Compositions of bacterial consortium and methods of use

Abstract

The present disclosure provides, in part, microbiome compositions comprising a bacterial consortium, or an isolated plurality of bacterial species / isolates, and methods of preparing and using the same, e.g., for establishing a healthy microbiome and / or treating cancer.

Description

Atorney Docket No.: 137085-5001 -PCCOMPOSITIONS OF BACTERIAL CONSORTIUM AND METHODS OF USEFIELD

[0001] The present disclosure relates to, in part, microbiome compositions comprising bacterial consortia and methods of preparing and using the same, e.g., for establishing a healthy microbiome and / or treating cancer.CROSS-REFERENCE TO RELATED APPLICATIONS

[0002] This application claims the benefit or and priority to U.S. Provisional Application Nos. 63 / 696,151, 63 / 696,157, and 63 / 696,162, each filed September 18, 2024, the contents of each of which are incorporated by reference in their entirety.SEQUENCE LISTING

[0003] The present disclosure includes a sequence listing submitted in XML format via Patentcenter, the entire contents of which is incorporated by reference. The XML file was created on September 17, 2025, is named “137085-5001 _Sequence_Listing.xml,” and is approximately 1 ,695,744 bytes in size.BACKGROUND

[0004] Microbiome-based products have enjoyed recent attention due to the increasingly robust data that have revealed the interplay between host-microbiota interactions. Microbiome-relevant locations in humans are not simply confined to the gastrointestinal tract (gut). Studies have uncovered that microbiomehost interactions play profound roles in the functioning of the lung and respiratory tract, scalp / skin, the immune system, liver, and even the brain. However, modern lifestyle factors have shown to negatively impact microbiota, for example, ranging from the use of non-nutritive and artificial sweeteners, adoption of diets lacking in fiber and / or micronutrients, increasingly stressful and sedentary lifestyles, widespread antibiotic use (e.g., in cleaning products), and the use of harsh cosmetics, haircare, and skincare products. There is also increasing evidence to suggest that responses to medical treatments (e.g., antibiotics, chemotherapy, and biologies) are guided in part by whole body microbiome composition.

[0005] The host-microbiome interplay has revealed to be more complicated than originally thought, spurring the development of numerous products aimed at shaping the microbiome. Relevant uses for microbiome products include improvement of digestion, modulation of metabolism, acne / dermatitis / eczema reduction, modulation of liver disease (alcohol-based and non-alcohol based), conditioning of the immuneDBl / 161604598.2 1Atorney Docket No.: 137085-5001 -PC system, modulation of mood disorders, and reducing the onset and / or progression of neurodegeneration. Traditional ingestible microbiome-focused products include foods (e.g., dairy, fermented foods, carbonated beverages), dietary supplements (e.g., probiotics), and plant-derived products. Common commerciallyrelevant dietary and food-based live cultures used as probiotics include the genera of Bacillus, Bifidobacterium {e.g., B. animalis or B. longum), Enterococcus, Escherichia, Lactobacillus e.g., L. rhamnosus or L. bulgaricus), Saccharomyces, and Streptococcus {e.g., S. theimophilus).

[0006] However, bacteria-based microbiome products are generally limited in their complexity - having only a few distinct species / isolates. Commercially-available ingestible bacterial combinations are generally focused solely on homofermentative and / or heterofermentative lactic acid bacteria (e.g., food-based probiotics), or only selective few live cultures that can be infused into food products. More sophisticated microbiome products rely on donors for fecal microbiome transplantation (FMT). However, this form of product does not start from isolated bacterial stocks and includes the risks of transfer of antibiotic-resistant strains / isolates and pathogens, as well as inducing immunological and gastrointestinal adverse events (AEs) in the recipient. Moreover, there are practical considerations, including regulatory and manufacturing hurdles in starting from fecal material and heterogeneity among the bacterial species, strains, and isolates between individual FMT and the relative abundance and function of the components therein. Several practical caveats have emerged in the development of bacteria-based microbiome products and very little successful development has been achieved using larger bacterial consortia (e.g., 25+, 50+ 100+, etc. species, strains, isolates) from non-fecal sources.

