI00097, Gordonibacter pamelaeae, Bacteroides uniformis, Gordonibacter pamelaeae, Bacteroides fragilis, Phascolarctobacterium faecium, Monoglobus pectinolyticus, Clostridium aldenense, Ruthenibacterium lactatiformans, Bacteroides ovatus, Bifidobacterium bifidum, Anaerotruncus massiliensis, Clostridium aldenense, Sutterella wadsworthensis, Catabacter hongkongensis, Alistipes senegalensis、Ruminococcaceae sp.FBI00233, Alistipes shahii, Dielma fastidiosa, Eubacterium siraeum, Faecalibacterium prausnitzii, Turicibacter sanguinis, Eubacterium rectale, Bacteroides caccae, Methanobrevibacter smithii, Barnesiella intestinihominis, Alistipes onderdonkii, and Methanobrevibacter smithii, or their functional equivalents, or. b) FBI00004, FBI00012, FBI00015, FBI00018, FBI00019, FBI00021, FBI00038, FBI00040, FBI00046, FBI00061, FBI00066, FBI00075, FBI0 0077, FBI00080, FBI00081, FBI00085, FBI00092, FBI00097, FBI00099, FBI00112, FBI00132, FBI00137, FBI00140, FBI00149, FBI00151, FB This involves expanding a microorganism in a second mixed culture or composition containing I00176, FBI00189, FBI00197, FBI00208, FBI00212, FBI00224, FBI00226, FBI00229, FBI00233, FBI00235, FBI00237, FBI00243, FBI00244, FBI00258, FBI00260, FBI00263, FBI00270, FBI00273, FBI00277, and FBI00292, or their functional equivalents.

[0141] In a particular embodiment, this method a) Bifidobacterium adolescentis, Bifidobacterium longum, Bifidobacterium pseudocatenulatum, Bacteroides thetaiotaomicron, Coprococcus comes, Fusicatenibacter saccharivorans, Eggerthella lenta, Eubacterium eligens, Bacteroides xylanisolvens, Lactobacillus rogosae, Clostridium citoniae, Collinsella aerofaciens, Blautia obeum, Eggerthella lenta, Blautia wexlerae, Lachnoclostridium pacaense, Bacteroides vulgatus, Parabacteroides merdae, Dorea formicigenerans, Ruminococcus faecis, Roseburia hominis, Anaerostipes hadrus, Bifidobacterium adolescentis, Bifidobacterium pseudocatenulatum, Clostridium bolteae, Eisenbergiella tayi, Dorea longicatena, Eggerthella lenta, Bacteroides stercoris, Hungatella hathawayi, and Bacteroides xylanisolvens, or their functional equivalents, or b) FBI00009, FBI00011, FBI00016, FBI00020, FBI00025, FBI00027, FBI00030, FBI00047, FBI00052, FBI00053, FBI00056, FBI00062, FBI00078, FBI00096, FBI00104, FBI00110, FBI00111, FBI00113, FB This involves expanding microorganisms in a third mixed culture or composition containing I00115, FBI00116, FBI00123, FBI00124, FBI00126, FBI00135, FBI00147, FBI00159, FBI00167, FBI00170, FBI00232, FBI00255, and FBI00271, or their functional equivalents.

[0142] In a particular embodiment, this method a)Alistipes putredinis, Dialister succinatiphilus, Akkermansia muciniphila, Ruminococcus bromii, Dialister invisus, Bacteroides massiliensis, Bilophila wadsworthia, Holdemanella biformis, Parasutterella excrementihominis, Alistipes sp.FBI00180, Bacteroides coprocola, Alistipes sp.FBI00238, Alistipes putredinis, Eubacterium xylanophilum, and Senegalimassilia anaerobia, or their functional equivalents, or b) comprising expanding a fourth mixed culture or composition containing FBI00022, FBI00049, FBI00068, FBI00069, FBI00152, FBI00165, FBI00171, FBI00175, FBI00177, FBI00180, FBI00182, FBI00238, FBI00269, FBI00274, and FBI00281, or their functional equivalents.

[0143] In certain embodiments, the method includes expanding each of the three O. formigenes microorganisms of FB-001 in a single culture. In certain embodiments, the method includes expanding a microorganism in a first single culture (or fifth composition) containing a) a first O. formigenes strain, or b) FBI00067 or its functional equivalent. In certain embodiments, the method includes expanding a microorganism in a second single culture (or sixth composition) containing a) a second O. formigenes strain, or b) FBI00133 or its functional equivalent. In certain embodiments, the method includes expanding a microorganism in a third single culture (or seventh composition) containing a) a third O. formigenes strain, or b) FBI00289 or its functional equivalent.

[0144] In certain embodiments, the method includes lyophilized cultures and compositions described herein. In certain embodiments, the cultures and compositions include a lyoprotectant. In certain embodiments, the lyoprotectant includes maltodextrin. In certain embodiments, the lyoprotectant includes inulin. In certain embodiments, the lyoprotectant includes maltodextrin and inulin. In certain embodiments, maltodextrin is present at a concentration of about 8%. In certain embodiments, inulin is present at a concentration of about 0.5%.

[0145] In certain embodiments, the method involves blending and / or mixing the lyophilized cultures and compositions outlined above. Additional information regarding the strains for each composition can be found in Table 1 or Table 2.

[0146] In certain embodiments, DS1, as described in Table 1, is prepared using the method shown in Figure 17. In certain embodiments, DS2, as described in Table 1, is prepared using the method shown in Figure 18. In certain embodiments, DS3, as described in Table 1, is prepared using the method shown in Figure 19. In certain embodiments, DS4, as described in Table 1, is prepared using the method shown in Figure 20. In certain embodiments, for FB-001, DS5-DS7 (i.e., the preparation of O. formigenes) as described in Table 21 are prepared using the method shown in Figure 16. In certain embodiments, the preparation of FB-001 and FB-003 involves separate preparations of each of DS1-DS4 (and DS5-DS7 for FB-001) as shown in Figures 16-20, followed by blending to achieve a uniform distribution of each of the DS. In a particular embodiment, a blend of DS1-DS4 (for FB-003) and DS1-DS7 (for FB-003) is encapsulated for oral administration.

[0147] Pharmaceutical composition This disclosure also provides pharmaceutical compositions containing an effective amount of the microbial consortium described herein. The compositions can be formulated for use in various delivery systems. For appropriate formulation, one or more physiologically acceptable buffers or carriers may also be included in the compositions. Suitable formulations for use in this disclosure can be found in Remington's Pharmaceutical Sciences, Mack Publishing Company, Philadelphia, Pa., 17th ed., 1985. For a brief review of methods for drug delivery, see, for example, Langer (Science 249:1527-1533, 1990).

[0148] In certain embodiments, the pharmaceutical compositions disclosed herein include Consortia I. In certain embodiments, the pharmaceutical compositions disclosed herein include Consortia II. In certain embodiments, the pharmaceutical compositions disclosed herein include Consortia I. In certain embodiments, the pharmaceutical compositions disclosed herein include Consortia III. In certain embodiments, the pharmaceutical compositions disclosed herein include Consortia IV. In certain embodiments, the pharmaceutical compositions disclosed herein include Consortia V. In certain embodiments, the pharmaceutical compositions disclosed herein include Consortia VI. In certain embodiments, the pharmaceutical compositions disclosed herein include Consortia VII. In certain embodiments, the pharmaceutical compositions disclosed herein include Consortia VIII. In certain embodiments, the pharmaceutical compositions disclosed herein include Consortia IX. In certain embodiments, the pharmaceutical compositions disclosed herein include Consortia X. In certain embodiments, the pharmaceutical compositions disclosed herein include Consortia XI. In certain embodiments, the pharmaceutical compositions disclosed herein include Consortia XII. In certain embodiments, the pharmaceutical compositions disclosed herein include Consortia XIII. In certain embodiments, the pharmaceutical compositions disclosed herein include Consortia XIV. In certain embodiments, the pharmaceutical compositions disclosed herein include Consortia XV. In certain embodiments, the pharmaceutical compositions disclosed herein include Consortia XVI. In certain embodiments, the pharmaceutical compositions disclosed herein include Consortia XVII. In certain embodiments, the pharmaceutical compositions disclosed herein include Consortia XVIII. In certain embodiments, the pharmaceutical compositions disclosed herein include Consortia XIX. In certain embodiments, the pharmaceutical compositions disclosed herein include Consortia A. In certain embodiments, the pharmaceutical compositions disclosed herein include Consortia B.

[0149] In certain embodiments, the pharmaceutical composition disclosed herein includes FB-001. In certain embodiments, the pharmaceutical composition disclosed herein includes FB-003.

[0150] In certain embodiments, the pharmaceutical compositions disclosed herein contain at least about 10 of each strain (e.g., each strain of FB-001 or FB-003), at least about 10 2 , at least about 10 3 , at least about 10 4 , at least about 10 5 , at least about 10 6 , at least about 10 7 , at least about 10 8 , at least about 10 9 , at least about 10 10 , at least about 10 11 , at least about 10 12 , or at least about 10 13 This includes the amount of microorganisms. In certain embodiments, the pharmaceutical compositions disclosed herein contain about 10 to about 10 for each strain (e.g., each strain of FB-001 or FB-003). 13 , about 10 2 ~about 10 13 , about 10 3 ~about 10 13 , about 10 4 ~about 10 13 , about 10 5 ~about 10 13 , about 10 6 ~about 10 13 , about 10 7 ~about 10 13 , about 10 8 ~about 10 13 , about 10 9 ~about 10 13 , about 10 10 ~about 10 13 , about 10 11 ~about 10 13 , about 10 12 ~about 10 13 , about 10 2 ~about 10 12 , about 10 2 ~about 10 11 , about 10 2~about 10 10 、about 10 2 ~about 10 9 、about 10 2 ~about 10 8 、about 10 2 ~about 10 7 、about 10 2 ~about 10 6 、about 10 2 ~about 10 5 、about 10 2 ~about 10 4 、about 10<x 2 ~about 10 3 、about 10 2 ~about 10 9 、about 10 3 ~about 10 9 、about 10 4 ~about 10 9 、about 10 5 ~about 10 9 、about 10 6 ~about 10 9 、about 10 7 ~about 10 9 、about 10 8 ~about 10 9 、about 10 2 ~about 10 6 、about 10 3 ~about 10 6 、about 10 4 ~about 10 6 、or about 10 5 ~about 10 6 of microorganisms. In certain embodiments, each strain can be present in different amounts. For example, without any limitation, a pharmaceutical composition comprising a first strain, a second strain, and a third strain can comprise 10 microorganisms of the first strain, 10 7 of microorganisms of the second strain, 10 3 of microorganisms of the third strain.

[0151] In certain embodiments, the pharmaceutical compositions disclosed herein comprise at least about 10, at least about 10 2 、at least about 10 3 、at least about 10 4 、at least about 10 5 、at least about 10 6, at least about 10 7 , at least about 10 8 , at least about 10 9 , at least about 10 10 , at least about 10 11 , at least about 10 12 , or at least about 10 13 This includes an amount of CFU. In certain embodiments, the pharmaceutical compositions disclosed herein contain about 10 to about 10 for each strain (e.g., each strain of FB-001 or FB-003). 13 , about 10 2 ~about 10 13 , about 10 3 ~about 10 13 , about 10 4 ~about 10 13 , about 10 5 ~about 10 13 , about 10 6 ~about 10 13 , about 10 7 ~about 10 13 , about 10 8 ~about 10 13 , about 10 9 ~about 10 13 , about 10 10 ~about 10 13 , about 10 11 ~about 10 13 , about 10 12 ~about 10 13 , about 10 2 ~about 10 12 , about 10 2 ~about 10 11 , about 10 2 ~about 10 10 , about 10 2 ~about 10 9 , about 10 2 ~about 10 8 , about 10 2 ~about 10 7 , about 10 2 ~about 10 6 , about 10 2 ~about 10 5 , about 10 2 ~about 10 4 , about 10 2 ~about 10 3 , about 10 2 ~about 10 9 , about 103 ~about 10 9 , about 10 4 ~about 10 9 , about 10 5 ~about 10 9 , about 10 6 ~about 10 9 , about 10 7 ~about 10 9 , about 10 8 ~about 10 9 , about 10 2 ~about 10 6 , about 10 3 ~about 10 6 , about 10 4 ~about 10 6 , or about 10 5 ~about 10 6 Contains CFUs of 10 of the first strain and 10 of the second strain. In certain embodiments, each strain may be present in different amounts. For example, without any limitations, a pharmaceutical composition comprising a first strain, a second strain, and a third strain may contain 10 CFUs of the first strain and 10 CFUs of the second strain. 7 CFU, 3rd share 10 3 It can include CFU.

[0152] In certain embodiments, the pharmaceutical compositions disclosed herein include at least about 10 -1 , at least about 10 -2 , at least about 10 -3 , at least about 10 -4 , at least about 10 -5 , at least about 10 -6 , at least about 10 -7 , at least about 10 -8 , at least about 10 -9 , at least about 10 -10 , at least about 10 -11 , or at least about 10 -12 , or at least about 10 13 This includes the amount of each strain (e.g., each strain FB-001 or FB-003) in grams. In certain embodiments, each strain may be present in different amounts. For example, without any limitations, a pharmaceutical composition comprising a first strain, a second strain, and a third strain may be 10 -4 Gram's first strain, 10 -3Gram's second strain, 10 -6 It may include a third strain of Gram.

[0153] In certain embodiments, the pharmaceutical compositions disclosed herein include at least about 10, at least about 10 2 , at least about 10 3 , at least about 10 4 , at least about 10 5 , at least about 10 6 , at least about 10 7 , at least about 10 8 , at least about 10 9 , at least about 10 10 , at least about 10 11 , at least about 10 12 , or at least about 10 13 The total amount of microorganisms (for example, the total amount of microorganisms FB-001 or the total amount of microorganisms FB-003) is included. In certain embodiments, the pharmaceutical compositions disclosed herein are about 10 to about 10 13 , about 10 2 ~about 10 13 , about 10 3 ~about 10 13 , about 10 4 ~about 10 13 , about 10 5 ~about 10 13 , about 10 6 ~about 10 13 , about 10 7 ~about 10 13 , about 10 8 ~about 10 13 , about 10 9 ~about 10 13 , about 10 10 ~about 10 13 , about 10 11 ~about 10 13 , about 10 12 ~about 10 13 , about 10 2 ~about 10 12 , about 10 2 ~about 10 11 , about 10 2 ~about 10 10 , about 10 2 ~about 10 9 , about 102 ~about 10 8 , about 10 2 ~about 10 7 , about 10 2 ~about 10 6 , about 10 2 ~about 10 5 , about 10 2 ~about 10 4 , about 10 2 ~about 10 3 , about 10 2 ~about 10 9 , about 10 3 ~about 10 9 , about 10 4 ~about 10 9 , about 10 5 ~about 10 9 , about 10 6 ~about 10 9 , about 10 7 ~about 10 9 , about 10 8 ~about 10 9 , about 10 2 ~about 10 6 , about 10 3 ~about 10 6 , about 10 4 ~about 10 6 , or about 10 5 ~about 10 6 This includes the total amount of microorganisms.

[0154] In certain embodiments, the pharmaceutical compositions disclosed herein include at least about 10, at least about 10 2 , at least about 10 3 , at least about 10 4 , at least about 10 5 , at least about 10 6 , at least about 10 7 , at least about 10 8 , at least about 10 9 , at least about 10 10 , at least about 10 11 , at least about 10 12 , or at least about 10 13This includes the total amount of CFUs (for example, the total CFUs of FB-001 or the total CFUs of FB-003). In certain embodiments, the pharmaceutical compositions disclosed herein are about 10 to about 10 13 , about 10 2 ~about 10 13 , about 10 3 ~about 10 13 , about 10 4 ~about 10 13 , about 10 5 ~about 10 13 , about 10 6 ~about 10 13 , about 10 7 ~about 10 13 , about 10 8 ~about 10 13 , about 10 9 ~about 10 13 , about 10 10 ~about 10 13 , about 10 11 ~about 10 13 , about 10 12 ~about 10 13 , about 10 2 ~about 10 12 , about 10 2 ~about 10 11 , about 10 2 ~about 10 10 , about 10 2 ~about 10 9 , about 10 2 ~about 10 8 , about 10 2 ~about 10 7 , about 10 2 ~about 10 6 , about 10 2 ~about 10 5 , about 10 2 ~about 10 4 , about 10 2 ~about 10 3 , about 10 2 ~about 10 9 , about 10 3 ~about 10 9 , about 10 4 ~about 10 9 , about 10 5 ~about 10 9 , about 10 6 ~about 10 9 , about 10 7 ~about 109 , about 10 8 ~about 10 9 , about 10 2 ~about 10 6 , about 10 3 ~about 10 6 , about 10 4 ~about 10 6 , or about 10 5 ~about 10 6 This includes the total amount of CFU. In certain embodiments, the pharmaceutical compositions disclosed herein are about 10 5 ~about 10 13 , about 10 6 ~about 10 13 , about 10 7 ~about 10 13 , about 10 8 ~about 10 13 , about 10 9 ~about 10 13 , about 10 10 ~about 10 13 , about 10 11 ~about 10 13 , about 10 12 ~about 10 13 , about 10 5 ~about 10 12 , about 10 6 ~about 10 12 , about 10 7 ~about 10 12 , about 10 8 ~about 10 12 , about 10 9 ~about 10 12 , about 10 10 ~about 10 12 , about 10 11 ~about 10 12 , about 10 5 ~about 10 11 , about 10 6 ~about 10 11 , about 10 7 ~about 10 11 , about 10 8 ~about 10 11 , about 10 9 ~about 10 11 , about 10 10 ~about 10 11 , about 10 5 ~about 10 10 , about 10 6 ~about 1010 , about 10 7 ~about 10 10 , about 10 8 ~about 10 10 , about 10 9 ~about 10 10 , about 10 5 ~about 10 9 , about 10 6 ~about 10 9 , about 10 7 ~about 10 9 , about 10 8 ~about 10 9 , about 5×10 9 ~Approx. 5×10 10 , about 5×10 9 ~Approx. 5×10 11 , about 5×10 9 ~Approx. 5×10 12 , about 5×10 10 ~Approx. 5×10 12 , about 5×10 11 ~Approx. 5×10 12 , or approximately 5 x 10 10 ~Approx. 5×10 11 Contains 5 x 10 viable cells. In certain embodiments, the pharmaceutical compositions disclosed herein contain about 5 x 10 9 ~Approx. 5×10 12 Contains 5 x 10 viable cells. In certain embodiments, the pharmaceutical compositions disclosed herein contain about 5 x 10 9 ~Approx. 5×10 10 Contains 5 x 10 viable cells. In certain embodiments, the pharmaceutical compositions disclosed herein contain about 5 x 10 10 ~Approx. 5×10 11 Contains 5 x 10 viable cells. In certain embodiments, the pharmaceutical compositions disclosed herein contain about 5 x 10 11 ~Approx. 5×10 12 Contains individual surviving cells.

[0155] In certain embodiments, the pharmaceutical compositions disclosed herein may be up to approximately 10 5 , up to about 10 6 , up to about 10 7 , up to about 10 8 , up to about 10 9 , up to about 10 10 , up to about 10 11, up to about 10 12 , or up to approximately 10 13 Contains 10 living cells. In certain embodiments, the pharmaceutical compositions disclosed herein contain up to about 10 11 Contains 10 living cells. In certain embodiments, the pharmaceutical compositions disclosed herein contain up to about 10 12 Contains individual surviving cells.

[0156] In certain embodiments, the pharmaceutical compositions disclosed herein may exist in the form of a food product containing the consortium disclosed herein (e.g., FB-001 or FB-003). As used herein, the term “food product” refers to a composition intended for ingestion by an individual (e.g., a human subject). Non-limiting examples of food products encompassed herein include juices, soft drinks, tea drinks, beverage preparations, jelly drinks, functional beverages, milk, dairy drinks, ice cream, cheese, yogurt, biscuits, cookies, candy, chewing gum, gummies, jelly, cream caramel, frozen desserts, and instant foods. Furthermore, these examples also include health foods and beverages prepared in the form of powders, granules, tablets, capsules, liquids, pastes, and jellies. In certain embodiments, the food product containing the consortium disclosed herein further includes a prebiotic. As used herein, the term “prebiotic” refers to a substance that can promote the growth of the microorganisms in the consortium. Non-exclusive examples of prebiotics include fructose, galactose, mannose, soy, inulin, dietary fiber, or combinations thereof.

[0157] In certain embodiments, the microbial cells of this disclosure are collected by microfiltration and centrifugation. In certain embodiments, microfiltration is carried out in a membrane containing a non-reactive polymer. For example, in certain non-limiting embodiments, the membrane contains polyvinylidene fluoride, polysulfone, or nitrocellulose. In certain embodiments, the membrane for microfiltration has a pore size of about 0.2 μm to about 0.45 μm. In a particular embodiment, the cells are approximately 1000g to 30000g, 5000g to 30000g, 10000g to 30000g, 15000g to 30000g, 20000g to 30000g, 25000g to 30000g, 1000g to 25000g, 5000g to 25000g, 10000g to 25000g, 15000g to 25000g, and 200 Centrifugation is performed using forces of approximately 0g to 25000g, approximately 1000g to 20000g, approximately 5000g to 20000g, approximately 10000g to 20000g, approximately 15000g to 20000g, approximately 1000g to 15000g, approximately 5000g to 15000g, approximately 10000g to 15000g, approximately 1000g to 10000g, approximately 5000g to 10000g, or approximately 1000g to 5000g.

[0158] In a particular embodiment, the cells are approximately 1 × 10⁶ per milliliter. 6 CFU ~ approximately 1 x 10⁶ per milliliter 12 CFU of approximately 1 x 10⁶ per milliliter 7 CFU ~ approximately 1 x 10⁶ per milliliter 12 CFU of approximately 1 x 10⁶ per milliliter 8 CFU ~ approximately 1 x 10⁶ per milliliter 12 CFU of approximately 1 x 10⁶ per milliliter 9 CFU ~ approximately 1 x 10⁶ per milliliter 12 CFU of approximately 1 x 10⁶ per milliliter 10 CFU ~ approximately 1 x 10⁶ per milliliter 12 CFU of approximately 1 x 10⁶ per milliliter 11 CFU ~ approximately 1 x 10⁶ per milliliter 12CFU of approximately 1 x 10⁶ per milliliter 6 CFU ~ approximately 1 x 10⁶ per milliliter 11 CFU of approximately 1 x 10⁶ per milliliter 7 CFU ~ approximately 1 x 10⁶ per milliliter 11 CFU of approximately 1 x 10⁶ per milliliter 8 CFU ~ approximately 1 x 10⁶ per milliliter 11 CFU of approximately 1 x 10⁶ per milliliter 9 CFU ~ approximately 1 x 10⁶ per milliliter 11 CFU of approximately 1 x 10⁶ per milliliter 10 CFU ~ approximately 1 x 10⁶ per milliliter 11 CFU of approximately 1 x 10⁶ per milliliter 6 CFU ~ approximately 1 x 10⁶ per milliliter 10 CFU of approximately 1 x 10⁶ per milliliter 7 CFU ~ approximately 1 x 10⁶ per milliliter 10 CFU of approximately 1 x 10⁶ per milliliter 8 CFU ~ approximately 1 x 10⁶ per milliliter 10 CFU of approximately 1 x 10⁶ per milliliter 9 CFU ~ approximately 1 x 10⁶ per milliliter 10 CFU of approximately 1 x 10⁶ per milliliter 6 CFU ~ approximately 1 x 10⁶ per milliliter 9 CFU of approximately 1 x 10⁶ per milliliter 7 CFU ~ approximately 1 x 10⁶ per milliliter 9 CFU of approximately 1 x 10⁶ per milliliter 8 CFU ~ approximately 1 x 10⁶ per milliliter 9 CFU of approximately 1 x 10⁶ per milliliter 6 CFU ~ approximately 1 x 10⁶ per milliliter 8 CFU of approximately 1 x 10⁶ per milliliter 7 CFU ~ approximately 1 x 10⁶ per milliliter 8 CFU of 10¹⁶ CFU, or approximately 1 × 10¹⁶ CFU per milliliter. 6 CFU ~ approximately 1 x 10⁶ per milliliter 7It is concentrated into CFU.

[0159] In certain embodiments, the microbial cells of the Disclosure are frozen. In certain embodiments, the microbial cells of the Disclosure are mixed with one or more cryoprotective agents (CPAs) before freezing. In certain embodiments, the cell-to-CPA ratio is approximately 25:1, 10:1, 5:1, 4:1, 3:1, 2:1, 1:1, 1:2, 1:3, 1:4, 1:5, 1:10, or 1:25. In certain embodiments, the CPA comprises one or more of glycerol, maltodextrin, sucrose, inulin, trehalose, and alginate. In certain embodiments, the CPA further comprises one or more antioxidants. In certain embodiments, the antioxidants are selected from the list of cysteine, ascorbic acid, and riboflavin.

[0160] In certain embodiments, the microbial cells of the Disclosure are freeze-dried. In certain embodiments, the freeze-dried cells are used to prepare the oral doses of the Disclosure. In certain embodiments, primary drying is carried out at approximately below -20°C. In certain embodiments, primary drying is followed by secondary drying at a higher temperature, for example, above 0°C, above 5°C, or above 10°C.

[0161] A drug product that is functionally equivalent to and identical to FB-001. The strains included in FB-001 are described herein by their 16S RNA sequences and functional characteristics. Based on this, a consortium of equivalent strains to FB-001 can be generated by screening multiple identical strains to find equivalent strains with equivalent functionality to those containing FB-001. Thus, identical strains may theoretically have different functionalities, and strains can be screened using 16S RNA and Biolog as described herein to identify functionally identical and equivalent strains from any fecal collection using the collection methods described herein.

[0162] It is important to note that FB-001 is explicitly designed to have multiple identical strains in a consortium. The reason for this is to have redundancy to ensure function; however, such redundancy is not required for equivalent function as long as one of the redundant strains is included in the final drug product in a sufficient number of viable cells to achieve in vivo function in the subject. Therefore, a consortium equivalent to or identical to FB-001 may contain all redundancies (see Table 1), or alternatively, may contain no redundancy per strain, or less redundancy, as long as the included strains achieve in vivo function in the subject.

[0163] An alternative approach to creating a functionally equivalent consortium to FB-001 is that a consortium of supportive microorganisms from a healthy fecal donor can be recreated and supplemented with one or more O. formigenes strains. In certain embodiments, the supportive microorganisms are supplemented with two or more O. formigenes strains, or specifically three O. formigenes strains. The supportive microorganisms may consist of any number of microorganisms, from 10 to 200, insofar as such a supportive community supports and promotes the growth, health, and establishment of the O. formigenes strain(s) in the subject. FB-001 was designed to have 148 microorganisms to mimic a complete and healthy microbiome. Therefore, an equivalent consortium may consist of approximately 148 microorganisms, including the O. formigenes strain(s). However, it is interesting to note that older subjects often have smaller microbiomes; therefore, a functionally equivalent consortium to FB-001 may also have far fewer microorganisms (e.g., 30-40, 40-50, 50-60, 60-70, 70-80, 8-90, 90-100, 100-110, 110-120, 120-130, 130-140, or 140-150 microorganisms, including O. formigenes strains).

[0164] A drug product that is functionally equivalent to and identical to FB-003. The strains included in FB-003 are described herein by their 16S RNA sequences and functional characteristics. Based on this, a consortium of equivalent strains to FB-003 can be generated by screening multiple identical strains to find equivalent strains with equivalent functionality to those containing FB-003. Thus, identical strains may theoretically have different functionalities, and strains can be screened using 16S RNA and Biolog as described herein to identify functionally identical and equivalent strains from any fecal collection using the collection methods described herein.

[0165] It is important to note that FB-003 is explicitly designed to have multiple identical strains in a consortium. The reason for this is to have redundancy to ensure function; however, such redundancy is not required for equivalent function as long as one of the redundant strains is included in the final drug product in a sufficient number of viable cells to achieve in vivo function in the subject. Therefore, a consortium equivalent to or identical to FB-003 may contain all redundancies (see Table 2), or alternatively, may contain no redundancy per strain, or less redundancy, as long as the included strains achieve in vivo function in the subject.

[0166] therapeutic use This disclosure provides a consortium that can be implanted in one or more niches of the gastrointestinal tract, where the consortium can treat dysbiosis that causes or contributes to disease in an animal. In certain embodiments, the animal is a human.

[0167] In certain embodiments of this disclosure, when administered to animals, the animals are pre-treated with one or more antibiotics prior to administration of the consortium. In certain embodiments, the one or more antibiotics are selected from ampicillin, enrofloxacin, clarithromycin, and metronidazole. In certain embodiments, the animals are pre-treated with a polyethylene glycol enteral preparation procedure.

[0168] In certain embodiments, the consortium is used to treat a subject who has or is at risk of developing gastrointestinal dysbiosis. In certain embodiments, the dysbiosis is caused by or develops irritable bowel disease (IBD), colitis, ulcerative colitis, or Crohn's disease. In certain embodiments, the dysbiosis is caused by or develops IBD. In certain embodiments, the dysbiosis is caused by or develops colitis. In certain embodiments, the dysbiosis is caused by or develops ulcerative colitis. In certain embodiments, the dysbiosis is caused by or develops Crohn's disease.

[0169] In certain embodiments, the consortium significantly alters the profile and / or concentration of bile acids present in the animal. For example, in certain non-limiting embodiments, the consortium significantly alters the profile and / or concentration of Tβ-MCA, Tα-MCA, TUDCA, THDCA, TCA, 7β-CA, 7-oxo-CA, TCDCA, Tω-MCA, TDCA, α-MCA, β-MCA, ω-MCA, Muro-CA, d4-CA, CA, TLCA, UDCA, HDCA, CDCA, DCA, and LCA in the animal. In a particular embodiment, FB-003 alters the profile and / or concentration of one or more of the following in animals: Tβ-MCA, Tα-MCA, TUDCA, THDCA, TCA, 7β-CA, 7-oxo-CA, TCDCA, Tω-MCA, TDCA, α-MCA, β-MCA, ω-MCA, Muro-CA, d4-CA, CA, TLCA, UDCA, HDCA, CDCA, DCA, and LCA.

[0170] In certain embodiments, the highly complex intestinal microbial community defined in this disclosure can be used to treat animals with cholestatic diseases such as primary sclerosing cholangitis, primary biliary cholangitis, progressive familial intrahepatic cholestasis, or non-alcoholic steatohepatitis. For example, in certain non-limiting embodiments, the animal may be a mammal, and more specifically, a human.

[0171] In certain embodiments, the consortium may be administered via an enteric coating. For example, in certain non-limiting embodiments, the microbial consortium may be administered orally, rectally (e.g., by enema, suppository, or colonoscopy), or orally or via a nasogastric tube.

[0172] In certain embodiments, the consortium is administered orally. In certain embodiments, oral administration is in the form of a powder. In certain embodiments, oral administration is in the form of a slurry. In certain embodiments, oral administration is in the form of a tablet or capsule.

[0173] In certain embodiments, the consortium can be administered to specific locations along the gastrointestinal tract. For example, in certain non-limiting embodiments, the microbial consortium can be administered to one or more gastrointestinal locations, including the mouth, esophagus, stomach, small intestine (duodenum, jejunum, ileum), large intestine (cecum, ascending colon, transverse colon, descending colon), or rectum. In certain embodiments, the microbial consortium can be administered to any region of the gastrointestinal tract.

[0174] In certain embodiments, FB-001 and FB-003 can be administered orally via tablets or capsules.

[0175] How to treat dysbiosis and IBD This disclosure provides a method for preventing and / or treating dysbiosis in a subject. In certain embodiments, the method may include administering an effective amount of the consortium or a pharmaceutically acceptable composition thereof disclosed herein. In certain embodiments, the consortium is FB-001 or a functional equivalent thereof. In certain embodiments, the consortium is FB-003 or a functional equivalent thereof. In certain embodiments, administration of the consortium or a pharmaceutically acceptable composition thereof results in the engraftment of the consortium's microorganisms. In certain embodiments, administration of the consortium or a pharmaceutically acceptable composition thereof results in an increase in the microbial diversity of the gastrointestinal tract. In certain embodiments, administration of the consortium or a pharmaceutically acceptable composition thereof results in an increase in short-chain fatty acids (SCFAs) (e.g., in the gastrointestinal tract of the subject). In certain embodiments, administration of the consortium or a pharmaceutically acceptable composition thereof results in an increase in secondary bile acids (e.g., in the gastrointestinal tract of the subject). In certain embodiments, administration of the consortium or a pharmaceutically acceptable composition thereof results in a decrease in bacterial pathogens (e.g., in the gastrointestinal tract of the subject).

[0176] This disclosure also provides a method for reducing dysbiosis in a subject (e.g., gastrointestinal dysbiosis). In certain embodiments, the method may include administering an effective amount of the consortium or its pharmaceutically acceptable composition disclosed herein. In certain embodiments, the consortium is FB-001 or its functional equivalent. In certain embodiments, the consortium is FB-003 or its functional equivalent. In certain embodiments, administration of the consortium or its pharmaceutically acceptable composition results in the establishment of the consortium's microorganisms. In certain embodiments, administration of the consortium or its pharmaceutically acceptable composition results in an increase in the microbial diversity of the gastrointestinal tract. In certain embodiments, administration of the consortium or its pharmaceutically acceptable composition results in an increase in short-chain fatty acids (SCFAs) (e.g., in the gastrointestinal tract of the subject). In certain embodiments, administration of the consortium or its pharmaceutically acceptable composition results in an increase in secondary bile acids (e.g., in the gastrointestinal tract of the subject). In certain embodiments, administration of the consortium or its pharmaceutically acceptable composition results in a reduction in bacterial pathogens (e.g., in the gastrointestinal tract of the subject).

[0177] Furthermore, this disclosure provides a method for restoring the microbiome in a subject. In certain embodiments, the method may include administering an effective amount of the consortium or its pharmaceutical composition disclosed herein. In certain embodiments, the consortium is FB-001 or its functional equivalent. In certain embodiments, the consortium is FB-003 or its functional equivalent. In certain embodiments, administration of the consortium or its pharmaceutical composition results in the engraftment of the consortium's microorganisms. In certain embodiments, administration of the consortium or its pharmaceutical composition results in an increase in the microbial diversity of the gastrointestinal tract. In certain embodiments, administration of the consortium or its pharmaceutical composition results in an increase in short-chain fatty acids (SCFAs) (e.g., in the gastrointestinal tract of the subject). In certain embodiments, administration of the consortium or its pharmaceutical composition results in an increase in secondary bile acids (e.g., in the gastrointestinal tract of the subject). In certain embodiments, administration of the consortium or its pharmaceutical composition results in a decrease in bacterial pathogens (e.g., in the gastrointestinal tract of the subject).

[0178] Furthermore, this disclosure provides a method for restoring a healthy microbiome in a subject that has undergone a dysbiosis-inducing event. In certain non-limiting embodiments, the dysbiosis-inducing event may be, for example, antibiotic treatment, an infectious disease, or an underlying disease, without any limitation. In certain non-limiting embodiments, the underlying disease may be IBD, colitis, ulcerative colitis, or Crohn's disease. In certain embodiments, the method may include administering an effective amount of the consortium or its pharmaceutical composition disclosed herein. In certain embodiments, the consortium is FB-001 or its functional equivalent. In certain embodiments, the consortium is FB-003 or its functional equivalent. In certain embodiments, administration of the consortium or its pharmaceutical composition results in the engraftment of the consortium's microorganisms. In certain embodiments, administration of the consortium or its pharmaceutical composition results in an increase in the microbial diversity of the gastrointestinal tract. In certain embodiments, administration of the consortium or its pharmaceutical composition results in an increase in short-chain fatty acids (SCFAs) (for example, in the gastrointestinal tract of the subject). In certain embodiments, administration of the consortium or its pharmaceutical composition results in an increase in secondary bile acids (e.g., in the gastrointestinal tract of the subject). In certain embodiments, administration of the consortium or its pharmaceutical composition results in a decrease in bacterial pathogens (e.g., in the gastrointestinal tract of the subject).

[0179] This disclosure further provides methods for reducing the severity of at least one symptom of a gastrointestinal disorder (e.g., associated with dysbiosis of the gastrointestinal tract) in a subject. Non-limiting examples of gastrointestinal disorders include irritable bowel syndrome, diarrhea, constipation, celiac disease, and leaky gut syndrome. In certain embodiments, the method may include administering an effective amount of the consortium or its pharmaceutically equivalent disclosed herein. In certain embodiments, the consortium is FB-001 or its functional equivalent. In certain embodiments, the consortium is FB-003 or its functional equivalent. In certain embodiments, administration of the consortium or its pharmaceutically equivalent results in the engraftment of the consortium's microorganisms. In certain embodiments, administration of the consortium or its pharmaceutically equivalent results in an increase in the microbial diversity of the gastrointestinal tract. In certain embodiments, administration of the consortium or its pharmaceutically equivalent results in an increase in short-chain fatty acids (SCFAs) (e.g., in the gastrointestinal tract of a subject). In certain embodiments, administration of the consortium or its pharmaceutical composition results in an increase in secondary bile acids (e.g., in the gastrointestinal tract of the subject). In certain embodiments, administration of the consortium or its pharmaceutical composition results in a decrease in bacterial pathogens (e.g., in the gastrointestinal tract of the subject).

[0180] This disclosure further provides methods for treating diseases in subjects. In certain embodiments, the diseases are irritable bowel syndrome, diarrhea, constipation, celiac disease, and leaky gut syndrome, colitis, ulcerative colitis, or Crohn's disease. In certain embodiments, the method may include administering an effective amount of the consortium or its pharmaceutically equivalent disclosed herein. In certain embodiments, the consortium is FB-001 or its functional equivalent. In certain embodiments, the consortium is FB-003 or its functional equivalent. In certain embodiments, administration of the consortium or its pharmaceutically equivalent results in the engraftment of the consortium's microorganisms. In certain embodiments, administration of the consortium or its pharmaceutically equivalent results in an increase in the microbial diversity of the gastrointestinal tract. In certain embodiments, administration of the consortium or its pharmaceutically equivalent results in an increase in short-chain fatty acids (SCFAs) (e.g., in the gastrointestinal tract of the subject). In certain embodiments, administration of the consortium or its pharmaceutically equivalent results in an increase in secondary bile acids (e.g., in the gastrointestinal tract of the subject). In certain embodiments, administration of the consortium or its pharmaceutical composition results in a reduction of bacterial pathogens (for example, in the gastrointestinal tract of the subject).

[0181] This disclosure further provides methods for treating inflammatory bowel disease (IBD) in subjects. In certain embodiments, the method may include administering an effective amount of the consortium or its pharmaceutically equivalent disclosed herein. In certain embodiments, the consortium is FB-001 or its functional equivalent. In certain embodiments, the consortium is FB-003 or its functional equivalent. In certain embodiments, administration of the consortium or its pharmaceutically equivalent results in the engraftment of the consortium's microorganisms. In certain embodiments, administration of the consortium or its pharmaceutically equivalent results in an increase in the microbial diversity of the gastrointestinal tract. In certain embodiments, administration of the consortium or its pharmaceutically equivalent results in an increase in short-chain fatty acids (SCFAs) (e.g., in the gastrointestinal tract of the subject). In certain embodiments, administration of the consortium or its pharmaceutically equivalent results in an increase in secondary bile acids (e.g., in the gastrointestinal tract of the subject). In certain embodiments, administration of the consortium or its pharmaceutically equivalent results in a decrease in bacterial pathogens (e.g., in the gastrointestinal tract of the subject).

[0182] IBD (including colitis, ulcerative colitis, and Crohn's disease) is a debilitating disease, and despite approved commercial products, there is still a great unmet need for its treatment. It is a disorder characterized by chronic inflammation and increased intestinal permeability. There is no known pharmacological care for IBD; rather, current standard care relies on symptom control, maintenance of remission, prevention of relapse, and palliative care. With over 1.7 million people living with IBD in the United States alone as of 2022, disease-modifying therapies with a favorable tolerability profile would be game-changer. Furthermore, there are no therapies to treat the dysbiosis underlying IBD.

[0183] In certain embodiments, FB-001 is a disease modification therapy for the treatment of IBD. In certain embodiments, FB-001 treats the underlying dysbiosis of IBD. In certain embodiments, a functional equivalent of FB-001 is a disease modification therapy for the treatment of IBD. In certain embodiments, a functional equivalent of FB-001 treats the underlying dysbiosis of IBD.

[0184] In certain embodiments, FB-003 is a disease-modifying therapy for the treatment of IBD. In certain embodiments, FB-003 treats the underlying dysbiosis of IBD. In certain embodiments, a functional equivalent of FB-003 is a disease-modifying therapy for the treatment of IBD. In certain embodiments, a functional equivalent of FB-003 treats the underlying dysbiosis of IBD.