[0007] Developing higher complexity consortia aimed at achieving diverse microbiological and biochemical effects becomes increasingly difficult considering co-culture and manufacture implications. Understanding how to select individual species / isolates to craft an overall consortium is challenging. Additionally, there is a need for greater understanding of the combinations of bacterial species / isolates that are most compatible with establishing a healthy microbiome. In light of this, there remains a need for guidance in the field to develop bacteria-based microbiome products which establish and / or maintain a healthy microbiome in humans, e.g., for clinically-relevant uses outside of simply functioning as a probiotic.SUMMARY

[0008] Accordingly, the present disclosure provides, in part, bacterial consortia, or compositions of bacterial species / isolates which incorporate more complex combinations aimed at achieving diverse microbiological and biochemical effects selected based on a combination of in silico, in vitro, and in vivoDBl / 161604598.2 2Atorney Docket No.: 137085-5001 -PC screening and analysis. The present disclosure provides, in part, bacteria- based microbiome products to establish and / or maintain a healthy microbiome in humans, e.g., for clinically-relevant uses outside of simply functioning as a probiotic. In embodiments, the present disclosure provides methods for screening bacterial species, strains, and / or isolates to build and test bacterial consortia.

[0009] In aspects, described herein is composition comprising an isolated plurality of bacterial species, the plurality of bacterial species comprising a total of at least about 100 isolates from at least about 50 bacterial species, where at least about 7 isolates are selected from at least about 5 species having about or at least about 95% sequence identity to the 16S rRNA sequence of bacterial species selected from Table 1 a, at least about 12 isolates are selected from at least about 10 species having about or at least about 95% sequence identity to the 16S rRNA sequence of bacterial species selected from Table 1c, at least about 12 isolates are selected from at least about 10 species having about or at least about 95% sequence identity to the 16S rRNA sequence of bacterial species selected from Table 1 d, at least about 12 isolates are selected from at least about 10 species having about or at least about 95% sequence identity to the 16S rRNA sequence of bacterial species selected from Table 1e and / or Table 1f, the remaining of the at least about 100 isolates from the at least about 50 bacterial species have about or at least about 95% sequence identity to the 16S rRNA sequence of bacterial species selected from Table 1 b.

[0010] In embodiments, the plurality of bacterial species is suitable for co-culturing in no more than 5 bioreactors, no more than 4 bioreactors, no more than 3 bioreactors, no more than 2 bioreactors, or no more than a single bioreactor.

[0011] In embodiments, the plurality of bacterial species comprises between about 50 bacterial species and about 100 bacterial species, between about 100 bacterial species and 150 bacterial species, or between about 150 bacterial species and 200 bacterial species. In embodiments, the plurality of bacterial species comprises between about 50 bacterial species and about 60 bacterial species, between about 60 bacterial species and about 70 bacterial species, between about 70 bacterial species and about 80 bacterial species, between about 80 bacterial species and about 90 bacterial species, between about 90 bacterial species and about 100 bacterial species, between about 100 bacterial species and about 110 bacterial species, between about 110 bacterial species and about 120 bacterial species, between about 120 bacterial species and about 130 bacterial species, between about 130 bacterial species and about 140 bacterial species, or between about 140 bacterial species and about 150 bacterial species.DBl / 161604598.2 3Atorney Docket No.: 137085-5001 -PC

[0012] In embodiments, the plurality of bacterial species comprises between about 100 bacterial isolates and about 150 bacterial isolates, between about 150 bacterial isolates and about 200 bacterial isolates, or between about 200 bacterial isolates and about 250 bacterial isolates. In embodiments, the plurality of bacterial species comprises between about 100 bacterial isolates and about 110 bacterial isolates, between about 110 bacterial isolates and about 120 bacterial isolates, between about 120 bacterial isolates and about 130 bacterial isolates, between about 130 bacterial isolates and about 140 bacterial isolates, between about 140 bacterial isolates and about 150 bacterial isolates, between about 150 bacterial isolates and about 160 bacterial isolates, between about 160 bacterial isolates and about 170 bacterial isolates, between about 170 bacterial isolates and about 180 bacterial isolates, between about 180 bacterial isolates and about 190 bacterial isolates, or between about 190 bacterial isolates and about 200 bacterial isolates.