[0185] As a result of dysbiosis in IBD patients, microbial diversity, short-chain fatty acids (SCFAs), and secondary bile acids are all reduced, while the presence of bacterial pathogens increases. In certain embodiments, FB-001 or its functional equivalent can increase (or restore to normal and / or healthy levels) microbial diversity in IBD patients, increase SCFAs in IBD patients, increase secondary bile acids in IBD patients, and decrease the presence of bacterial pathogens, thereby restoring the gut ecosystem and promoting a healthy barrier response. In certain embodiments, FB-003 or its functional equivalent can increase (or restore to normal and / or healthy levels) microbial diversity in IBD patients, increase SCFAs in IBD patients, increase secondary bile acids in IBD patients, and decrease the presence of bacterial pathogens, thereby restoring the gut ecosystem and promoting a healthy barrier response.

[0186] Limitations in the field of IBD microbiome therapy include low microbial diversity. For example, certain microbiome therapies for IBD include spore preparations that limit diversity based on how the spores are isolated and produced (i.e., spore preparation results in a loss of microbial diversity, and complete taxonomic reproduction of a healthy microbiome is impossible; see, e.g., Figure 13), as well as small, defined consortia of fewer than 20 strains (i.e., limited microbial diversity, if present, and no complete or near-complete taxonomic reproduction of a healthy microbiome). In certain embodiments, the consortia described herein address the unmet need for microbiome therapies with taxonomic and functional diversity for the treatment of IBD. In certain embodiments, the consortia is FB-001 or its functional equivalent. In certain embodiments, the consortia is FB-003 or its functional equivalent.

[0187] In certain embodiments, FB-001 or its functional equivalent, and FB-003 or its functional equivalent, engraft in the patient's gastrointestinal tract. In certain embodiments, FB-001 or its functional equivalent, and FB-003 or its functional equivalent, engraft robustly in the patient's gastrointestinal tract. In certain embodiments, FB-001 or its functional equivalent, and FB-003 or its functional equivalent, engraft in the patient's gastrointestinal tract and restore microbial diversity. In certain embodiments, FB-001 or its functional equivalent, and FB-003 or its functional equivalent, engraft in the patient's gastrointestinal tract and restore important functions of a healthy gut microbiome. In certain embodiments, important functions include 1) increasing microbial diversity, 2) increasing SCFAs, 3) increasing secondary bile acids, 4) reducing the presence of bacterial pathogens, and / or 5) promoting a healthy barrier response.

[0188] In certain embodiments, the consortium is used to treat IBD, colitis, ulcerative colitis, and / or Crohn's disease. In certain embodiments, FB-001 is used to treat IBD, colitis, ulcerative colitis, and / or Crohn's disease. In certain embodiments, FB-003 is used to treat IBD, colitis, ulcerative colitis, and / or Crohn's disease.

[0189] In certain embodiments, the consortium is administered as a single dose or as multiple doses. In certain embodiments, the consortium is administered once daily for 2, 3, 4, 5, 6 days, 1 week, 2 weeks, 3 weeks, 1 month, 2 months, 3 months, 4 months, 5 months, 6 months, or 1 year. In certain embodiments, the consortium is administered multiple times a day. In certain embodiments, the consortium is administered twice, three, four, or five times a day. In certain embodiments, the consortium is administered intermittently. In certain embodiments, the consortium is administered once a week, once a month, or whenever the subject needs it. In certain embodiments, the consortium is FB-001 or FB-003. In certain embodiments, the consortium is FB-003.

[0190] In certain embodiments, the consortia are administered at an effective dose to enable engraftment and substrate metabolism. In certain embodiments, the consortia are administered at an effective dose to enable engraftment and significant SCFA production. In certain embodiments, the consortia are administered at an effective dose to enable engraftment and reduction of gastrointestinal inflammation.

[0191] In certain embodiments, the consortium is administered with a first loading dose, followed by a maintenance dose. In certain embodiments, the first loading dose is administered for 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 days. In certain embodiments, the loading dose is administered for 1 to 3 days. In certain embodiments, the loading dose is administered for 2 to 4 days. In certain embodiments, the loading dose is administered for 2 to 3 days. In certain embodiments, the loading dose is administered for 3 to 5 days. In certain embodiments, the loading dose is administered for 4 to 6 days. In certain embodiments, the loading dose is administered for 5 to 7 days. In certain embodiments, the loading dose is administered for 1 day. In certain embodiments, the loading dose is administered for 3 days. In certain embodiments, the loading dose is administered for 2 days. In certain embodiments, the maintenance dose is administered for 5 to 10 days after the last loading dose. In certain embodiments, the maintenance dose is administered for 7 to 12 days after the last loading dose. In certain embodiments, the maintenance dose is administered for 10 to 14 days after the last loading dose. In certain embodiments, the maintenance dose is administered for 14 to 21 days after the last loading dose. In certain embodiments, the maintenance dose is administered for 21 to 28 days after the last loading dose. In certain embodiments, the maintenance dose is administered for 14 days after the last loading dose. In certain embodiments, the maintenance dose is administered for 21 days after the last loading dose. In certain embodiments, the maintenance dose is administered for 28 days after the last loading dose. In certain embodiments, the maintenance dose is administered for approximately 8 days after the last loading dose. In certain embodiments, the maintenance dose is administered for approximately 7 days after the last loading dose. In certain embodiments, the maintenance dose is administered for approximately 6 days after the last loading dose. In certain embodiments, the maintenance dose is administered for approximately 9 days after the last loading dose. In certain embodiments, the maintenance dose is administered for approximately 10 days after the last loading dose. In certain embodiments, the loading dose is administered for 2 days and the maintenance dose for 6 days (over a total of 8 days of treatment). In certain embodiments, the loading dose is administered for 2 days and the maintenance dose for 7 days (over a total of 9 days of treatment).In certain embodiments, the loading dose is administered for 2 days and the maintenance dose for 8 days (over a total of 10 days of treatment). In certain embodiments, the loading dose is administered for 9 days and the maintenance dose for 9 days (over a total of 11 days of treatment). In certain embodiments, the loading dose is administered for 2 days and the maintenance dose for 10 days (over a total of 12 days of treatment). In certain embodiments, the consortium is FB-001. In certain embodiments, the loading dose follows prior treatment with antibiotics as described in the following combination therapy section. In certain embodiments, the loading dose follows prior treatment with bowel preparation as described in the following combination therapy section. In certain embodiments, the loading dose follows prior treatment with antibiotics and bowel preparation as described in the following combination therapy section.

[0192] In certain embodiments, FB-001 is formulated by blending seven lyophilized DS containing 148 microbial species and filling them into coated enteric capsules. In certain embodiments, FB-003 is formulated by blending four lyophilized DS containing 145 microbial species and filling them into coated enteric capsules. In certain embodiments, capsules of FB-001 or FB-003 are provided in blister packaging or alternative packaging (e.g., packaging for maintaining the viability of anaerobic microorganisms) to allow for anaerobic or hypoxic exposure. In certain embodiments, each capsule contains 5 × 10 10 ~5×10 11 This includes a range of individual viable cells / capsules. In a particular embodiment, each capsule contains 5 × 10 9 ~5×10 10 This includes a range of individual viable cells / capsules. In a particular embodiment, each capsule contains 5 × 10 11 ~5×10 12 This includes a range of individual viable cells / capsules. In certain embodiments, FB-001 or FB-003 may contain up to 10 viable cells / capsules on days 1 and 2. 12 10 surviving cells, and up to 10 between days 3 and 10.11 It is administered orally to individual living cells. In certain embodiments, maltodextrin is included as an excipient in the capsule.

[0193] In a particular embodiment, each capsule of FB-001 or FB-003 is 5 × 10 10 ~5×10 11 Including the range of individual viable cells / capsule and viable cell counting criteria, the relative abundance values ​​for 145 strains (with the absence of O. formigenes, which is present only in FB-001) range from 18% to 0.015%.

[0194] In certain embodiments, the methods disclosed herein include diagnosing dysbiosis in a subject and then treating the subject with the consortium or its pharmaceutical composition. For example, but not limited to, a method for treating a subject having dysbiosis may include (a) diagnosing the subject having dysbiosis and (b) administering an effective amount of the consortium (e.g., FB-001 or FB-003) or its pharmaceutical composition to the subject. In certain embodiments, a method for diagnosing dysbiosis may include an organic acid test, comprehensive digestive stool analysis (CDSA), a hydrogen breath test, or a combination thereof.

[0195] In certain embodiments, the methods disclosed herein include diagnosing IBD in a subject and then treating the subject with the consortium or a pharmaceutical composition thereof. For example, a method for treating a subject having IBD may include, but is not limited to, (a) diagnosing the subject having IBD and (b) administering an effective amount of the consortium (e.g., FB-001 or FB-003) or a pharmaceutical composition thereof to the subject. In certain embodiments, a method for diagnosing IBD may include endoscopy, colonoscopy, flexible sigmoidoscopy, upper endoscopy, capsule endoscopy, analysis of c-reactive protein (CPR) in a blood sample, analysis of erythrocyte sedimentation rate in a blood sample, detection of calprotectin in stool, detection of lactoferrin in stool, or a combination thereof.

[0196] In certain embodiments, the consortia described herein is used to treat dysbiosis caused by chemical injury. In certain embodiments, the consortia described herein is used to treat diseases associated with dysbiosis caused by chemical injury. In certain embodiments, FB-003, FB-001, Consortia A, or Consortia B described herein is used to treat dysbiosis caused by chemical injury. In certain embodiments, FB-003, FB-001, Consortia A, or Consortia B described herein is used to treat diseases associated with dysbiosis caused by chemical injury.

[0197] In certain embodiments, the consortia described herein is used to treat inflammation-induced dysbiosis. In certain embodiments, the consortia described herein is used to treat diseases associated with inflammation-induced dysbiosis. In certain embodiments, FB-003, FB-001, Consortia A, or Consortia B described herein is used to treat inflammation-induced dysbiosis. In certain embodiments, FB-003, FB-001, Consortia A, or Consortia B described herein is used to treat diseases associated with inflammation-induced dysbiosis.

[0198] In certain embodiments, the consortia described herein is used to treat dysbiosis caused by infectious diseases. In certain embodiments, the consortia described herein is used to treat diseases associated with dysbiosis caused by infectious diseases. In certain embodiments, FB-003, FB-001, Consortia A, or Consortia B described herein is used to treat dysbiosis caused by infectious diseases. In certain embodiments, FB-003, FB-001, Consortia A, or Consortia B described herein is used to treat diseases associated with dysbiosis caused by infectious diseases.

[0199] In certain embodiments, the consortium described herein is used to treat dysbiosis by improving the epithelial barrier of the intestine and / or colon. In certain embodiments, the consortium described herein is used to treat dysbiosis by fixing the epithelial barrier of the intestine and / or colon. In certain embodiments, the consortium described herein is used to treat dysbiosis by transforming the epithelial barrier of the intestine and / or colon into the epithelial barrier of a healthy individual. In certain embodiments, the consortium is FB-003, FB-001, Consortium A, or Consortium B.

[0200] Combination therapy In certain embodiments, the consortium may be administered in combination with other agents. In certain embodiments, the consortium may be administered with antimicrobial agents, antifungal agents, antiviral agents, antiparasitic agents, or prebiotics. In certain embodiments, the consortium may be administered after the administration of antimicrobial agents, antifungal agents, antiviral agents, antiparasitic agents, or prebiotics. In certain embodiments, the administration may be continuous over a period of several hours or several days, or it may be simultaneous.

[0201] For example, in certain non-limiting embodiments, a microbial consortium may be administered with, or pre-administered with, one or more antimicrobial agents selected from fluoroquinolone antibiotics (ciprofloxacin, levaquin, phloxin, tequin, avelox, and norflox), cephalosporin antibiotics (cephalexin, cefuroxime, cefadroxil, cefazolin, cephalothin, cefaclor, cephamandol, cefoxitin, cefprodil, and ceftoviprole); penicillin antibiotics (amoxicillin, ampicillin, penicillin V, dicloxacillin, carbenicillin, vancomycin, and methicillin); tetracycline antibiotics (tetracycline, minocycline, oxytetracycline, and doxycycline); and carbapenem antibiotics (ertapenem, doripenem, imipenem / cilastatin, and meropenem).

[0202] For example, in a certain non-limiting embodiment, the microbial consortium may include abacavir, acyclovir, adefovir, amprenavir, atazanavir, cidofovir, darunavir, delavirdin, didanosine, docosanol, efavirenz, elvitegravir, emtricitabine, enfuvirtide, etravirine, famciclovir, foscamet, homivirsen, ganciclovir, indinavir, idoxuridine, lamivudine, lopinavir It can be administered with one or more antiviral agents selected from virmaraviroc, MK-2048, nelfinavir, nevirapine, penciclovir, raltegravir, rilpivirine, ritonavir, saquinavir, stabudine, tenofovir trifluridine, valacyclovir, valganciclovir, vidarabine, ivacitabine, amantadine, oseltamivir, rimantidine, tipranavir, zalcitabine, zanamivir, and zidovudine.

[0203] In certain embodiments, the microbial consortium includes triazole antifungal substances such as miconazole, ketoconazole, clotrimazole, econazole, omoconazole, bifonazole, butoconazole, fenticonazole, isoconazole, oxyconazole, sertaconazole, sulconazole, and thioconazole; fluconazole, itraconazole, isabconazole, rabconazole, posaconazole, voriconazole, terconazole, and albaconazole; and It can be administered with one or more antifungal agents selected from thiazole antifungal agents such as bafandin; allylamine antifungal agents such as terbinafine, naphthifine, and butenafine; as well as echinocandin antifungal agents such as anidurafungin, caspofungin, and micafungin; polygodial; benzoic acid; cyclopirox; tolnaphthate; undecylenic acid; flucytosine or 5-fluorocytosine; griseofulvin; and haloprogin.

[0204] In certain embodiments, the microbial consortium may be administered with one or more anti-inflammatory and / or immunosuppressant agents selected from cyclophosphamide, mycophenolate mofetil, corticosteroids, mesalazine, mesalamine, sulfasalazine, sulfasalazine derivatives, cyclosporine A, mercaptopurine, azathioprine, prednisone, methotrexate, antihistamines, glucocorticoids, epinephrine, theophylline, cromolyn sodium, anti-leukotrienes, anticholinergics, monoclonal anti-IgE, immunomodulatory peptides, immunomodulatory small molecules, immunomodulatory cytokines, immunomodulatory antibodies, and vaccines.

[0205] In certain embodiments, the consortium may be administered with one or more prebiotics selected from, but not limited to, amino acids, biotin, fructooligosaccharides, galactooligosaccharides, inulin, lactulose, mannan-oligosaccharides, oligofructose-concentrated inulin, oligofructose, oligodextrose, tagatose, transgalactooligosaccharides, and xylooligosaccharides.

[0206] In certain embodiments, the consortium described herein is administered in combination with an anti-inflammatory agent.

[0207] In certain embodiments, the consortium described herein is administered in combination with an antidiarrheal agent.

[0208] In certain embodiments, the consortium described herein is administered in combination with an analgesic. In certain embodiments, the consortium described herein is administered in combination with a nonsteroidal anti-inflammatory drug (NSAID).

[0209] In certain embodiments, the consortium described herein is administered in combination with vitamins and supplements.

[0210] In certain embodiments, the consortia described herein is administered in combination with an aminosalicylic acid.

[0211] In certain embodiments, the consortium described herein is administered in combination with an antibiotic.

[0212] In certain embodiments, the consortium described herein is administered in combination with a biological agent. In certain embodiments, the biological agent blocks signals from the immune system that cause inflammation.

[0213] In certain embodiments, the consortium described herein is administered in combination with a corticosteroid or a steroid.

[0214] In certain embodiments, the consortium described herein is administered in combination with an immunomodulator.

[0215] In certain embodiments, the consortium combination therapy includes prior treatment with antibiotics.

[0216] In certain embodiments, bowel preparation (e.g., MiraLax) is administered late afternoon or early evening after the final dose of antibiotics.

[0217] kit The subject matter disclosed herein provides kits for treating or preventing gastrointestinal dysbiosis. In certain embodiments, the dysbiosis is caused by or causes IBD, colitis, ulcerative colitis, and / or Crohn's disease. In certain embodiments, the kit comprises an effective amount of the consortium disclosed herein or a pharmaceutical composition containing it.

[0218] In certain embodiments, the kit comprises an effective amount of FB-001 or a pharmaceutical composition containing it. In certain embodiments, the kit comprises an effective amount of a consortium functionally equivalent to FB-001 or a pharmaceutical composition containing it. In certain embodiments, the kit comprises an effective amount of a consortium functionally identical to FB-001 or a pharmaceutical composition containing it.

[0219] In certain embodiments, the kit comprises an effective amount of FB-003 or a pharmaceutical composition containing the same. In certain embodiments, the kit comprises an effective amount of a consortium functionally equivalent to FB-003 or a pharmaceutical composition containing the same. In certain embodiments, the kit comprises an effective amount of a consortium functionally identical to FB-003 or a pharmaceutical composition containing the same.

[0220] In certain embodiments, the kit includes a sterile container, which may be a box, ampoule, bottle, vial, tube, bag, pouch, blister pack, or other suitable container form known in the art. Such containers may be made of plastic, glass, laminated paper, metal foil, or other material suitable for holding pharmaceuticals. In certain non-limiting embodiments, the kit includes an anaerobic container for holding the consortium(s) described herein. In certain non-limiting embodiments, the kit includes a blister pack for holding the consortium(s) described herein in the presence of oxygen-free or limited amounts of oxygen. In certain non-limiting embodiments, the kit includes a blister pack having a desiccant for holding the consortium(s) described herein in the presence of oxygen-free or limited amounts of oxygen. In certain non-limiting embodiments, the kit includes a bottle having a desiccant for holding the consortium(s) described herein in the presence of oxygen-free or limited amounts of oxygen.

[0221] In certain embodiments, the kit includes instructions for administering the consortium as described herein. In certain embodiments, the instructions include instructions for administering loading and maintenance doses.

[0222] In certain embodiments, the kit includes storage instructions. In certain embodiments, the storage instructions are for storage at approximately -20°C. In certain embodiments, the storage instructions are for storage below -5°C. In certain embodiments, the storage instructions are for storage at approximately -15 to -20°C, -10 to -20°C, -10 to -15°C, -5 to -10°C, 0 to -5°C, below 0°C, or below 0 to -20°C. In certain embodiments, the storage instructions are for storage at approximately below 4°C. In certain embodiments, the storage instructions are for storage at room temperature.

[0223] In certain embodiments, the kit includes instructions for maintaining a consortium under oxygen-free or hypoxic conditions.

[0224] In a particular embodiment, the kit includes instructions for the subject to maintain a complete antibiotic cessation during treatment by the consortium.

[0225] In a particular embodiment, the kit includes FB-001 and instructions for administering FB-001.

[0226] In a particular embodiment, the kit includes FB-003 and instructions for administering FB-003. [Examples]

[0227] Example 1: Design of a Consortium While microbial consortia of two or more microbial strains have been previously created, limitations existed that hindered their manufacture and clinical efficacy. Specifically, manufacturing limitations have prevented the design and generation of large-scale consortia capable of engrafting in the gastrointestinal tract and constructing functional microbiota systems.

[0228] Isolation of donor-derived microbial strains. Microbial strains were isolated and identified using the method described in PCT / US2021 / 021790.

[0229] Consortium Generation. Using microbial strains identified using the isolation and identification methods described in PCT / US2021 / 021790, more than 30 large consortia were constructed and investigated for their functional ability to metabolize oxalates, phage absence, acceptable endotoxin levels, and their ability to be manufactured with multi-strain APIs. The reason for the large number of experimental consortia is that it was unclear what combinations of microbial strains would be necessary considering the above considerations. Furthermore, the combinations of microbial strains could not be predicted by algorithms and required wet laboratory work to determine efficacy and manufacturability.

[0230] Nineteen exemplary consortia are provided to Consortia I through XIX.

[0231] Consortia V was most effective in the metabolism and degradation of oxalates (i.e., Consortia V had the lowest urinary oxalate concentrations), but further investigation and modification of the consortia were necessary to design products for the treatment of diseases, specifically, diseases caused by or resulting in a reduction or inability to effectively metabolize and degrade oxalates in the gastrointestinal tract. Therefore, modifications of Consortia V were made to determine which microbiota provide functional benefits, including but not limited to consortia growth, oxalate metabolism and degradation, consortia engraftment, and consortia survival, and which microbiota are not necessary or confer a loss to patients receiving the consortia as a treatment for a disease, or are not necessary or confer a loss to the overall function of the consortia (including but not limited to consortia growth, oxalate metabolism and degradation, consortia engraftment, and consortia survival). Examples of such designed and investigated consortia are Consortia IX-XVI.

[0232] Of the designed and tested consortia IX–XVI, consortia IX was selected as the lead for clinical development. The main modifications made as variations of the consortia were made to modify the treatment of diseases that cause or result in a reduced or inability to effectively metabolize and break down oxalates in the gastrointestinal tract. This includes removing the Citrobacter freundii strain because it was determined to be a facultative anaerobe through experimental methods (see, for example, the removal of strains between consortia XIII and XV, and between consortia XXIV, XIII, and XII), replacing one Bacteroides kribbi species with another Bacteroides kribbi species cluster (see, for example, the replacement of strains between consortia XV and XVI), replacing one Blautia faecis species with another Blautia faecis species (see, for example, the replacement of strains between consortia XV and XVI), removing strains determined to be duplicates based on whole-genome sequencing clusters (see, for example, the removal of strains between consortia XVII and XVI), and replacing one Bifidobacterium adolescentis with another Bifidobacterium to improve growth in culture. Replacement with adolescentis (see, for example, strain replacement between consortia X and XII), replacement of one Bifidobacterium pseudocatenulatum with Bifidobacterium pseudoactenulatum to improve growth in culture (see, for example, strain replacement between consortia X and XII), replacement of one Bacteroides xylanisolvens with Bacteroides xylanisolvens to improve growth in culture (see, for example, strain replacement between consortia X and XII), replacement of one Clostridium citroniae with ClostridiumThis includes substitution with citroniae (see, for example, strain substitution between consortia X and XII), substitution of one Blautia faecis with another Blautia faecis to identify a Blautia strain that can grow sufficiently to generate a master cell bank (see, for example, strain substitution between consortia X and XII), removal of Holdemanella biformis to eliminate the risk of phages because phages were not detected in co-culture but were detected using bioinformatics (see, for example, strain substitution between consortia X and XII), as well as removal of Faecalibacterium prasnitzii to eliminate the risk of phages because phages were not detected in co-culture but were detected using bioinformatics (see, for example, strain substitution between consortia X and XII).

[0233] Example 2: Design and manufacture of drug products As shown in Example 1, the consortia described herein was designed to be a complex community of anaerobic microbiota capable of engrafting and functioning in the gastrointestinal tract. However, conventional methods known to those skilled in the art were not capable of producing such a large-scale consortia. Therefore, a novel manufacturing method was needed to grow the microbiota in individual groups (i.e., active pharmaceutical ingredients) to form the final drug product.

[0234] Traditionally, live biotherapeutic products (LBPs) are manufactured one strain at a time (i.e., monostrain manufacturing). Monostrain manufacturing requires fermentation scale-up of each monostrain followed by lyophilization to produce individual active pharmaceutical ingredients (each "DS"). Subsequently, multiple DSs of the individual lyophilized dyes are blended into a mixture and filled into capsules or other suitable packaging / fillings to produce the final drug product ("DP"). While this works for small consortia, it is not feasible to grow more than 100 strains separately, produce more than 100 DSs, and then blend more than 100 DSs into a stable DP. In addition to stability limitations, current technology would require more than a year to produce a single DP. Therefore, conventional manufacturing using current technology was not an option for DPs containing more than 100 strains, and preferably more than 145 strains, such as those offered to Consortia IX.

[0235] The consortia were designed and modified as described in Examples 1 and 2, so we have developed a manufacturing method that can produce consortia of more than 145 strains, including more than 90 species and more than 4 or 6 taxonomic phyla found in the human gastrointestinal tract microbiome. Furthermore, we have developed a method to modify Consortia IX, which includes approximately 99 species across the taxonomic phyla Bacteroidetes, Firmicutes, Actinobacteria, Proteobacteria, and Archaea. The method developed and described herein is a mixed co-culture method that can stably grow more than 50 strains in a single co-culture to produce DS having more than 50 strains.

[0236] Strains were selected for co-culture based on their growth rate, and the manufacturing process was initially designed to add strains to the co-culture at different times throughout the manufacturing process to achieve growth for each strain. This approach was referred to as “addition time” manufacturing. The rationale behind this initial approach was to increase the effectiveness of engraftment (i.e., to ensure that the strains were reactivated in the gastrointestinal tract to enable engraftment before the strains were expelled). Reactivation and engraftment of lyophilized strains requires that the strains be preserved in an “active state” (i.e., an active growth state). However, this “addition time” manufacturing approach was unsuccessful because the growth rates of the strains in the consortia described herein are highly variable, making it difficult to achieve exponential growth simultaneously for diverse strains in co-culture. Therefore, it was determined that additional experimental methods were needed to understand the unique growth kinetics of each strain so that strains could be binned based on their growth rate and the addition time to the bioreactor could be further modified. Growth kinetic assays were performed using HTP anaerobic growth kinetic assays for each individual strain in each of the consortia IX-XVI at eight different inoculation densities.

[0237] Experimental methods to understand the unique growth dynamics of each strain proved useful, along with the addition time manufacturing process. However, ultimately, the highly variable nature of the growing strains from lyophilized powder to active consortia in the bioreactor proved undesirable for the addition time method.

[0238] Therefore, a second approach for co-culture was developed. Instead of applying different inoculation times, the second approach synchronized control of growth and strain distribution at harvest from co-culture by using inoculation density adjustment for each strain ("inoculation density" manufacturing). A growth zone was determined for each strain using unique growth dynamics determined for each strain in the consortium, specifically in Consortia IX-XVI. In doing so, it was determined that co-culture was effective and feasible if each strain was added to the culture at an initial stage based on the inoculation density (i.e., the number of cells per strain added to the co-culture), such that a higher inoculation density for a particular strain resulted in a shorter growth delay time for such strains. Based on this, higher inoculation densities for slow-growing strains and lower inoculation densities for fast-growing strains resulted in synchronized harvest times. As illustrated by the examples in Figures 1A and 1B, modifying the inoculation density of individual strains allowed for improved control over strain distribution and strain recovery in co-culture (i.e., uniform distribution of strains and recovery of a larger number of strains are achieved by adjusting the inoculation density). Figure 1A shows an example of co-culture of 21 fast-growing strains, where only 4 of the 21 strains were undetectable by metagenomics in the final product. However, it is important to note that even if a strain is undetectable in the final product, it may still provide a community advantage that allows for more efficient and robust growth of other strains that are detectable in the final product. Figure 1B shows a further modified experiment of the one shown in Figure 1A, with modified timing of sampling and strain detection. As shown, different timings of growth and culture resulted in better distribution of strains and detection of all 21 strains.

[0239] Further modifications to the co-culture process were necessary to improve fermentation. For example, additional modifications were made to control pH and achieve growth conditions based on the bioreactor vessel (i.e., vessel type and size).

[0240] Using the methods developed and described herein, consortia IX–XVI were each manufactured using only seven DS strains. One exemplary seven DS drug product comprises three O. formigenes single cultures: strain DS1 (e.g., listed in Table 1), strain DS2 (e.g., listed in Table 1), strain DS3 (e.g., listed in Table 1), and strain DS4 (e.g., listed in Table 1).

[0241] Using the methods developed and described herein, the microorganisms listed in Table 2 (FB-003 or FB-003 Consortium) were produced using only four DS strains. One exemplary four DS drug product includes strain DS1 (e.g., listed in Table 1), strain DS2 (e.g., listed in Table 1), strain DS3 (e.g., listed in Table 1), and strain DS4 (e.g., listed in Table 1).

[0242] Identifier strains were developed to identify each DS without sequencing the entire genome of all strains and to ensure proper growth throughout the co-culture process. For DS1, the identifier strains were Bacteroides thetaiotaomicron, Bifidobacterium pseudocatenulatum, and Megasphaera massiliensis. For DS2, the identifier strains were Bacteroides ovatus, Faecalibacterium prausnitzii, and Phascolarctobacterium faecium. For DS3, the identifier strains were Blautia wexlerae, Anaerostipes hadrus, and Clostridium bolteae. For DS4, the identifier strains were Holdemanella biformis, Parasutterella excrementihominis, and Dialister invisus.

[0243] As described herein, the number of strains detected at the end of co-culture may be less than the number of strains added at the start of the culture. This may be a result of limited detection methods. Furthermore, not all strains may be detected at the end of the co-culture process, but the inclusion of undetected strains may still be important for the survival and proliferation of other detected strains.

[0244] In one experiment, DS1 consisted of 54 initial strains, with 50 strains detected at the end of the co-culture process; DS2 consisted of 47 initial strains, with 39 strains detected at the end of the co-culture process; DS3 consisted of 33 initial strains, with 30 strains detected at the end of the co-culture process; and DS4 consisted of 14 initial strains, with 11 strains detected at the end of the co-culture process.

[0245] The detection of this strain was achieved through the development of a fermentation process that enables the growth of diverse strains in co-culture. Variables investigated included the growth dynamics of each strain, the nutritional requirements for each strain, competition for nutrient sources in each DS, and the selection of initial inoculum concentrations to achieve strain growth and distribution in each DS. For example, growth curves were created and used to define the DS buckets and initial inoculum compositions, which are shown in Figures 2A and 2B. Figure 2A shows the design of strain isolation into four DS buckets based on slow-growing and fast-growing strains. Figure 2B shows the initial inoculum species design for fast-growing and very-fast-growing strains. Using five iterations of the strain isolation and inoculum species design methods, for example, DS1 was able to increase its yield from approximately 35 / 54 strains detected at the end of the co-culture process to 50 / 54 strains detected at the end of the co-culture process.

[0246] To successfully produce DS on a large scale, additional experimental methods were required. For example, experimental methods were performed on the sterilization procedure and raw materials used in the culture medium, gas solubility in the bioreactor (i.e., fermenter), shear stress caused by impeller and gas spraying in the bioreactor, and mass transfer and mixing time. Each of these factors is necessary to develop a process that can successfully produce complex consortia, such as any of the consortia described herein. For example, through experimental methods, it was determined that nitrogen spraying resulted in higher shear and influencing gas solubility. Therefore, experiments were performed to adjust the sparger speed, sparger position, and substitution of spraying with gas overlay. The data showed that gas overlay was the only approach that provided successful co-culture of DS. For example, data from different spraying conditions allowed for the detection of only a maximum of 36 strains out of 54 from DS1, while gas overlay allowed for the detection of an additional 11 strains (i.e., 47 / 54 strains) at the end of co-culture.

[0247] The next step in the manufacturing process that needed to be developed was a method for storing the final product in a way that preserved the stability and activity of the strain. Freezing and freeze-drying methods were investigated to determine what would preserve the activity and viability of the strain for each DS.

[0248] To determine whether lyophilization is better than freezing for preserving the activity and viability of the strains in each DS, a lyophilization process had to be developed, given that the complexity of the DSs and consortia provided herein is not known in the art. Key variables investigated to develop a lyophilization process for each DS include, but are not limited to, the formulation of the broth or alternative microbiota suspension medium, methods for preventing oxygen contamination during the lyophilization process, the excipient:broth ratio, parameters for freezing the microbiota suspension before lyophilization, cycle parameters for lyophilization, sterilization requirements, methods for reviving the microbiota after lyophilization storage, buffers for reviving the microbiota, and storage of the lyophilized DS.

[0249] As an example, high-throughput foil-coated plates were used as one of the test options for storing lyophilized DS. This was assumed to work because the foil coating should prevent oxygen exposure. However, it was determined that the foil-coated plates could not actually prevent oxygen contamination because there was no way to partially stop the plates. Another storage method investigated was glass and plastic tray vials with multiple stoppers. The theoretical advantage of this approach was assumed to be the ability to perform high-throughput screening without having to stop each vial individually, since the multiple stoppers could be pushed into the vial in a single step. However, this method proved ineffective because oxygen contamination occurred with the removal of the multiple stoppers. After exploring additional options for how to store lyophilized products, it was determined that individual glass vials with individual stoppers would allow for long-term storage without oxygen contamination.

[0250] In the second example, it was necessary to determine the correct formulation for the lyophilized buffer / culture medium. To determine the correct formulation for each DS, the following lyophilized protective agents were investigated: sorbitol, maltodextrin, OPS diagnostics buffer, sucrose, inulin, alginate, mannitol, trehalose, and skim milk. For example, Figure 3A shows an example of different viability rates for DS2 based on different lyophilized protective agents, and Figure 3B shows an example of different viability rates for DS1 based on different lyophilized protective agents. The addition of reducing agents, including but not limited to cysteine ​​HCl and riboflavin, was also investigated, as shown in Figures 4A (DS2) and 4B (DS1). The additional lyophilized formulations tested included 8% maltodextrin + 0.5% inulin + RA, 5% sucrose + 10% glycerol + 0.3% inulin + RA, 7% trehalose + 8% maltodextrin + RA, 3% sucrose + 5% maltodextrin + 0.5% inulin + RA, 5% maltodextrin + OPS Diag + 0.5% inulin + RA, and 5% maltodextrin + 10% glycerol + 0.3% inulin + RA.

[0251] Based on freeze-thaw and freeze-drying experiments, the data suggested that 10–12% solid content was the selected dose. However, additional experiments were conducted to determine if lower doses were possible. One exemplary experiment for DS2 is shown in Figure 5A, and a second exemplary experiment is shown in Figure 5B.

[0252] Next, assays were performed to determine the success rate of cell regeneration. Cell regeneration was carried out using Anaerobe Systems YCFAC medium, and the dilution scheme was performed using a 100-fold dilution of lyophilized powder (e.g., 50 mg (0.05 g) of powder diluted in 5.0 mL of YCFAC medium). Regeneration was then detected using flow cytometry and a Coulter counter.

[0253] The experiments conducted and the data generated herein determined that freeze-dried material resulted in equivalent colony formation of the strain in mice.

[0254] Example 3: Synthetic Consortium Isolation and Processing. Isolation of bacterial strains for creating a synthetic consortium: Bacterial strains for creating a consortium were isolated and homogenized from healthy human stool samples collected under anaerobic conditions, and then the bacterial species from each sample were identified using whole-genome sequencing (WGS). From there, the bacterial strains and their abundances were determined.

[0255] Next, stool samples were processed and bacterial strains were isolated for cultivation on appropriate culture media (e.g., BHI, blood agar). Isolation of strains specific to the metabolism of oxalate degradation products and EH-related pathways was prioritized, along with preferred and unique strains and strains associated with a healthy gut microbiome. After culturing, the strains were purified and sequenced using metagenomics. From the cultured and isolated strains, we created communities for treating enteric hyperoxaluria based on our bacterial concept, to fill important functional niches in the gut, support normal GI physiology, support the engraftment of specific strains such as O. formigenes, and degrade oxalates.

[0256] Diversity of Synthetic Consortia: Each consortium described herein contains unique species and strains to cover a variety of metabolic phenotypes (e.g., bile acid metabolism, short-chain fatty acid synthesis, oxalate degradation). The core set of 31 bacterial strains was similar across the synthetic consortia, and each community had its own unique signature as shown in the Venn diagram. As shown in Figures 6A and 6B, the number of species present in each consortium created ranged from 40 to 103, and the number of strains ranged from 75 to 195. The species and strains contained varying proportions of phylum-level diversity, where the ratio of Bacteroidetes to firmicutes ranged from 51% to 96%, indicating variation in the general composition.

[0257] Example 4: Production of threonine-dependent microorganisms Certain microorganisms are nutrient dependency strains. This means that the microorganism is unable to synthesize certain organic compounds required for its growth. One such organic compound that certain microorganisms are incapable of synthesizing is threonine. Furthermore, some microorganisms are not nutrient dependency strains of threonine themselves, but they are inefficient threonine-producing strains that hinder effective growth in commonly used growth media.

[0258] N-acetylgalactosamine (GalNAc) is an amino sugar derivative of galactose, which is typically the first monosaccharide that links serine or threonine in a specific form of protein O-glycosylation. While it is possible to grow threonine nutrient addicts by supplementing certain small-batch growth media with GalNAc without adding threonine, such supplementation is undesirable for large-scale batch production because GalNAc is expensive and large quantities are required for the effective growth of microorganisms that require such galactose derivatives. Furthermore, certain media, such as YCFAC medium, are incapable of effectively growing certain threonine nutrient addicts even in the presence of GalNAc.

[0259] Therefore, in order to effectively grow such microorganisms, methods are needed to expand and improve the growth of inefficient threonine-producing strains.

[0260] One such microorganism included in the consortium described herein is Akkermansia muciniphilia. Akkermansia is unable to synthesize threonine itself and therefore cannot effectively expand and grow in cultures lacking a GalNAc source (or a primary source that can be metabolized to GalNAc). Furthermore, GalNAc is a preferred carbon source for Akkermansia, and therefore, known methods for effectively growing and producing Akkermansia include adding GalNAc to the growth medium.

[0261] Therefore, the experiment was designed to identify a novel method for growing Akkermansia in large batches without large amounts of GalNAc. Specifically, three different growth media were tested: YCFAC + GalNAc, YCFAC + GalNAc + threonine, and YCFAC + threonine. BHI medium was used as a positive control because it is an animal-based medium containing threonine (specifically, BHI medium + GalNAc + hemin + vitamin K). GalNAc was expected to be necessary in all media to enable microbial expansion and growth, as it is a preferred carbon source for Akkermansia; however, the anticipated question was not whether GalNAc was unnecessary at all when threonine was also added, but rather how much GalNAc was needed. Surprisingly, we determined that 1) YCFAC + 0.5 g / L GalNAc did not support Akkermansia growth, 2) YCFAC + 0.5 g / L GalNAc + 10 mM threonine did not support growth, and 3) only YCFAC + 10 mM threonine supported Akkermansia growth. In these experiments, seed cultures containing 0.5 g / L GalNAc in YCFAC were used to initiate cell growth, and then transferred to large fermenters for growth and expansion using the three media described above.

[0262] However, certain consortia described herein contain more than 100 different microorganisms, and Akkermansia is only one of these more than 100 different microorganisms. Furthermore, the production methods described herein allow for the growth and production of multiple microorganisms in a single large batch culture (e.g., in a fermenter). The question then became how to grow Akkermansia in large-scale co-cultures, given that Akkermansia is the only microorganism that is a threonine nutrient requirement with a preferred carbon source for GalNAc. Therefore, we designed an experiment to determine whether it is possible to start a seed culture of Akkermansia alone and then combine it with a second seed culture of multiple microorganisms for large-scale batch expansion.

[0263] This experiment included: 1) first growing a seed culture before scaling up to a large batch fermenter to allow Akkermansia to begin growing in a small 10 mL culture (i.e., a seed culture); 2) simultaneously growing a seed culture of Akkermansia and separately growing a second 100 mL seed culture of all other microorganisms in the active pharmaceutical ingredient; 3) combining a 100 mL seed co-culture with a 10 mL Akkermansia seed culture in a large batch fermenter (e.g., 1 L or more); and 4) detecting strains of the active pharmaceutical ingredient and evaluating the ability of Akkermansia to grow and expand in the co-culture. A diagram of this experiment is shown in Figure 7A.

[0264] As shown in Figure 8, it was surprising to see that Akkermansia could not grow in YCFAC medium supplemented with GalNAc, hemin, and vitamin K compared to BHI medium supplemented with GalNAc, hemin, and vitamin K (0.0000% Akkermansia was detected). Therefore, we concluded that YCFAC + GalNAc does not support the growth of Akkermansia. The next question was whether the addition of threonine could restore the growth of Akkermansia.

[0265] The next question was whether GalNAc was necessary when threonine was added. Specifically, the question was how Akkermansia would grow in YCFAC + 10mM threonine (72 hours of growth) compared to medium containing YCFAC + 10mM threonine + 0.5g / L GalNAc (48 hours of growth). Surprisingly, the results showed comparable growth regardless of the presence or absence of GalNAc (0.25 OD without GalNAc and 0.35 OD with GalNAc).

[0266] A co-culture experiment similar to the one described above and shown in Figure 7A was designed to evaluate the requirements for GalNAc and threonine. This experiment used two seed cultures: 1) Akkermansia species grown in YCFAC + 10 mM threonine + 0.5 g / L GalNAc, and 2) other microorganisms in the active pharmaceutical ingredient (14 microorganisms) grown in YCFAC alone. The seed cultures were then combined into a large batch fermenter containing YCFAC + 10 mM threonine (i.e., without GalNAc). See Figure 7B. This study showed that GalNAc is not required in the presence of 10 mM threonine in the large batch fermenter for Akkermansia to grow in co-culture with other microorganisms that are not threonine nutrient requirements. Furthermore, Akkermansia was detected at all growth stages in YCFAC medium with 10 mM threonine (Figure 13).