[0013] In embodiments, the plurality of bacterial species belong to one or more bacterial genera of Acetatifactor, Agathobacter, Agathobaculum, Akkermansia, Alistipes, Anaerobutyricum, Anaerostipes, Anaerotignum, Anaerotmncus, Avimicrobium, Bacteroides, Bariatricus, Bamesiella, Bifidobacterium, Bilophila, Bittarella, Blautia, Butyricicoccus, Butyricimonas, Catenibacterium, Candidatus (UBA1417), Choladousia, Christensenella, Clostridium, Clostridiales (KLE1615), Coprobacillus, Coprobacter, Coprococcus, Copromonas, Dialister, Diplocloster, Dorea, Dysosmobacter, Eggerthella, Eisenbergiella, ER4, Eubacterium, Faecalibacillus, Faecalibacterium, Firmicutes (CAG), Fimivivens, Flavonifractor, Fusicatenibacter, Gemmiger, Harryflintia, Holdemanella, Hominisplanchenecus, Hungatella, Intestinimonas, Lachnoclostridium, Lachnospira (UBA3402), Lacrimispora, Ligilactobacillus, Longibaculum, Mediterraneibacter, Monoglobus, Muricomes, Odoribacter, Oliverpabstia, Parabacteroides, Paraprevotella, Peptostreptococcus, Phascolarctobacterium, Phocaeicola, Prevotella, Roseburia, Ruminococcus, Ruthenibacterium, Sarcina, Slackia, Sutterella, Thomasclavelia, Tractidigestivibacter, Turicibacter, and Wujia.

[0014] In embodiments, the plurality of bacterial species belong to one or more bacterial genera of Agathobacter, Agathobaculum, Akkermansia, Alistipes, Anaerobutyricum, Anaerostipes, Anaerotignum, Avimicrobium, Bacteroides, Bariatricus, Bamesiella, Bifidobacterium, Bilophila, Bittarella, Blautia_A, Butyricicoccus, Butyricimonas, CAG-317, CAG-41, Christensenella, Clostridium, Coprobacter, Coprococcus_A, Copromonas, Diplocloster, Dorea, Dorea_A, Dysosmobacter, Eisenbergiella, Eubacterium_G, Faecalibacillus, Faecalibacterium, Flavonifractor, Fusicatenibacter, Gemmiger, Harryflintia, Hungatella, Intestinimonas, KLE1615, Lachnoclostridium_B, Lachnospira, Mediterraneibacter, Monoglobus, Muricomes, Odoribacter, Oliverpabstia, Parabacteroides, Peptostreptococcus, Phocaeicola, Prevotella,DBl / 161604598.2 4Atorney Docket No.: 137085-5001 -PCRoseburia, Ruminococcus_B, Ruminococcus_D, Ruminococcus_E, Ruthenibacterium, Slackia_A, Turicibacter, UBA3402, and Wujia.

[0015] In embodiments, the plurality of bacterial species belong to one or more bacterial genera of Agathobacter, Akkermansia, Anaerobutyricum, Anaerostipes, Bacteroides, Clostridium, Faecalibacterium, Gemmiger, and Phocaeicola.

[0016] In embodiments, the plurality of bacterial species comprises no more than about 15 individual bacterial species per genera, no more than about 10 individual bacterial species per genera, no more than about 8 individual bacterial species per genera, no more than about 6 individual bacterial species per genera, no more than about 5 individual bacterial species per genera, no more than about 4 individual bacterial species per genera, no more than about 3 individual bacterial species per genera, no more than about 2 individual bacterial species per genera, or no more than a single individual bacterial species per genera.

[0017] In embodiments, the plurality of bacterial species comprises about or at least about 85 distinct bacterial genera, about or at least about 80 distinct bacterial genera, about or at least about 75 distinct bacterial genera, about or at least about 70 distinct bacterial genera, about or at least about 65 distinct bacterial genera, about or at least about 60 distinct bacterial genera, about or at least about 50 distinct bacterial genera, or about or at least about 40 distinct bacterial genera.