[0267] Further experiments showed that GalNAc was not even necessary in the seed culture to achieve Akkermansia growth.

[0268] Given that GalNAc is a preferred carbon source for Akkermansia, the ability to grow Akkermansia without GalNAc was quite remarkable. Furthermore, the ability to grow Akkermansia in a GalNAc-free medium provides a means for producing GalNAc-containing microbial drug products in which Akkermansia grows in co-cultures of multiple microorganisms.

[0269] Example 5: Selection of Clinical Candidates Consortium IX was selected as a clinical candidate for clinical trials for the treatment of enteric hyperoxaluria and designated FB-001. FB-003 was selected as a clinical trial candidate for clinical trials for the treatment of IBD, ulcerative colitis, Crohn's disease, and other related dysbiotic diseases and conditions. FB-001 contains 148 different anaerobic microbial strains, and FB-003 contains 145 different anaerobic microbial strains. Both FB-001 and FB-003 were designed to mimic the metabolic and phylogenetic diversity of a healthy human microbiome (Figure 13) and were divided into seven (for FB-001) and four (for FB-003) different active pharmaceutical ingredients for manufacturing purposes. Tables 1 and 2 show the different active pharmaceutical ingredients. Species were identified by 16S rRNA gene sequencing and RCB whole-genome sequencing. The species in the consortium span six major phyla found in the GI tubes of healthy adults, deliberately excluding Fusobacteria, a phylum generally associated with human infections and enriched in opportunistic pathogens (King, Desai et al. 2019). Both strains FB-001 and FB-003 comprise 10 distinct classes, 18 orders, 26 families, and 59 genera.

[0270] Prior to lyophilization, cell pellets containing the FB-001 or FB-003 microbial strain were resuspended in YCFAC medium with a lyophilization protectant, and then lyophilized. YCFAC medium and the lyophilization protectant were selected to stabilize the DS during the lyophilization step. The combination of 8% maltodextrin + 0.5% inulin as the lyophilization protectant showed high viability of the FB-001 and FB-003 microbial strains in formulation development studies, and was therefore selected for the final DS formulation.

[0271] Maltodextrin was also added as a filler during DP manufacturing.

[0272] Capsules for encapsulating DP were enterically coated to release DP in the small intestine and to resist stomach acid as it passes through the gastrointestinal tract. These capsules were dissolved in USP at a pH of 1.2. <701> The capsules were tested according to the specified parameters and showed no disintegration over a 2-hour period. At a pH of 6.8, the capsules completely disintegrated within 30 minutes, which is the target release pH in a GI tube for FB-001 and FB-003 DP (Hydroxypropyl Methylcellulose [HPMC] Capsule COA).

[0273] Functional characteristics of FB-001 and FB-003. FB-001 and FB-003 are prepared using seven or four individual active pharmaceutical ingredients (DS), respectively, containing a total of 148 and 145 anaerobic microbial strains, and are concentrated with species that perform beneficial or normalizing functions in the human GI tube.

[0274] Regarding FB-001, the first of these beneficial or normalizing functions is oxalate degradation, which is the primary EH disease modification mechanism of FB-001. Oxalobacter formigenes are the main drivers of oxalate degradation in the human GI tubule. O. formigenes use oxalate as its exclusive energy source and metabolize considerable concentrations of oxalate for energy production and biomass production. Oxalate metabolism is mediated by a series of enzymatic and transport reactions that ultimately consume oxalate and release CO2 and formate.

[0275] Formate, a byproduct of oxalate metabolism, can ultimately further inhibit oxalate metabolism in vitro if not removed. Therefore, FB-001 also contains strains capable of formate degradation. Bacteria that utilize these formate help remove potentially inhibitory metabolic byproducts of oxalate metabolism.

[0276] FB-001 and FB-003 also contain strains that are oxalate-tolerant and can grow in the presence of oxalate concentrations that are greater than or equal to the magnitude of physiologically normal concentrations of oxalate. This enrichment of oxalate-tolerant strains in the FB-001 and FB-003 consortium may support stable engraftment despite potentially elevated levels of free oxalate in the GI lumen of patients with EH, as the abundance of major oxalotrophs naturally increases with spikes in oxalate concentration.

[0277] The FB-001 and FB-003 consortia were specifically designed to contain phylogenetically diverse microbial species that function mutually to improve malabsorption-related dysbiosis. This was achieved by including numerous species intended to support the community by restoring essential metabolic functions. The strains comprising the FB-001 and FB-003 consortia were selected based on their predictive ability to perform various supportive metabolic functions that contribute to engraftment, regardless of patient physiological or dietary differences. Metabolism of macronutrients and dietary molecules not digested or utilized by host cells can result in the release of metabolites that supply other members of the microbiome community.

[0278] Other strains of FB-001 and FB-003 were evaluated for their unique and potentially beneficial biological functions in the GI tubule, including short-chain fatty acid (SCFA) production, trophic symbiotic (cross-feeding) activity, and mucin degradation. SCFAs are known to confer a wide range of health-promoting functions by being absorbed by the host and acting as a major energy substrate for colon cells, intestinal cells, and hepatocytes, while also acting as signaling molecules recognized by specific G protein-coupled receptors in the lamina propria of the intestinal mucosa, primarily targeting enteroendocrine and immune cells. The strains of FB-001 and FB-003 were evaluated for their trophic symbiosis, a process in which bacteria produce by-products that they supply to other bacteria. Tropic symbiosis stabilizes the gut microbiome and creates novel niches. The strains of FB-001 and FB-003 were also evaluated for their putative protective and / or anti-inflammatory properties.

[0279] Table 3 summarizes the number of strains in FB-001 that contribute to each of these functional characteristics, and the characteristics associated with each FB-001 strain are summarized in Table 4. [Table 3] [Table 4-1] [Table 4-2] [Table 4-3] [Table 4-4]

[0280] Formate Metabolism. The FB-001 and FB-003 DP Consortia contain bacteria that utilize formate to maintain the maximum carbon flux through the pathway. Symbiotic bacterial species, such as methanobacteria found in human GI tubes, can efficiently remove formate by reduction to methane in the presence of hydrogen gas produced by microbial fermenters. Therefore, the FB-001 and FB-003 Consortia include Methanobrevibacter smithii (DS-CoC2), the most common and abundant archaeal methanobacter in the gut that efficiently metabolizes formate, as well as the acetate-producing enteric commensal Blautia hydrogenotrophica (DS-CoC1), which utilizes formate to produce acetate for short-chain fatty acid (SCFA) synthesis, and a panel of anaerobic bacteria expressing cytochrome-dependent formate dehydrogenases that oxidize formate to CO2 (e.g., Sutterella and Parasutterella found in DS-CoC2 and DS-CoC4).

[0281] Supportive metabolic function. FB-001 and FB-003 also contain a diverse panel of broadly functional commensal symbiotes that fulfill unique and potentially beneficial biological functions in the GI tube, including macronutrient metabolism, short-chain fatty acid production, nutrient symbiosis, and mucin degradation.

[0282] Composition of FB-001 and FB-003 DP. FB-001 DP is a very complex mixed fermentation of 148 microbial strains selected for their potential role in supporting healthy GI tubes. Similarly, FB-003 DP is a very complex mixed fermentation of 145 microbial strains selected for their potential role in supporting healthy GI tubes.

[0283] To support clinical research, FB-001 DP was characterized using metagenomic sequencing for the relative abundance of individual species in the final DP and for the total O. formigenes content. In the metagenomic sequencing and analysis, the presence of the strain in the sample was first confirmed by positive identification of a pre-specified biomarker (short DNA sequence) unique to the strain of interest. The results of the metagenomic sequencing were then reported as the relative abundance of each strain, which approximates the percentage of genome copies belonging to each strain and can range from 0 to 100%. The relative abundance was then calculated by comparing the number and frequency of detected biomarkers against the total number of strain-specific biomarkers and the number of sequencing reads. The contribution percentage of each strain in FB-001 DP includes the following dominant portions of the three O. formigenes strains identified by 16S RNA and carbon source analysis described below: approximately 32% of O. formigenes on a relative abundance basis (i.e., approximately 40% on a viable cell count basis), and the other 145 strains have relative abundance values ​​ranging from 18% to 0.015% (typical distribution of the human microbiome).

[0284] FB-001 DP was manufactured as a single batch. Single capsules of DP were collected and stored at -20°C ± 5°C until DNA extraction. FB-001 DP was sequenced via shotgun metagenomics, and the metagenomic sequence of DP was analyzed to determine the composition of FB-001 DP. The results are reported as the relative abundance of each strain. The relative abundance approximates the percentage of FB-001 DP genome copies belonging to each strain, which can range from 0 to 100%. A total of 60 strains out of 148 strains, including 21 strains from DS-CoC1, 13 strains from DS-CoC2, 16 strains from DS-CoC3, 7 strains from DS-CoC4, and each of DS-OF1, DS-OF2, and DS-OF3, were detected at or above their qualified detection limits. The absence of a strain in detection should not be interpreted as its absence from the active pharmaceutical ingredient. The 60 strains detected account for 95.932% of the biomarkers detected in FB-001 DP. Therefore, the remaining 88 strains account for 4.068% of the biomarkers. Relative abundance profiles are expected to vary between batches, and data will continue to be collected during development to understand the magnitude of these variations. Furthermore, the exact percentages should not be interpreted as restrictive or exclusive; rather, each batch of DP may vary in its microbial distribution based on the natural growth of bacteria in co-culture. Table 5 provides an example of the relative abundance profile of microorganisms in one lot of FB-001. [Table 5-1] [Table 5-2]

[0285] Process Development. A blending process was developed for DP production for FB-001 and FB-003 to produce a homogeneous mixture of DS. During the development phase, the blend-sieve-blend technique was tested for mixing DS. Using this technique, several DS were blended in a Turbula mixer at 43 rpm for 15 minutes, followed by sieving the material through a #50 sieve. The material was blended again at 43 rpm for 15 minutes. Aliquots of the blended material were taken from the top, middle, and bottom of the container and evaluated for strain distribution by TCC, VCC, and relative abundance. The results of the blending study showed that the DS material was homogeneously mixed by the blend-sieve-blend technique. For FB-001 DP, the VCC / g, TCC / g, and relative abundance of the three O. formigenes strains in the top, middle, and bottom of the mixing container were very similar, indicating a homogeneous blend of DS in the blending container.

[0286] A diagram illustrating the co-culture method for manufacturing is provided in Figure 10.

[0287] Preparation of DS1. Yeast casitone fatty acid (YCFAC) medium containing carbohydrates, pH 7, was prepared at a 1:1 concentration in 4 L batches for seed 1 fermentation and seed 2 fermentation, respectively. The medium was prepared by adding the components shown in Table 6 to 3.46 kg of sterile water for injection, boiling for 5-10 minutes, and then allowing the medium to cool. Once the temperature reached below 50°C, the medium was sprayed with N2 while adding the remaining components in the following order: sodium bicarbonate, 50-fold volatile fatty acid solution, L-cysteine ​​HCl monohydrate, 0.5% hemin solution, and 25-fold vitamin solution. The pH was adjusted to 7 with 10N NaOH or sulfuric acid, and the medium was autoclaved at 122.5°C for 45 minutes. The medium was incubated at 37°C for a minimum of 24 hours before inoculation for contamination checking. [Table 6]

[0288] A 5x concentrated culture medium was also prepared for use in the main fermentation. The 5x stock was scaled up to 5x using the same proportions as listed in Table 6. The 5x culture medium was diluted to 1x concentration before the main fermentation process.

[0289] A resuspension medium was also prepared, containing YCFAC medium with the reducing agent L-cysteine ​​HCl and riboflavin, pH 7. To prepare the resuspension medium, 0.6 g of riboflavin and 2.0 g of cysteine-HCl were added per 1 kg of YCFAC medium. The medium was stirred until completely dissolved, and then titrated with 10N NaOH or sulfuric acid to obtain a final pH of 7. The medium was filtered through a 0.22 μm polyethersulfone (PES) filter. The final concentration of riboflavin in the YCFAC medium was 0.06%, and the final concentration of L-cysteine ​​HCl was 0.2%.

[0290] A volatile fatty acid solution (50-fold dilution) was prepared using YCFAC medium and contained glacial acetic acid (65.7% w / w at 50-fold dilution; 1.31% w / w at 1-fold dilution), propionic acid (24.2% w / w at 50-fold dilution; 0.48% w / w at 1-fold dilution), isobutyric acid (3.1% w / w at 50-fold dilution; 0.06% w / w at 1-fold dilution), n-valeric acid (3.5% w / w at 50-fold dilution; 0.07% w / w at 1-fold dilution), and isovaleric acid (3.5% w / w at 50-fold dilution; 0.07% w / w at 1-fold dilution).

[0291] The vitamin solution (25x dilution) in YCFAC medium contained biotin powder (1.31 g / 6 kg WFI(g)), folic acid (1.31 g / 6 kg WFI(g)), pyridoxine hydrochloride (6.56 g / 6 kg WFI(g)), thiamine-HCl-2H2O (3.28 g / 6 kg WFI(g)), riboflavin (0.13 g / 6 kg WFI(g)), nicotinic acid (3.28 g / 6 kg WFI(g)), calcium D-pantothenate (3.28 g / 6 kg WFI(g)), vitamin B12 (0.07 g / 6 kg WFI(g)), 4-aminobenzoic acid (3.28 g / 6 kg WFI(g)), and DL-alpha-lipoic acid (3.28 g / 6 kg WFI(g)).

[0292] Microbial strains intended to be FB-001 and FB-003 DS-CoC1 were isolated from stool samples obtained after extensive donor screening. An overview of the strain isolation and purification process, RCB banking, and RCB identity / purity testing is provided in Figures 11 and 12. Homogenization and aliquoting of the entire stool sample were performed under anaerobic conditions, starting with transferring the stool sample to an anaerobic chamber within 15–30 minutes of collection, followed by homogenization, addition of a 1:1 solution of PBS and 50% glycerol, aliquoting into 6–9 separate frozen vials, and transferring to below -65°C for storage until further processing.

[0293] To isolate individual strains, fecal samples were serially diluted and then plated onto various agar plates containing anaerobic microbial culture media (counted as passage 1). The plates were incubated at 37°C under anaerobic conditions. Single colonies from these initial growth plates were collected for further isolation on appropriate microbial culture agar plates (counted as passage 2). After incubation at 37°C, if single colony plating yielded isolated colonies with homogeneous morphology, the cultures were further characterized for strain identification. Preliminary strain identification was performed either by 16S rRNA gene sequencing or by creating and analyzing proteomic fingerprints using high-throughput matrix-assisted laser desorption / ionization time-of-flight spectroscopy. If single colony plating yielded multiple colony morphologies, each unique colony type was collected from this plating for further isolation on appropriate culture agar plates until homogeneous colony morphology was achieved (counted as passage 3 or higher). Table 7 lists the subculturing history of each strain in FB-001 and FB-003 DS-CoC1, as well as the agar and broth media used. [Table 7-1] [Table 7-2] [Table 7-3]

[0294] To bank the RCBs used in FB-001 and FB-003 DS-CoC1, single cultures were inoculated into culture tubes containing appropriate broth medium and incubated at 37°C under anaerobic conditions until sufficient growth was observed. Sterile glycerol solution was added to achieve a final glycerol concentration of 25%, and approximately 0.2 mL was aliquoted into 2D barcoded frozen vials. After removing the frozen vials from the anaerobic gas chamber, the 2D barcode at the bottom of the vials was quickly scanned, and the vials were transferred to below -65°C as the final step in RCB banking.

[0295] After freezing for at least 10 hours, one vial of each purified frozen RCB was retrieved from the freezer, thawed under anaerobic conditions, and subsequently plated onto an agar plate containing appropriate growth medium. The plate was incubated at 37°C under anaerobic conditions. Growth on the plate was observed to confirm resurrection and homogeneous colony morphology for each purified isolate. Following confirmation of homogeneous colony morphology for each RCB, individual colonies were analyzed by 16S rRNA gene sequencing (see sequence listing). The RCBs were further characterized using whole-genome sequencing, followed by genome assembly. Strain-level identification was performed using both 16S rRNA gene sequencing and whole-genome assembly.

[0296] Clear criteria for including each strain in FB-001 and FB-003 DS-CoC1 were that they demonstrated susceptibility to at least two FDA-approved antibiotics. Anaerobic microorganisms in FB-001 DS-CoC1 were tested against several FDA-approved and clinically relevant antimicrobial agents, most of which exhibited particularly potent activity against anaerobic bacteria. All strains in FB-001 and FB-003 DS-CoC1 were found to be susceptible in vitro to two or more clinically relevant antibiotics, meaning there are readily available means for biological control. Importantly, strains in FB-001 or FB-00...

Claims

1. A method for preventing, reducing, and / or treating dysbiosis in a subject, a) Clostridium citroniae, Bacteroides saliersiae, Blautia obeum, Parabacteroides merdae, Parabacteroides distasonis, Anaerotypes hadrus, Lachnospiraceae sp. FBI00033, Eubacterium eligens, Bifidobacterium dentium, Blautia wexlerae, Fusicatenibacter saccharivorans, Bacteroides nordii, Dorea formicigenans, Dorea longicatena, Bacteroides stercorirosoris, Bifidobacterium longum, Bacteroides kribbi, Lachnospiraceae sp. FBI00071, Bacteroides thetaiotaomicron, Clostridium clostridioforme, Clostridium scindens, Roseburia hominis, Clostridium fessum, Coprococcus comes, Blautia faecis, Hungatella hathawayi, Bacteroides stercoris, Collinsella aerofaciens, Hungatella effluvii, Bifidobacterium adolescentis, Bifidobacterium catenulatum, Lactobacillus rogosa, Bacteroides faeces, Bacteroides finegoldii, Clostridium sp. FBI00191, Ruminococcus faeces, Lachnoclostridium pacaense, Clostridium boltea, Longicathena caecimuris, Eggerthella lenta, Blautia massiliensis, Bacteroides xylanisolvens, Bacteroides vulgatus, MegasphereMassiliensis, Butyricimonas faecichominis, Eisenbergella tayi, Acidaminococcus intestini, Emergencia timonensis, Bifidobacterium pseudocatenulatum, Eubacterium hallii, Anaerofustis stercorihominis, Eubacterium ventriosum, Blautia hydrogenotropha, and Lachnospiraceae sp. FBI00290, or their functional equivalents, or b) FBI00001, FBI00002, FBI00010, FBI00013, FBI00029, FBI00032, FBI00033, FBI 00034, FBI00043, FBI00044, FBI00048, FBI00050, FBI00051, FBI00057, FBI00059 , FBI00060, FBI00070, FBI00071, FBI00076, FBI00079, FBI00087, FBI00093, FBI0 0102, FBI00109, FBI00117, FBI00120, FBI00125, FBI00127, FBI00128, FBI00145, F A method comprising administering an effective amount of a microbial consortium or a pharmaceutically acceptable composition thereof, comprising BI00162, FBI00174, FBI00184, FBI00190, FBI00191, FBI00194, FBI00198, FBI00199, FBI00200, FBI00201, FBI00205, FBI00206, FBI00211, FBI00220, FBI00221, FBI00236, FBI00245, FBI00248, FBI00251, FBI00254, FBI00267, FBI00278, FBI00288, and FBI00290, or their functional equivalents.

2. The microbial consortium or its pharmaceutical composition a) Acute bacter timonensis, Alistipes onderdonkii, Bacteroides uniformis, Eubacterium rectale, Alistipes timonensis, Bacteroides kribbi, Coprococcus eutactus, Bilophila wadsworthia, Bacteroides caccae, Alistipes shahii, Parasutterella Excrement hominis, Paraprevotella clara, Sutterella wadsworthensis, Sutterella massiliensis, Porphyromonas asaccharolytica, Ruminococcus bromii, Monoglobus pectinilyticus, Ruminococcaceae sp. FBI00097, Gordonibacter pamelaeae, Bacteroides uniformis, Gordonibacter pamelaea, Bacteroides fragilis, Phascolarctobacterium faecium, Monoglobus pectinolyticus, Clostridium aldenense, Ruthenibacterium lactatiformans, Bacteroides ovatus, Bifidobacterium bifidum, Anaerotruncus massiliensis, Clostridium aldenense, Sutterella wadsworthensis, Catabacter hongkongensis, Alistipes senegalensis, Ruminococcaceae sp. FBI00233, Alistipes shahii, Dielma fastidiosa, Eubacterium siraeum, Faecalibacterium prausnitzii, Turicibacter sanguinis, Eubacterium rectale, Bacteroides caccae, Methanobrevibacter smythii、Brnesimlstintestinihominis, Alistipes onderdonkii, and Methanobrevibacter smithii, or their functional equivalents, b) Bifidobacterium adolescentis, Bifidobacterium longum, Bifidobacterium pseudocatenulatum, Bacteroides thetaiotaomicron, Coprococcus comes, Fusicatenibacter saccharivorans, Eggerthella lenta, Eubacterium elegans, Bacteroides xylanisolvens, Lactobacillus rogosae, Clostridium citroniae, Collinsella aerofaciens, Blautia obeum, Eggerthella lenta, Blautia wexlerae, Lachnoclostridium pacaense, Bacteroides vulgatus, Parabacteroides merdae, Dorea formicigenans, Ruminococcus faecis, Roseburia hominis, Anaerotypes hadrus、Bifidobacteriumm adolescentis、｢ifidobacteriumm pseudocatenulatumm、Clostridium bolteae、Eisenbergiella tayi、Dorea longicatena, Eggerthella lenta, Bacteroides stercoris, Hungatella hathawayi, and Bacteroides xylanisolvens, or their functional equivalents, and / or c) Alistipes putredinis, Dialister succinatiphilus, Akkermansia muciniphila, Ruminococcus bromii, Dialister invisus, Bacteroides massiliensis, Bilophila wadsworthia, Holdemanella biformis, Parasutterella excrementihominis, Alistipes sp. FBI00180, Bacteroides coprocola, Alistipes sp. The method according to claim 1, further comprising FBI00238, Alistipes putredinis, Eubacterium xylanophyllum, and Senegalimassilia anaerobia, or functional equivalents thereof.

3. The microbial consortium or its pharmaceutical composition a) FBI00004, FBI00012, FBI00015, FBI00018, FBI00019, FBI00021, FBI00038, FBI00040, FBI00046, FBI00061, FBI00066, FBI00 075, FBI00077, FBI00080, FBI00081, FBI00085, FBI00092, FBI00097, FBI00099, FBI00112, FBI00132, FBI00137, FBI00140, FBI 00149, FBI00151, FBI00176, FBI00189, FBI00197, FBI00208, FBI00212, FBI00224, FBI00226, FBI00229, FBI00233, FBI00235, FBI00237, FBI00243, FBI00244, FBI00258, FBI00260, FBI00263, FBI00270, FBI00273, FBI00277, and FBI00292, or their functional equivalents, b) FBI00009, FBI00011, FBI00016, FBI00020, FBI00025, FBI00027, FBI00030, FBI00047, FB I00052, FBI00053, FBI00056, FBI00062, FBI00078, FBI00096, FBI00104, FBI00110, FBI0011 1. FBI00113, FBI00115, FBI00116, FBI00123, FBI00124, FBI00126, FBI00135, FBI00147, FBI00159, FBI00167, FBI00170, FBI00232, FBI00255, and FBI00271, or their functional equivalents, and / or c) The method of claim 1, further comprising FBI00022, FBI00049, FBI00068, FBI00069, FBI00152, FBI00165, FBI00171, FBI00175, FBI00177, FBI00180, FBI00182, FBI00238, FBI00269, FBI00274, and FBI00281, or functional equivalents thereof.

4. The method according to claim 2 or 3, wherein the microbial consortium or its pharmaceutical composition further comprises a first strain of Oxalobacter formigenes or FBI00067.

5. The method according to claim 4, wherein the microbial consortium or its pharmaceutical composition further comprises a second strain of Oxalobacter formigenes or FBI00133.

6. The method according to claim 5, wherein the microbial consortium or its pharmaceutical composition further comprises a third strain of Oxalobacter formigenes or FBI00289.

7. The microbial consortium or its pharmaceutical composition a) Clostridium citroniae, Bacteroides saliersiae, Blautia obeum, Parabacteroides merdae, Parabacteroides distasonis, Anaerotypes hadrus, Lachnospiraceae sp. FBI00033, Eubacterium eligens, Bifidobacterium dentium, Blautia wexlerae, Fusicatenibacter saccharivorans, Bacteroides nordii, Dorea formicigenans, Dorea longicatena, Bacteroides stercorirosoris, Bifidobacterium longum, Bacteroides kribbi, Lachnospiraceae sp. FBI00071, Bacteroides thetaiotaomicron, Clostridium clostridioforme, Clostridium scindens, Roseburia hominis, Clostridium fessum, Coprococcus comes, Blautia faecis, Hungatella hathawayi, Bacteroides stercoris, Collinsella aerofaciens, Hungatella effluvii, Bifidobacterium adolescentis, Bifidobacterium catenulatum, Lactobacillus rogosa, Bacteroides faeces, Bacteroides finegoldii, Clostridium sp. FBI00191, Ruminococcus faeces, Lachnoclostridium pacaense, Clostridium boltea, Longicathena caecimuris, Eggerthella lenta, Blautia massiliensis, Bacteroides xylanisolvens, Bacteroides vulgatus, MegasphereMassilensis, Butyricimonas faecihominis, Eisenbergiella tayi, Acidaminococcos intestini, Emergence timonensis, Bifidobacterium pseudocatenulatum, Eubacterium hallii, Anaerofustis stercorihominis, Eubacterium ventriosum, Blautia hydrogenotrophica, and Lachnospiraceae sp.FBI00290、 b) Acute bacterium timonensis, Alistipes onderdonkii, Bacteroides uniformis, Eubacterium rectale, Alistipes timonensis, Bacteroides kribbi, Coprococcus eutactus, Bilophila wadsworthia, Bacteroides caccae, Alistipes shahii, Parasutterella Excrement hominis, Paraprevotella clara, Sutterella wadsworthensis, Sutterella massiliensis, Porphyromonas asaccharolytica, Ruminococcus bromii, Monoglobus pectinilyticus, Ruminococcaceae sp. FBI00097, Gordonibacter pamelaeae, Bacteroides uniformis, Gordonibacter pamelaea, Bacteroides fragilis, Phascolarctobacterium faecium, Monoglobus pectinolyticus, Clostridium aldenense, Ruthenibacterium lactatiformans, Bacteroides ovatus, Bifidobacterium bifidum, Anaerotruncus massiliensis, Clostridium aldenense, Sutterella wadsworthensis, Catabacter hongkongensis, Alistipes senegalensis, Ruminococcaceae sp. FBI00233, Alistipes shahii, Dielma fastidiosa, Eubacterium siraeum, Faecalibacterium prausnitzii, Turicibacter sanguinis, Eubacterium rectale, Bacteroides caccae, Methanobrevibacter smythii、Brnesimlstintestinihominis, Alistipes onderdonkii, and Methanobrevibacter smithii, or their functional equivalents, c) Bifidobacterium adolescentis, Bifidobacterium longum, Bifidobacterium pseudocatenulatum, Bacteroides thetaiotaomicron, Coprococcus comes, Fusicatenibacter saccharivorans, Eggerthella lenta, Eubacterium elegans, Bacteroides xylanisolvens, Lactobacillus rogosae, Clostridium citroniae, Collinsella aerofaciens, Blautia obeum, Eggerthella lenta, Blautia wexlerae, Lachnoclostridium pacaense, Bacteroides vulgatus, Parabacteroides merdae, Dorea formicigenans, Ruminococcus faecis, Roseburia hominis, Anaerotypes hadrus、Bifidobacteriumm adolescentis、｢ifidobacteriumm pseudocatenulatumm、Clostridium bolteae、Eisenbergiella tayi、Dorea longicatena, Eggerthella lenta, Bacteroides stercoris, Hungatella hathawayi, and Bacteroides xylanisolvens, or their functional equivalents, and d) Alistipes putredinis, Dialister succinatiphilus, Akkermansia muciniphila, Ruminococcus bromii, Dialister invisus, Bacteroides massiliensis, Bilophila wadsworthia, Holdemanella biformis, Parasutterella excrementihominis, Alistipes sp. FBI00180, Bacteroides coprocola, Alistipes sp. The method according to claim 1, comprising FBI00238, Alistipes putredinis, Eubacterium xylanophyllum, and Senegalimassilia anaerobia, or functional equivalents thereof.

8. The microbial consortium or its pharmaceutical composition a) FBI00001, FBI00002, FBI00010, FBI00013, FBI00029, FBI00032, FBI0003 3, FBI00034, FBI00043, FBI00044, FBI00048, FBI00050, FBI00051, FBI0005 7, FBI00059, FBI00060, FBI00070, FBI00071, FBI00076, FBI00079, FBI0008 7, FBI00093, FBI00102, FBI00109, FBI00117, FBI00120, FBI00125, FBI0012 7. FBI00128, FBI00145, FBI00162, FBI00174, FBI00184, FBI00190, FBI00191, FBI00194, FBI00198, FBI00199, FBI00200, FBI00201, FBI00205, FBI00206, FBI00211, FBI00220, FBI00221, FBI00236, FBI00245, FBI00248, FBI00251, FBI00254, FBI00267, FBI00278, FBI00288, and FBI00290, or their functional equivalents, b) FBI00004, FBI00012, FBI00015, FBI00018, FBI00019, FBI00021, FBI00038, FBI00040, FBI00046, FBI00061, FBI00066, FBI00 075, FBI00077, FBI00080, FBI00081, FBI00085, FBI00092, FBI00097, FBI00099, FBI00112, FBI00132, FBI00137, FBI00140, FBI 00149, FBI00151, FBI00176, FBI00189, FBI00197, FBI00208, FBI00212, FBI00224, FBI00226, FBI00229, FBI00233, FBI00235, FBI00237, FBI00243, FBI00244, FBI00258, FBI00260, FBI00263, FBI00270, FBI00273, FBI00277, and FBI00292, or their functional equivalents, c) FBI00009, FBI00011, FBI00016, FBI00020, FBI00025, FBI00027, FBI00030, FBI00047, F BI00052, FBI00053, FBI00056, FBI00062, FBI00078, FBI00096, FBI00104, FBI00110, FBI00 111, FBI00113, FBI00115, FBI00116, FBI00123, FBI00124, FBI00126, FBI00135, FBI00147, FBI00159, FBI00167, FBI00170, FBI00232, FBI00255, and FBI00271, or their functional equivalents, and d) The method of claim 1, comprising FBI00022, FBI00049, FBI00068, FBI00069, FBI00152, FBI00165, FBI00171, FBI00175, FBI00177, FBI00180, FBI00182, FBI00238, FBI00269, FBI00274, and FBI00281, or functional equivalents thereof.

9. The method according to claim 7, wherein the microbial consortium or its pharmaceutical composition further comprises a first strain of Oxalobacter formigenes or FBI00067, a second strain of Oxalobacter formigenes or FBI00133, and a third strain of Oxalobacter formigenes or FBI00289.

10. The method according to claim 8, wherein the microbial consortium or its pharmaceutical composition further comprises a first strain of Oxalobacter formigenes or FBI00067, a second strain of Oxalobacter formigenes or FBI00133, and a third strain of Oxalobacter formigenes or FBI00289.

11. The method according to claim 1, wherein the microbial consortium or its pharmaceutical composition is FB-001 or a functional equivalent thereof.

12. The method according to claim 1, wherein the microbial consortium or its pharmaceutical composition is FB-003 or a functional equivalent thereof.

13. The method according to any one of claims 1 to 12, wherein the microbial consortium or its pharmaceutical composition increases the microbial diversity of the gastrointestinal tract.

14. The method according to any one of claims 1 to 13, wherein the microbial consortium or its pharmaceutical composition increases short-chain fatty acids (SCFAs).

15. The method according to any one of claims 1 to 14, wherein the microbial consortium or its pharmaceutical composition increases secondary bile acids.

16. The method according to any one of claims 1 to 15, wherein the microbial consortium or its pharmaceutical composition reduces the bacterial pathogens in the gastrointestinal tract of the target.

17. The microbial consortium or its pharmaceutical composition is approximately 5 × 10 ９ ~Approx. 5×10 １２ The method according to any one of claims 1 to 16, comprising a single living cell.

18. The microbial consortium or its pharmaceutical composition is approximately 5 × 10 ９ ~Approx. 5×10 １０ The method according to any one of claims 1 to 16, comprising a single living cell.

19. The microbial consortium or its pharmaceutical composition is approximately 5 × 10 １０ ~Approx. 5×10 １１ The method according to any one of claims 1 to 16, comprising a single living cell.

20. The microbial consortium or its pharmaceutical composition is approximately 5 × 10 １１ ~Approx. 5×10 １２ The method according to any one of claims 1 to 16, comprising a single living cell.

21. The method according to any one of claims 1 to 20, wherein the microbial consortium or its pharmaceutical composition comprises up to about 10 １１ viable cells.

22. The microbial consortium or its pharmaceutical composition may be up to approximately 10 １２ The method according to any one of claims 1 to 20, comprising a single living cell.

23. The method according to claim 1, wherein the method comprises administering a loading dose and one or more maintenance doses.

24. The method according to claim 23, wherein the loading dose is administered for one, two, three, four, five, six, seven, eight, nine, or ten days.

25. The method according to claim 23 or 24, wherein the loading dose is administered for 2 to 3 days, 3 to 5 days, 4 to 6 days, or 5 to 7 days.

26. The method according to any one of claims 23 to 25, wherein one or more maintenance doses are administered for at least 21 days after the last loading dose.

27. The method according to any one of claims 1 to 26, further comprising administering an antibacterial agent, antiviral agent, antifungal agent, anti-inflammatory agent, immunosuppressant, and / or prebiotic.

28. The method according to claim 27, wherein the antibacterial agent is selected from the group consisting of ciprofloxacin, levaquin, floxin, tequin, avelox, norflox, cephalexin, cefuroxime, cefadroxil, cefazolin, cephalothin, cefaclor, cephamandol, cefoxitin, cefprodil, ceftoviprole, amoxicillin, ampicillin, penicillin V, dicloxacillin, carbenicillin, vancomycin, and methicillin, tetracycline, minocycline, oxytetracycline, doxycycline, ertapenem, doripenem, imipenem / cilastatin, and meropenem.

29. The aforementioned antiviral agents include abacavir, acyclovir, adefovir, amprenavir, atazanavir, cidofovir, darunavir, delavirdin, didanosine, docosanol, efavirenz, elvitegravir, emtricitabine, enfvirtide, etravirine, famciclovir, foscamet, homivirsen, ganciclovir, indinavir, idoxuridine, lamivudine, lopinavir maraviloc, mk- The method according to claim 27, selected from the group consisting of 2048, nelfinavir, nevirapine, nilmatrelvir, penciclovir, raltegravir, rilpivirine, ritonavir, saquinavir, stabudine, tenofovir trifluridine, valacyclovir, valganciclovir, vidarabine, ivacitabine, amantadine, oseltamivir, rimantidine, tipranavir, zalcitabine, zanamivir, and zidovudine.

30. The method according to claim 27, wherein the antifungal agent is selected from the group consisting of miconazole, ketoconazole, clotrimazole, econazole, omoconazole, bifonazole, butoconazole, fenticonazole, isoconazole, oxyconazole, sertaconazole, sulconazole, thioconazole, fluconazole, itraconazole, isabconazole, ravconazole, posaconazole, voriconazole, terconazole, albaconazole, abafandin, terbinafine, naftifine, butenafine, anidurafungin, caspofungin, micafungin, polygodial, benzoic acid, cyclopirox, tolnaphthate, undecylenic acid, flucytosine or 5-fluorocytosine, griseofulvin, and haloprozine.

31. The method according to claim 27, wherein the anti-inflammatory agent and / or immunosuppressant is selected from the group consisting of cyclophosphamide, mycophenolate mofetil, corticosteroids, mesalazine, mesalamine, sulfasalazine, sulfasalazine derivatives, cyclosporine A, mercaptopurine, azathioprine, prednisone, methotrexate, antihistamines, glucocorticoids, epinephrine, theophylline, cromolyn sodium, anti-leukotrienes, anticholinergics, monoclonal anti-IgE, immunomodulatory peptides, immunomodulatory small molecules, immunomodulatory cytokines, immunomodulatory antibodies, and vaccines.

32. The method according to claim 27, wherein the prebiotic is selected from the group consisting of amino acids, biotin, fructooligosaccharides, galactooligosaccharides, inulin, lactulose, mannan-oligosaccharides, oligofructose-concentrated inulin, oligofructose, oligodextrose, tagatose, transgalactooligosaccharides, and xylooligosaccharides.

33. The method according to any one of claims 1 to 32, wherein the microbial consortium or its pharmaceutical composition is present in a food product.

34. A method for restoring a microbiome in a subject and / or for restoring a healthy microbiome, a) Clostridium citroniae, Bacteroides saliersiae, Blautia obeum, Parabacteroides merdae, Parabacteroides distasonis, Anaerotypes hadrus, Lachnospiraceae sp. FBI00033, Eubacterium eligens, Bifidobacterium dentium, Blautia wexlerae, Fusicatenibacter saccharivorans, Bacteroides nordii, Dorea formicigenans, Dorea longicatena, Bacteroides stercorirosoris, Bifidobacterium longum, Bacteroides kribbi, Lachnospiraceae sp. FBI00071, Bacteroides thetaiotaomicron, Clostridium clostridioforme, Clostridium scindens, Roseburia hominis, Clostridium fessum, Coprococcus comes, Blautia faecis, Hungatella hathawayi, Bacteroides stercoris, Collinsella aerofaciens, Hungatella effluvii, Bifidobacterium adolescentis, Bifidobacterium catenulatum, Lactobacillus rogosa, Bacteroides faeces, Bacteroides finegoldii, Clostridium sp. FBI00191, Ruminococcus faeces, Lachnoclostridium pacaense, Clostridium boltea, Longicathena caecimuris, Eggerthella lenta, Blautia massiliensis, Bacteroides xylanisolvens, Bacteroides vulgatus, MegasphereMassiliensis, Butyricimonas faecihominis, Eisenbergella tayi, Acidaminococcus intestini, Emergencia timonensis, Bifidobacterium pseudocatenulatum, Eubacterium hallii, Anaerofustis stercorihominis, Eubacterium ventriosum, Blautia hydrogenotropha, and Lachnospiraceae sp. FBI00290, or their functional equivalents, or b) FBI00001, FBI00002, FBI00010, FBI00013, FBI00029, FBI00032, FBI00033, FBI 00034, FBI00043, FBI00044, FBI00048, FBI00050, FBI00051, FBI00057, FBI00059 , FBI00060, FBI00070, FBI00071, FBI00076, FBI00079, FBI00087, FBI00093, FBI0 0102, FBI00109, FBI00117, FBI00120, FBI00125, FBI00127, FBI00128, FBI00145, F A method comprising administering an effective amount of a microbial consortium or a pharmaceutically acceptable composition thereof, comprising BI00162, FBI00174, FBI00184, FBI00190, FBI00191, FBI00194, FBI00198, FBI00199, FBI00200, FBI00201, FBI00205, FBI00206, FBI00211, FBI00220, FBI00221, FBI00236, FBI00245, FBI00248, FBI00251, FBI00254, FBI00267, FBI00278, FBI00288, and FBI00290, or their functional equivalents.