[0018] In embodiments, the plurality of bacterial species comprises at least about 7 isolates selected from at least about 5 species having about or at least about 96%, about or at least about 97%, about or at least about 98%, or about or at least about 99% sequence identity to the 16S rRNA sequence of bacterial species selected from Table 1 a. In embodiments, the plurality of bacterial species comprises at least about 12 isolates selected from at least about 8 species having about or at least about 96%, about or at least about 97%, about or at least about 98%, or about or at least about 99% sequence identity to the 16S rRNA sequence of bacterial species selected from Table 1c. In embodiments, the plurality of bacterial species comprises at least about 12 isolates selected from at least about 8 species having about or at least about 96%, about or at least about 97%, about or at least about 98%, or about or at least about 99% sequence identity to the 16S rRNA sequence of bacterial species selected from Table 1d. In embodiments, the plurality of bacterial species comprises at least about 12 isolates selected from at least about 8 species having about or at least about 96%, about or at least about 97%, about or at least about 98%, or about or at least about 99% sequence identity to the 16S rRNA sequence of bacterial species selected from Table 1e and / or Table 1f. In embodiments, at least about 40 isolates selected from at least about 20 species having about or atDBl / 161604598.2 5Atorney Docket No.: 137085-5001 -PC least about 96%, about or at least about 97%, about or at least about 98%, or about or at least about 99% sequence identity to the 16S rRNA sequence of bacterial species selected from Table 1 b.

[0019] In embodiments, the plurality of bacterial species comprises at least about 7 isolates selected from at least about 5 species, each having the 16S rRNA sequence of bacterial species selected from Table 1 a. In embodiments, the plurality of bacterial species comprises at least about 12 isolates selected from at least about 7 species, each having the 16S rRNA sequence of bacterial species selected from Table 1c. In embodiments, the plurality of bacterial species comprises at least about 12 isolates selected from at least about 8 species, each having the 16S rRNA sequence of bacterial species selected from Table 1 d. In embodiments, the plurality of bacterial species comprises at least about 12 isolates selected from at least about 8 species, each having the 16S rRNA sequence of bacterial species selected from Table 1e and / or Table 1f. In embodiments, the plurality of bacterial species comprises at least about 40 isolates selected from at least about 20 species, each having the 16S rRNA sequence of bacterial species selected from Table 1 b.

[0020] In embodiments, the plurality of bacterial species comprises about or at least about 8 isolates, about or at least about 9 isolates, about or at least about 10 isolates, about or at least about 11 isolates, about or at least about 12 isolates, about or at least about 13 isolates, about or at least about 14 isolates, about or at least about 15 isolates, about or at least about 17 isolates, about or at least about 18 isolates, about or at least about 19 isolates, about or at least about 20 isolates, or about or at least about 25 isolates, selected from about or at least about 6 species, about or at least about 7 species, about or at least about 8 species, about or at least about 9 species, about or at least about 10 species, about or at least about 11 species, about or at least about 12 species, about or at least about 13 species, about or at least about 14 species, about or at least about 15 species, or about or at least about 20 species, each having about or at least about 95%, about or at least about 96%, about or at least about 97%, about or at least about 98%, or about or at least about 99% sequence identity to a 16S rRNA sequence of a bacterial species selected from Table 1a.

[0021] In embodiments, the plurality of bacterial species comprises about or at least about 8 isolates, about or at least about 9 isolates, about or at least about 10 isolates, about or at least about 11 isolates, about or at least about 12 isolates, about or at least about 13 isolates, about or at least about 14 isolates, about or at least about 15 isolates, about or at least about 17 isolates, about or at least about 18 isolates, about or at least about 19 isolates, about or at least about 20 isolates, or about or at least about 25 isolates, selected from about or at least about 6 species, about or at least about 7 species, about or at least about 8DBl / 161604598.2 6Atorney Docket No.: 137085-5001 -PC species, about or at least about 9 species, about or at least about 10 species, about or at least about 11 species, about or at least about 12 species, about or at least about 13 species, about or at least about 14 species, about or at least about 15 species, or about or at least about 20 species selected from Table 1a.

[0022] In embodiments, the plurality of bacterial isolates and / or species selected from Table 1 a comprise one or more of Agathobacter rectalis, Akkermansia muciniphila_B, Anaerobutyricum soehngenii, Anaerostipes hadrus, Bacteroides thetaiotaomicron, Bacteroides uniformis, Clostridium _AP scindens, Faecalibacterium prausnitzii_D, Faecalibacterium prausnitziij, Phocaeicola vulgatus.