35. The microbial consortium or its pharmaceutical composition a) Acute bacter timonensis, Alistipes onderdonkii, Bacteroides uniformis, Eubacterium rectale, Alistipes timonensis, Bacteroides kribbi, Coprococcus eutactus, Bilophila wadsworthia, Bacteroides caccae, Alistipes shahii, Parasutterella Excrement hominis, Paraprevotella clara, Sutterella wadsworthensis, Sutterella massiliensis, Porphyromonas asaccharolytica, Ruminococcus bromii, Monoglobus pectinilyticus, Ruminococcaceae sp. FBI00097, Gordonibacter pamelaeae, Bacteroides uniformis, Gordonibacter pamelaea, Bacteroides fragilis, Phascolarctobacterium faecium, Monoglobus pectinolyticus, Clostridium aldenense, Ruthenibacterium lactatiformans, Bacteroides ovatus, Bifidobacterium bifidum, Anaerotruncus massiliensis, Clostridium aldenense, Sutterella wadsworthensis, Catabacter hongkongensis, Alistipes senegalensis, Ruminococcaceae sp. FBI00233, Alistipes shahii, Dielma fastidiosa, Eubacterium siraeum, Faecalibacterium prausnitzii, Turicibacter sanguinis, Eubacterium rectale, Bacteroides caccae, Methanobrevibacter smythii、Brnesimlstintestinihominis, Alistipes onderdonkii, and Methanobrevibacter smithii, or their functional equivalents, b) Bifidobacterium adolescentis, Bifidobacterium longum, Bifidobacterium pseudocatenulatum, Bacteroides thetaiotaomicron, Coprococcus comes, Fusicatenibacter saccharivorans, Eggerthella lenta, Eubacterium elegans, Bacteroides xylanisolvens, Lactobacillus rogosae, Clostridium citroniae, Collinsella aerofaciens, Blautia obeum, Eggerthella lenta, Blautia wexlerae, Lachnoclostridium pacaense, Bacteroides vulgatus, Parabacteroides merdae, Dorea formicigenans, Ruminococcus faecis, Roseburia hominis, Anaerotypes hadrus、Bifidobacteriumm adolescentis、｢ifidobacteriumm pseudocatenulatumm、Clostridium bolteae、Eisenbergiella tayi、Dorea longicatena, Eggerthella lenta, Bacteroides stercoris, Hungatella hathawayi, and Bacteroides xylanisolvens, or their functional equivalents, and / or c) Alistipes putredinis, Dialister succinatiphilus, Akkermansia muciniphila, Ruminococcus bromii, Dialister invisus, Bacteroides massiliensis, Bilophila wadsworthia, Holdemanella biformis, Parasutterella excrementihominis, Alistipes sp. FBI00180, Bacteroides coprocola, Alistipes sp. The method according to claim 34, further comprising FBI00238, Alistipes putredinis, Eubacterium xylanophyllum, and Senegalimassilia anaerobia, or functional equivalents thereof.

36. The microbial consortium or its pharmaceutical composition a) FBI00004, FBI00012, FBI00015, FBI00018, FBI00019, FBI00021, FBI00038, FBI00040, FBI00046, FBI00061, FBI00066, FBI00 075, FBI00077, FBI00080, FBI00081, FBI00085, FBI00092, FBI00097, FBI00099, FBI00112, FBI00132, FBI00137, FBI00140, FBI 00149, FBI00151, FBI00176, FBI00189, FBI00197, FBI00208, FBI00212, FBI00224, FBI00226, FBI00229, FBI00233, FBI00235, FBI00237, FBI00243, FBI00244, FBI00258, FBI00260, FBI00263, FBI00270, FBI00273, FBI00277, and FBI00292, or their functional equivalents, b) FBI00009, FBI00011, FBI00016, FBI00020, FBI00025, FBI00027, FBI00030, FBI00047, FB I00052, FBI00053, FBI00056, FBI00062, FBI00078, FBI00096, FBI00104, FBI00110, FBI0011 1. FBI00113, FBI00115, FBI00116, FBI00123, FBI00124, FBI00126, FBI00135, FBI00147, FBI00159, FBI00167, FBI00170, FBI00232, FBI00255, and FBI00271, or their functional equivalents, and / or c) The method of claim 34, further comprising FBI00022, FBI00049, FBI00068, FBI00069, FBI00152, FBI00165, FBI00171, FBI00175, FBI00177, FBI00180, FBI00182, FBI00238, FBI00269, FBI00274, and FBI00281, or functional equivalents thereof.

37. The method according to claim 35 or 36, wherein the microbial consortium or its pharmaceutical composition further comprises a first strain of Oxalobacter formigenes or FBI00067.

38. The method according to claim 37, wherein the microbial consortium or its pharmaceutical composition further comprises a second strain of Oxalobacter formigenes or FBI00133.

39. The method according to claim 38, wherein the microbial consortium or its pharmaceutical composition further comprises a third strain of Oxalobacter formigenes or FBI00289.

40. The microbial consortium or its pharmaceutical composition a) Clostridium citroniae, Bacteroides saliersiae, Blautia obeum, Parabacteroides merdae, Parabacteroides distasonis, Anaerotypes hadrus, Lachnospiraceae sp. FBI00033, Eubacterium eligens, Bifidobacterium dentium, Blautia wexlerae, Fusicatenibacter saccharivorans, Bacteroides nordii, Dorea formicigenans, Dorea longicatena, Bacteroides stercorirosoris, Bifidobacterium longum, Bacteroides kribbi, Lachnospiraceae sp. FBI00071, Bacteroides thetaiotaomicron, Clostridium clostridioforme, Clostridium scindens, Roseburia hominis, Clostridium fessum, Coprococcus comes, Blautia faecis, Hungatella hathawayi, Bacteroides stercoris, Collinsella aerofaciens, Hungatella effluvii, Bifidobacterium adolescentis, Bifidobacterium catenulatum, Lactobacillus rogosa, Bacteroides faeces, Bacteroides finegoldii, Clostridium sp. FBI00191, Ruminococcus faeces, Lachnoclostridium pacaense, Clostridium boltea, Longicathena caecimuris, Eggerthella lenta, Blautia massiliensis, Bacteroides xylanisolvens, Bacteroides vulgatus, MegasphereMassilensis, Butyricimonas faecihominis, Eisenbergiella tayi, Acidaminococcos intestini, Emergence timonensis, Bifidobacterium pseudocatenulatum, Eubacterium hallii, Anaerofustis stercorihominis, Eubacterium ventriosum, Blautia hydrogenotrophica, and Lachnospiraceae sp.FBI00290、 b) Acute bacterium timonensis, Alistipes onderdonkii, Bacteroides uniformis, Eubacterium rectale, Alistipes timonensis, Bacteroides kribbi, Coprococcus eutactus, Bilophila wadsworthia, Bacteroides caccae, Alistipes shahii, Parasutterella Excrement hominis, Paraprevotella clara, Sutterella wadsworthensis, Sutterella massiliensis, Porphyromonas asaccharolytica, Ruminococcus bromii, Monoglobus pectinilyticus, Ruminococcaceae sp. FBI00097, Gordonibacter pamelaeae, Bacteroides uniformis, Gordonibacter pamelaea, Bacteroides fragilis, Phascolarctobacterium faecium, Monoglobus pectinolyticus, Clostridium aldenense, Ruthenibacterium lactatiformans, Bacteroides ovatus, Bifidobacterium bifidum, Anaerotruncus massiliensis, Clostridium aldenense, Sutterella wadsworthensis, Catabacter hongkongensis, Alistipes senegalensis, Ruminococcaceae sp. FBI00233, Alistipes shahii, Dielma fastidiosa, Eubacterium siraeum, Faecalibacterium prausnitzii, Turicibacter sanguinis, Eubacterium rectale, Bacteroides caccae, Methanobrevibacter smythii、Brnesimlstintestinihominis, Alistipes onderdonkii, and Methanobrevibacter smithii, or their functional equivalents, c) Bifidobacterium adolescentis, Bifidobacterium longum, Bifidobacterium pseudocatenulatum, Bacteroides thetaiotaomicron, Coprococcus comes, Fusicatenibacter saccharivorans, Eggerthella lenta, Eubacterium elegans, Bacteroides xylanisolvens, Lactobacillus rogosae, Clostridium citroniae, Collinsella aerofaciens, Blautia obeum, Eggerthella lenta, Blautia wexlerae, Lachnoclostridium pacaense, Bacteroides vulgatus, Parabacteroides merdae, Dorea formicigenans, Ruminococcus faecis, Roseburia hominis, Anaerotypes hadrus、Bifidobacteriumm adolescentis、｢ifidobacteriumm pseudocatenulatumm、Clostridium bolteae、Eisenbergiella tayi、Dorea longicatena, Eggerthella lenta, Bacteroides stercoris, Hungatella hathawayi, and Bacteroides xylanisolvens, or their functional equivalents, and d) Alistipes putredinis, Dialister succinatiphilus, Akkermansia muciniphila, Ruminococcus bromii, Dialister invisus, Bacteroides massiliensis, Bilophila wadsworthia, Holdemanella biformis, Parasutterella excrementihominis, Alistipes sp. FBI00180, Bacteroides coprocola, Alistipes sp. The method according to claim 34, comprising FBI00238, Alistipes putredinis, Eubacterium xylanophyllum, and Senegalimassilia anaerobia, or functional equivalents thereof.

41. The microbial consortium or its pharmaceutical composition a) FBI00001, FBI00002, FBI00010, FBI00013, FBI00029, FBI00032, FBI0003 3, FBI00034, FBI00043, FBI00044, FBI00048, FBI00050, FBI00051, FBI0005 7, FBI00059, FBI00060, FBI00070, FBI00071, FBI00076, FBI00079, FBI0008 7, FBI00093, FBI00102, FBI00109, FBI00117, FBI00120, FBI00125, FBI0012 7. FBI00128, FBI00145, FBI00162, FBI00174, FBI00184, FBI00190, FBI00191, FBI00194, FBI00198, FBI00199, FBI00200, FBI00201, FBI00205, FBI00206, FBI00211, FBI00220, FBI00221, FBI00236, FBI00245, FBI00248, FBI00251, FBI00254, FBI00267, FBI00278, FBI00288, and FBI00290, or their functional equivalents, b) FBI00004, FBI00012, FBI00015, FBI00018, FBI00019, FBI00021, FBI00038, FBI00040, FBI00046, FBI00061, FBI00066, FBI00 075, FBI00077, FBI00080, FBI00081, FBI00085, FBI00092, FBI00097, FBI00099, FBI00112, FBI00132, FBI00137, FBI00140, FBI 00149, FBI00151, FBI00176, FBI00189, FBI00197, FBI00208, FBI00212, FBI00224, FBI00226, FBI00229, FBI00233, FBI00235, FBI00237, FBI00243, FBI00244, FBI00258, FBI00260, FBI00263, FBI00270, FBI00273, FBI00277, and FBI00292, or their functional equivalents, c) FBI00009, FBI00011, FBI00016, FBI00020, FBI00025, FBI00027, FBI00030, FBI00047, F BI00052, FBI00053, FBI00056, FBI00062, FBI00078, FBI00096, FBI00104, FBI00110, FBI00 111, FBI00113, FBI00115, FBI00116, FBI00123, FBI00124, FBI00126, FBI00135, FBI00147, FBI00159, FBI00167, FBI00170, FBI00232, FBI00255, and FBI00271, or their functional equivalents, and d) The method of claim 34, comprising FBI00022, FBI00049, FBI00068, FBI00069, FBI00152, FBI00165, FBI00171, FBI00175, FBI00177, FBI00180, FBI00182, FBI00238, FBI00269, FBI00274, and FBI00281, or functional equivalents thereof.

42. The method according to claim 40, wherein the microbial consortium or its pharmaceutical composition further comprises a first strain of Oxalobacter formigenes or FBI00067, a second strain of Oxalobacter formigenes or FBI00133, and a third strain of Oxalobacter formigenes or FBI00289.

43. The method according to claim 41, wherein the microbial consortium or its pharmaceutical composition further comprises a first strain of Oxalobacter formigenes or FBI00067, a second strain of Oxalobacter formigenes or FBI00133, and a third strain of Oxalobacter formigenes or FBI00289.

44. The method according to claim 34, wherein the microbial consortium or its pharmaceutical composition is FB-001 or a functional equivalent thereof.

45. The method according to claim 34, wherein the microbial consortium or its pharmaceutical composition is FB-003 or a functional equivalent thereof.

46. The method according to any one of claims 34 to 45, wherein the microbial consortium or its pharmaceutical composition increases the microbial diversity of the gastrointestinal tract.

47. The method according to any one of claims 34 to 46, wherein the microbial consortium or its pharmaceutical composition increases short-chain fatty acids (SCFAs).

48. The method according to any one of claims 34 to 47, wherein the microbial consortium or its pharmaceutical composition increases secondary bile acids.

49. The method according to any one of claims 34 to 48, wherein the microbial consortium or its pharmaceutical composition reduces bacterial pathogens in the gastrointestinal tract of the subject.

50. The microbial consortium or its pharmaceutical composition is approximately 5 × 10 ９ ~Approx. 5×10 １２ The method according to any one of claims 34 to 49, comprising a single living cell.

51. The microbial consortium or its pharmaceutical composition is approximately 5 × 10 ９ ~Approx. 5×10 １０ The method according to any one of claims 34 to 50, comprising a single living cell.

52. The microbial consortium or its pharmaceutical composition is approximately 5 × 10 １０ ~Approx. 5×10 １１ The method according to any one of claims 34 to 51, comprising a single living cell.

53. The microbial consortium or its pharmaceutical composition is approximately 5 × 10 １１ ~Approx. 5×10 １２ The method according to any one of claims 34 to 52, comprising a single living cell.

54. The microbial consortium or its pharmaceutical composition may be up to approximately 10 １１ The method according to any one of claims 34 to 53, comprising a single living cell.

55. The microbial consortium or its pharmaceutical composition may be up to approximately 10 １２ The method according to any one of claims 34 to 53, comprising a single living cell.

56. The method according to claim 34, wherein the method comprises administering a loading dose and one or more maintenance doses.

57. The method according to claim 56, wherein the loading dose is administered for one, two, three, four, five, six, seven, eight, nine, or ten days.

58. The method according to claim 56 or 57, wherein the loading dose is administered for 2 to 3 days, 3 to 5 days, 4 to 6 days, or 5 to 7 days.

59. The method according to any one of claims 56 to 58, wherein one or more maintenance doses are administered for at least 21 days after the last loading dose.

60. The method according to any one of claims 34 to 59, further comprising administering an antibacterial agent, antiviral agent, antifungal agent, anti-inflammatory agent, immunosuppressant, and / or prebiotic.

61. The method according to claim 60, wherein the antibacterial agent is selected from the group consisting of ciprofloxacin, levaquin, floxin, tequin, avelox, norflox, cephalexin, cefuroxime, cefadroxil, cefazolin, cephalothin, cefaclor, cephamandol, cefoxitin, cefprodil, ceftoviprole, amoxicillin, ampicillin, penicillin V, dicloxacillin, carbenicillin, vancomycin, and methicillin, tetracycline, minocycline, oxytetracycline, doxycycline, ertapenem, doripenem, imipenem / cilastatin, and meropenem.

62. The aforementioned antiviral agents include abacavir, acyclovir, adefovir, amprenavir, atazanavir, cidofovir, darunavir, delavirdin, didanosine, docosanol, efavirenz, elvitegravir, emtricitabine, enfvirtide, etravirine, famciclovir, foscamet, homivirsen, ganciclovir, indinavir, idoxuridine, lamivudine, lopinavir maraviloc, mk- The method according to claim 60, selected from the group consisting of 2048, nelfinavir, nevirapine, nilmatrelvir, penciclovir, raltegravir, rilpivirine, ritonavir, saquinavir, stabudine, tenofovir trifluridine, valacyclovir, valganciclovir, vidarabine, ivacitabine, amantadine, oseltamivir, rimantidine, tipranavir, zalcitabine, zanamivir, and zidovudine.

63. The method according to claim 60, wherein the antifungal agent is selected from the group consisting of miconazole, ketoconazole, clotrimazole, econazole, omoconazole, bifonazole, butoconazole, fenticonazole, isoconazole, oxyconazole, sertaconazole, sulconazole, thioconazole, fluconazole, itraconazole, isabconazole, ravconazole, posaconazole, voriconazole, terconazole, albaconazole, abafandin, terbinafine, naftifine, butenafine, anidurafungin, caspofungin, micafungin, polygodial, benzoic acid, cyclopirox, tolnaphthate, undecylenic acid, flucytosine or 5-fluorocytosine, griseofulvin, and haloprozine.

64. The method according to claim 60, wherein the anti-inflammatory agent and / or immunosuppressant is selected from the group consisting of cyclophosphamide, mycophenolate mofetil, corticosteroids, mesalazine, mesalamine, sulfasalazine, sulfasalazine derivatives, cyclosporine A, mercaptopurine, azathioprine, prednisone, methotrexate, antihistamines, glucocorticoids, epinephrine, theophylline, cromolyn sodium, anti-leukotrienes, anticholinergics, monoclonal anti-IgE, immunomodulatory peptides, immunomodulatory small molecules, immunomodulatory cytokines, immunomodulatory antibodies, and vaccines.

65. The method according to claim 60, wherein the prebiotic is selected from the group consisting of amino acids, biotin, fructooligosaccharides, galactooligosaccharides, inulin, lactulose, mannan-oligosaccharides, oligofructose-concentrated inulin, oligofructose, oligodextrose, tagatose, transgalactooligosaccharides, and xylooligosaccharides.

66. The method according to any one of claims 34 to 65, wherein the microbial consortium or its pharmaceutical composition is present in a food product.

67. A method for treating a disease in the subject, a) Clostridium citroniae, Bacteroides saliersiae, Blautia obeum, Parabacteroides merdae, Parabacteroides distasonis, Anaerotypes hadrus, Lachnospiraceae sp. FBI00033, Eubacterium eligens, Bifidobacterium dentium, Blautia wexlerae, Fusicatenibacter saccharivorans, Bacteroides nordii, Dorea formicigenans, Dorea longicatena, Bacteroides stercorirosoris, Bifidobacterium longum, Bacteroides kribbi, Lachnospiraceae sp. FBI00071, Bacteroides thetaiotaomicron, Clostridium clostridioforme, Clostridium scindens, Roseburia hominis, Clostridium fessum, Coprococcus comes, Blautia faecis, Hungatella hathawayi, Bacteroides stercoris, Collinsella aerofaciens, Hungatella effluvii, Bifidobacterium adolescentis, Bifidobacterium catenulatum, Lactobacillus rogosa, Bacteroides faeces, Bacteroides finegoldii, Clostridium sp. FBI00191, Ruminococcus faeces, Lachnoclostridium pacaense, Clostridium boltea, Longicathena caecimuris, Eggerthella lenta, Blautia massiliensis, Bacteroides xylanisolvens, Bacteroides vulgatus, MegasphereMassiliensis, Butyricimonas faecihominis, Eisenbergella tayi, Acidaminococcus intestini, Emergencia timonensis, Bifidobacterium pseudocatenulatum, Eubacterium hallii, Anaerofustis stercorihominis, Eubacterium ventriosum, Blautia hydrogenotropha, and Lachnospiraceae sp. FBI00290, or their functional equivalents, or b) FBI00001, FBI00002, FBI00010, FBI00013, FBI00029, FBI00032, FBI00033, FBI 00034, FBI00043, FBI00044, FBI00048, FBI00050, FBI00051, FBI00057, FBI00059 , FBI00060, FBI00070, FBI00071, FBI00076, FBI00079, FBI00087, FBI00093, FBI0 0102, FBI00109, FBI00117, FBI00120, FBI00125, FBI00127, FBI00128, FBI00145, The method involves administering an effective amount of a microbial consortium or its pharmaceutically acceptable composition containing FBI00162, FBI00174, FBI00184, FBI00190, FBI00191, FBI00194, FBI00198, FBI00199, FBI00200, FBI00201, FBI00205, FBI00206, FBI00211, FBI00220, FBI00221, FBI00236, FBI00245, FBI00248, FBI00251, FBI00254, FBI00267, FBI00278, FBI00288, and FBI00290, or their functional equivalents. The method wherein the disease is irritable bowel syndrome, diarrhea, constipation, celiac disease, and leaky gut syndrome, colitis, ulcerative colitis, or Crohn's disease.

68. The microbial consortium or its pharmaceutical composition a) Acute bacter timonensis, Alistipes onderdonkii, Bacteroides uniformis, Eubacterium rectale, Alistipes timonensis, Bacteroides kribbi, Coprococcus eutactus, Bilophila wadsworthia, Bacteroides caccae, Alistipes shahii, Parasutterella Excrement hominis, Paraprevotella clara, Sutterella wadsworthensis, Sutterella massiliensis, Porphyromonas asaccharolytica, Ruminococcus bromii, Monoglobus pectinilyticus, Ruminococcaceae sp. FBI00097, Gordonibacter pamelaeae, Bacteroides uniformis, Gordonibacter pamelaea, Bacteroides fragilis, Phascolarctobacterium faecium, Monoglobus pectinolyticus, Clostridium aldenense, Ruthenibacterium lactatiformans, Bacteroides ovatus, Bifidobacterium bifidum, Anaerotruncus massiliensis, Clostridium aldenense, Sutterella wadsworthensis, Catabacter hongkongensis, Alistipes senegalensis, Ruminococcaceae sp. FBI00233, Alistipes shahii, Dielma fastidiosa, Eubacterium siraeum, Faecalibacterium prausnitzii, Turicibacter sanguinis, Eubacterium rectale, Bacteroides caccae, Methanobrevibacter smythii、Brnesimlstintestinihominis, Alistipes onderdonkii, and Methanobrevibacter smithii, or their functional equivalents, b) Bifidobacterium adolescentis, Bifidobacterium longum, Bifidobacterium pseudocatenulatum, Bacteroides thetaiotaomicron, Coprococcus comes, Fusicatenibacter saccharivorans, Eggerthella lenta, Eubacterium elegans, Bacteroides xylanisolvens, Lactobacillus rogosae, Clostridium citroniae, Collinsella aerofaciens, Blautia obeum, Eggerthella lenta, Blautia wexlerae, Lachnoclostridium pacaense, Bacteroides vulgatus, Parabacteroides merdae, Dorea formicigenans, Ruminococcus faecis, Roseburia hominis, Anaerotypes hadrus、Bifidobacteriumm adolescentis、｢ifidobacteriumm pseudocatenulatumm、Clostridium bolteae、Eisenbergiella tayi、Dorea longicatena, Eggerthella lenta, Bacteroides stercoris, Hungatella hathawayi, and Bacteroides xylanisolvens, or their functional equivalents, and / or c) Alistipes putredinis, Dialister succinatiphilus, Akkermansia muciniphila, Ruminococcus bromii, Dialister invisus, Bacteroides massiliensis, Bilophila wadsworthia, Holdemanella biformis, Parasutterella excrementihominis, Alistipes sp. FBI00180, Bacteroides coprocola, Alistipes sp. The method according to claim 67, further comprising FBI00238, Alistipes putredinis, Eubacterium xylanophyllum, and Senegalimassilia anaerobia, or functional equivalents thereof.

69. The microbial consortium or its pharmaceutical composition a) FBI00004, FBI00012, FBI00015, FBI00018, FBI00019, FBI00021, FBI00038, FBI00040, FBI00046, FBI00061, FBI00066, FBI00 075, FBI00077, FBI00080, FBI00081, FBI00085, FBI00092, FBI00097, FBI00099, FBI00112, FBI00132, FBI00137, FBI00140, FBI 00149, FBI00151, FBI00176, FBI00189, FBI00197, FBI00208, FBI00212, FBI00224, FBI00226, FBI00229, FBI00233, FBI00235, FBI00237, FBI00243, FBI00244, FBI00258, FBI00260, FBI00263, FBI00270, FBI00273, FBI00277, and FBI00292, or their functional equivalents, b) FBI00009, FBI00011, FBI00016, FBI00020, FBI00025, FBI00027, FBI00030, FBI00047, FB I00052, FBI00053, FBI00056, FBI00062, FBI00078, FBI00096, FBI00104, FBI00110, FBI0011 1. FBI00113, FBI00115, FBI00116, FBI00123, FBI00124, FBI00126, FBI00135, FBI00147, FBI00159, FBI00167, FBI00170, FBI00232, FBI00255, and FBI00271, or their functional equivalents, and / or c) The method of claim 67, further comprising FBI00022, FBI00049, FBI00068, FBI00069, FBI00152, FBI00165, FBI00171, FBI00175, FBI00177, FBI00180, FBI00182, FBI00238, FBI00269, FBI00274, and FBI00281, or functional equivalents thereof.

70. The method according to claim 68 or 69, wherein the microbial consortium or its pharmaceutical composition further comprises a first strain of Oxalobacter formigenes or FBI00067.

71. The method according to claim 70, wherein the microbial consortium or its pharmaceutical composition further comprises a second strain of Oxalobacter formigenes or FBI00133.

72. The method according to claim 71, wherein the microbial consortium or its pharmaceutical composition further comprises a third strain of Oxalobacter formigenes or FBI00289.

73. The microbial consortium or its pharmaceutical composition a) Clostridium citroniae, Bacteroides saliersiae, Blautia obeum, Parabacteroides merdae, Parabacteroides distasonis, Anaerotypes hadrus, Lachnospiraceae sp. FBI00033, Eubacterium eligens, Bifidobacterium dentium, Blautia wexlerae, Fusicatenibacter saccharivorans, Bacteroides nordii, Dorea formicigenans, Dorea longicatena, Bacteroides stercorirosoris, Bifidobacterium longum, Bacteroides kribbi, Lachnospiraceae sp. FBI00071, Bacteroides thetaiotaomicron, Clostridium clostridioforme, Clostridium scindens, Roseburia hominis, Clostridium fessum, Coprococcus comes, Blautia faecis, Hungatella hathawayi, Bacteroides stercoris, Collinsella aerofaciens, Hungatella effluvii, Bifidobacterium adolescentis, Bifidobacterium catenulatum, Lactobacillus rogosa, Bacteroides faeces, Bacteroides finegoldii, Clostridium sp. FBI00191, Ruminococcus faeces, Lachnoclostridium pacaense, Clostridium boltea, Longicathena caecimuris, Eggerthella lenta, Blautia massiliensis, Bacteroides xylanisolvens, Bacteroides vulgatus, MegasphereMassilensis, Butyricimonas faecihominis, Eisenbergiella tayi, Acidaminococcos intestini, Emergence timonensis, Bifidobacterium pseudocatenulatum, Eubacterium hallii, Anaerofustis stercorihominis, Eubacterium ventriosum, Blautia hydrogenotrophica, and Lachnospiraceae sp.FBI00290、 b) Acute bacterium timonensis, Alistipes onderdonkii, Bacteroides uniformis, Eubacterium rectale, Alistipes timonensis, Bacteroides kribbi, Coprococcus eutactus, Bilophila wadsworthia, Bacteroides caccae, Alistipes shahii, Parasutterella Excrement hominis, Paraprevotella clara, Sutterella wadsworthensis, Sutterella massiliensis, Porphyromonas asaccharolytica, Ruminococcus bromii, Monoglobus pectinilyticus, Ruminococcaceae sp. FBI00097, Gordonibacter pamelaeae, Bacteroides uniformis, Gordonibacter pamelaea, Bacteroides fragilis, Phascolarctobacterium faecium, Monoglobus pectinolyticus, Clostridium aldenense, Ruthenibacterium lactatiformans, Bacteroides ovatus, Bifidobacterium bifidum, Anaerotruncus massiliensis, Clostridium aldenense, Sutterella wadsworthensis, Catabacter hongkongensis, Alistipes senegalensis, Ruminococcaceae sp. FBI00233, Alistipes shahii, Dielma fastidiosa, Eubacterium siraeum, Faecalibacterium prausnitzii, Turicibacter sanguinis, Eubacterium rectale, Bacteroides caccae, Methanobrevibacter smythii、Brnesimlstintestinihominis, Alistipes onderdonkii, and Methanobrevibacter smithii, or their functional equivalents, c) Bifidobacterium adolescentis, Bifidobacterium longum, Bifidobacterium pseudocatenulatum, Bacteroides thetaiotaomicron, Coprococcus comes, Fusicatenibacter saccharivorans, Eggerthella lenta, Eubacterium elegans, Bacteroides xylanisolvens, Lactobacillus rogosae, Clostridium citroniae, Collinsella aerofaciens, Blautia obeum, Eggerthella lenta, Blautia wexlerae, Lachnoclostridium pacaense, Bacteroides vulgatus, Parabacteroides merdae, Dorea formicigenans, Ruminococcus faecis, Roseburia hominis, Anaerotypes hadrus、Bifidobacteriumm adolescentis、｢ifidobacteriumm pseudocatenulatumm、Clostridium bolteae、Eisenbergiella tayi、Dorea longicatena, Eggerthella lenta, Bacteroides stercoris, Hungatella hathawayi, and Bacteroides xylanisolvens, or their functional equivalents, and d) Alistipes putredinis, Dialister succinatiphilus, Akkermansia muciniphila, Ruminococcus bromii, Dialister invisus, Bacteroides massiliensis, Bilophila wadsworthia, Holdemanella biformis, Parasutterella excrementihominis, Alistipes sp. FBI00180, Bacteroides coprocola, Alistipes sp. The method according to claim 67, comprising FBI00238, Alistipes putredinis, Eubacterium xylanophyllum, and Senegalimassilia anaerobia, or functional equivalents thereof.

74. The microbial consortium or its pharmaceutical composition a) FBI00001, FBI00002, FBI00010, FBI00013, FBI00029, FBI00032, FBI0003 3, FBI00034, FBI00043, FBI00044, FBI00048, FBI00050, FBI00051, FBI0005 7, FBI00059, FBI00060, FBI00070, FBI00071, FBI00076, FBI00079, FBI0008 7, FBI00093, FBI00102, FBI00109, FBI00117, FBI00120, FBI00125, FBI0012 7. FBI00128, FBI00145, FBI00162, FBI00174, FBI00184, FBI00190, FBI00191, FBI00194, FBI00198, FBI00199, FBI00200, FBI00201, FBI00205, FBI00206, FBI00211, FBI00220, FBI00221, FBI00236, FBI00245, FBI00248, FBI00251, FBI00254, FBI00267, FBI00278, FBI00288, and FBI00290, or their functional equivalents, b) FBI00004, FBI00012, FBI00015, FBI00018, FBI00019, FBI00021, FBI00038, FBI00040, FBI00046, FBI00061, FBI00066, FBI00 075, FBI00077, FBI00080, FBI00081, FBI00085, FBI00092, FBI00097, FBI00099, FBI00112, FBI00132, FBI00137, FBI00140, FBI 00149, FBI00151, FBI00176, FBI00189, FBI00197, FBI00208, FBI00212, FBI00224, FBI00226, FBI00229, FBI00233, FBI00235, FBI00237, FBI00243, FBI00244, FBI00258, FBI00260, FBI00263, FBI00270, FBI00273, FBI00277, and FBI00292, or their functional equivalents, c) FBI00009, FBI00011, FBI00016, FBI00020, FBI00025, FBI00027, FBI00030, FBI00047, F BI00052, FBI00053, FBI00056, FBI00062, FBI00078, FBI00096, FBI00104, FBI00110, FBI00 111, FBI00113, FBI00115, FBI00116, FBI00123, FBI00124, FBI00126, FBI00135, FBI00147, FBI00159, FBI00167, FBI00170, FBI00232, FBI00255, and FBI00271, or their functional equivalents, and d) The method of claim 67, comprising FBI00022, FBI00049, FBI00068, FBI00069, FBI00152, FBI00165, FBI00171, FBI00175, FBI00177, FBI00180, FBI00182, FBI00238, FBI00269, FBI00274, and FBI00281, or functional equivalents thereof.

75. The method according to claim 73, wherein the microbial consortium or its pharmaceutical composition further comprises a first strain of Oxalobacter formigenes or FBI00067, a second strain of Oxalobacter formigenes or FBI00133, and a third strain of Oxalobacter formigenes or FBI00289.

76. The method according to claim 74, wherein the microbial consortium or its pharmaceutical composition further comprises a first strain of Oxalobacter formigenes or FBI00067, a second strain of Oxalobacter formigenes or FBI00133, and a third strain of Oxalobacter formigenes or FBI00289.

77. The method according to claim 67, wherein the microbial consortium or its pharmaceutical composition is FB-001 or a functional equivalent thereof.

78. The method according to claim 67, wherein the microbial consortium or its pharmaceutical composition is FB-003 or a functional equivalent thereof.

79. The method according to any one of claims 67 to 78, wherein the microbial consortium or its pharmaceutical composition increases the microbial diversity of the gastrointestinal tract.

80. The method according to any one of claims 67 to 79, wherein the microbial consortium or its pharmaceutical composition increases short-chain fatty acids (SCFAs).

81. The method according to any one of claims 67 to 80, wherein the microbial consortium or its pharmaceutical composition increases secondary bile acids.

82. The method according to any one of claims 67 to 81, wherein the microbial consortium or its pharmaceutical composition reduces the bacterial pathogens in the gastrointestinal tract of the target.

83. The microbial consortium or its pharmaceutical composition is approximately 5 × 10 ９ ~Approx. 5×10 １２ The method according to any one of claims 67 to 82, comprising a single living cell.

84. The microbial consortium or its pharmaceutical composition is approximately 5 × 10 ９ ~Approx. 5×10 １０ The method according to any one of claims 67 to 83, comprising a single living cell.

85. The microbial consortium or its pharmaceutical composition is approximately 5 × 10 １０ ~Approx. 5×10 １１ The method according to any one of claims 67 to 84, comprising a single living cell.

86. The microbial consortium or its pharmaceutical composition is approximately 5 × 10 １１ ~Approx. 5×10 １２ The method according to any one of claims 67 to 85, comprising a single living cell.

87. The microbial consortium or its pharmaceutical composition may be up to approximately 10 １１ The method according to any one of claims 67 to 86, comprising a single living cell.

88. The microbial consortium or its pharmaceutical composition may be up to approximately 10 １２ The method according to any one of claims 67 to 86, comprising a single living cell.

89. The method according to claim 67, wherein the method comprises administering a loading dose and one or more maintenance doses.

90. The method according to claim 89, wherein the loading dose is administered for one, two, three, four, five, six, seven, eight, nine, or ten days.

91. The method according to claim 89 or 90, wherein the loading dose is administered for 2 to 3 days, 3 to 5 days, 4 to 6 days, or 5 to 7 days.

92. The method according to any one of claims 67 to 91, wherein one or more maintenance doses are administered for at least 21 days after the last loading dose.

93. The method according to any one of claims 67 to 92, further comprising administering an antibacterial agent, antiviral agent, antifungal agent, anti-inflammatory agent, immunosuppressant, and / or prebiotic.

94. The method according to claim 93, wherein the antibacterial agent is selected from the group consisting of ciprofloxacin, levaquin, floxin, tequin, avelox, norflox, cephalexin, cefuroxime, cefadroxil, cefazolin, cephalothin, cefaclor, cephamandol, cefoxitin, cefprodil, ceftoviprole, amoxicillin, ampicillin, penicillin V, dicloxacillin, carbenicillin, vancomycin, and methicillin, tetracycline, minocycline, oxytetracycline, doxycycline, ertapenem, doripenem, imipenem / cilastatin, and meropenem.

95. The aforementioned antiviral agents include abacavir, acyclovir, adefovir, amprenavir, atazanavir, cidofovir, darunavir, delavirdin, didanosine, docosanol, efavirenz, elvitegravir, emtricitabine, enfvirtide, etravirine, famciclovir, foscamet, homivirsen, ganciclovir, indinavir, idoxuridine, lamivudine, lopinavir maraviloc, mk- The method according to claim 93, selected from the group consisting of 2048, nelfinavir, nevirapine, nilmatrelvir, penciclovir, raltegravir, rilpivirine, ritonavir, saquinavir, stabudine, tenofovir trifluridine, valacyclovir, valganciclovir, vidarabine, ivacitabine, amantadine, oseltamivir, rimantidine, tipranavir, zalcitabine, zanamivir, and zidovudine.

96. The method according to claim 93, wherein the antifungal agent is selected from the group consisting of miconazole, ketoconazole, clotrimazole, econazole, omoconazole, bifonazole, butoconazole, fenticonazole, isoconazole, oxyconazole, sertaconazole, sulconazole, thioconazole, fluconazole, itraconazole, isabconazole, ravconazole, posaconazole, voriconazole, terconazole, albaconazole, abafandin, terbinafine, naftifine, butenafine, anidurafungin, caspofungin, micafungin, polygodial, benzoic acid, cyclopirox, tolnaphthate, undecylenic acid, flucytosine or 5-fluorocytosine, griseofulvin, and haloprozin.

97. The method according to claim 93, wherein the anti-inflammatory agent and / or immunosuppressant is selected from the group consisting of cyclophosphamide, mycophenolate mofetil, corticosteroids, mesalazine, mesalamine, sulfasalazine, sulfasalazine derivatives, cyclosporine A, mercaptopurine, azathioprine, prednisone, methotrexate, antihistamines, glucocorticoids, epinephrine, theophylline, cromolyn sodium, anti-leukotrienes, anticholinergics, monoclonal anti-IgE, immunomodulatory peptides, immunomodulatory small molecules, immunomodulatory cytokines, immunomodulatory antibodies, and vaccines.

98. The method according to claim 93, wherein the prebiotic is selected from the group consisting of amino acids, biotin, fructooligosaccharides, galactooligosaccharides, inulin, lactulose, mannan-oligosaccharides, oligofructose-concentrated inulin, oligofructose, oligodextrose, tagatose, transgalactooligosaccharides, and xylooligosaccharides.

99. The method according to any one of claims 67 to 98, wherein the microbial consortium or its pharmaceutical composition is present in a food product.

100. The method according to any one of claims 67 to 99, further comprising diagnosing IBD in the subject before administering the microbial consortium or its pharmaceutical composition.

101. A method for reducing dysbiosis in a subject, comprising administering to a patient a therapeutically effective amount of a pharmaceutical composition containing a consortium to reduce gastrointestinal dysbiosis in the patient.

102. The method according to claim 101, wherein reducing dysbiosis includes the establishment of microorganisms in the consortium, an increase in microbial diversity in the gastrointestinal tract, an increase in short-chain fatty acids (SCFAs), an increase in secondary bile acids, and / or a reduction in bacterial pathogens.

103. The method according to claim 101 or 102, wherein the consortium is FB-001 or a functional equivalent thereof.

104. The method according to claim 101 or 102, wherein the consortium is FB-003 or a functional equivalent thereof.

105. A method for restoring the microbiome in a patient, comprising administering to the patient a therapeutically effective amount of a pharmaceutical composition comprising a consortium.

106. The method according to claim 105, wherein the restoration of the microbiome includes the establishment of microorganisms in the consortium, an increase in microbial diversity in the gastrointestinal tract, an increase in short-chain fatty acids (SCFAs), an increase in secondary bile acids, and / or a decrease in bacterial pathogens.

107. The method according to claim 105 or 106, wherein the consortium is FB-001 or a functional equivalent thereof.

108. The method according to claim 105 or 106, wherein the consortium is FB-003 or a functional equivalent thereof.

109. A method for increasing the recovery of a healthy microbiome in a patient after a dysbiosis-inducing event, comprising administering a therapeutically effective amount of a pharmaceutical composition comprising a consortium to the target.

110. The method according to claim 109, wherein the restoration of the healthy microbiome includes the establishment of microorganisms in the consortium, an increase in microbial diversity in the gastrointestinal tract, an increase in short-chain fatty acids (SCFAs), an increase in secondary bile acids, and / or a decrease in bacterial pathogens.

111. The method according to claim 109 or 110, wherein the consortium is FB-001 or a functional equivalent thereof.

112. The method according to claim 109 or 110, wherein the consortium is FB-003 or a functional equivalent thereof.

113. The method according to any one of claims 109 to 112, wherein the dysbiosis-inducing event is treatment with one or more antibiotics, an infectious disease, or an underlying disease.

114. The method according to claim 113, wherein the underlying disease is IBD, colitis, ulcerative colitis, or Crohn's disease.

115. A composition for treating or reducing the severity of at least one symptom of a gastrointestinal disease, disorder, or condition associated with dysbiosis in a patient, comprising a consortium in an amount effective for aggregation and selective engraftment in the gastrointestinal tract of the patient.

116. The composition according to claim 115, wherein the gastrointestinal disease is selected from the group consisting of IBD, colitis, ulcerative colitis, and Crohn's disease.

117. The composition according to claim 115 or 116, wherein the dysbiosis is associated with a decrease in microbial diversity in the gastrointestinal tract, a decrease in short-chain fatty acids (SCFAs), a decrease in secondary bile acids, and / or an increase in bacterial pathogens.

118. The method according to any one of claims 115 to 117, wherein the consortium is FB-001 or a functional equivalent thereof.

119. The method according to any one of claims 115 to 117, wherein the consortium is FB-003 or a functional equivalent thereof.

120. A method for treating or reducing the severity of at least one symptom of a gastrointestinal disorder associated with dysbiosis, comprising administering an effective amount of a pharmaceutical composition comprising a consortium.

121. The method according to claim 120, wherein the consortium is FB-001 or a functional equivalent thereof.

122. The method according to claim 120, wherein the consortium is FB-003 or a functional equivalent thereof.

123. A composition comprising FB-003 or its functional equivalent.

124. A method for manufacturing FB-003 or a functional equivalent thereof.

125. A method for treating IBD, colitis, ulcerative colitis, or Crohn's disease by administering a consortium.

126. The method according to claim 125, wherein the consortium is FB-003 or FB-001.

127. A method for reducing symptoms associated with IBD, colitis, ulcerative colitis, or Crohn's disease by administering a consortium.

128. The method according to claim 127, wherein the consortium is FB-003 or FB-001.

129. Any method or composition described herein.

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