[0023] In embodiments, the plurality of bacterial species comprises about or at least about 13 isolates, about or at least about 14 isolates, about or at least about 15 isolates, about or at least about 16 isolates, about or at least about 17 isolates, about or at least about 18 isolates, about or at least about 19 isolates, about or at least about 20 isolates, about or at least about 21 isolates, about or at least about 22 isolates, about or at least about 23 isolates, about or at least about 24 isolates, about or at least about 25 isolates, about or at least about 30 isolates, or about or at least about 35 isolate, selected from about or at least about 11 species, about or at least about 12 species, about or at least about 13 species, about or at least about 14 species, about or at least about 15 species, about or at least about 16 species, about or at least about 17 species, about or at least about 18 species, about or at least about 19 species, about or at least about 20 species, or about or at least about 25 species, each having about or at least about 95%, about or at least about 96%, about or at least about 97%, about or at least about 98%, or about or at least about 99% sequence identity to a 16S rRNA sequence of a bacterial species selected from Table 1c.

[0024] In embodiments, the plurality of bacterial species comprises about or at least about 13 isolates, about or at least about 14 isolates, about or at least about 15 isolates, about or at least about 16 isolates, about or at least about 17 isolates, about or at least about 18 isolates, about or at least about 19 isolates, about or at least about 20 isolates, about or at least about 21 isolates, about or at least about 22 isolates, about or at least about 23 isolates, about or at least about 24 isolates, about or at least about 25 isolates, about or at least about 30 isolates, or about or at least about 35 isolate, selected from about or at least about 11 species, about or at least about 12 species, about or at least about 13 species, about or at least about 14 species, about or at least about 15 species, about or at least about 16 species, about or at least about 17 species, about or at least about 18 species, about or at least about 19 species, about or at least about 20 species, or about or at least about 25 species selected from Table 1c.DBl / 161604598.2 7Atorney Docket No.: 137085-5001 -PC

[0025] In embodiments, the plurality of bacterial isolates and / or species selected from Table 1c comprise one or more of Bilophila wadsworthia, Butyricimonas virosa, Clostridium cuniculi, Clostridium_Q fessum, Clostridium_Q symbiosum, Copromonas sp900066535, Dysosmobacter sp001916835, Dysosmobacter welbionis, Eisenbergiella sp900066775, ER4 sp900317525, Eubacterium_G sp000432355, Eubacterium_G ventriosum, Flavonifractor plautii, Intestinimonas butyriciproducens, Odoribacter splanchnicus, Wujia chipingensis.

[0026] In embodiments, the plurality of bacterial species comprises about or at least about 13 isolates, about or at least about 14 isolates, about or at least about 15 isolates, about or at least about 16 isolates, about or at least about 17 isolates, about or at least about 18 isolates, about or at least about 19 isolates, about or at least about 20 isolates, about or at least about 21 isolates, about or at least about 22 isolates, about or at least about 23 isolates, about or at least about 24 isolates, about or at least about 25 isolates, about or at least about 30 isolates, or about or at least about 35 isolates, selected from about or at least about 11 species, about or at least about 12 species, about or at least about 13 species, about or at least about 14 species, about or at least about 15 species, about or at least about 16 species, about or at least about 17 species, about or at least about 18 species, about or at least about 19 species, about or at least about 20 species, or about or at least about 25 species, each having about or at least about 95%, about or at least about 96%, about or at least about 97%, about or at least about 98%, or about or at least about 99% sequence identity to a 16S rRNA sequence of a bacterial species selected from Table 1 d.

[0027] In embodiments, the plurality of bacterial species comprises about or at least about 13 isolates, about or at least about 14 isolates, about or at least about 15 isolates, about or at least about 16 isolates, about or at least about 17 isolates, about or at least about 18 isolates, about or at least about 19 isolates, about or at least about 20 isolates, about or at least about 21 isolates, about or at least about 22 isolates, about or at least about 23 isolates, about or at least about 24 isolates, about or at least about 25 isolates, about or at least about 30 isolates, or about or at least about 35 isolates, selected from about or at least about 11 species, about or at least about 12 species, about or at least about 13 species, about or at least about 14 species, about or at least about 15 species, about or at least about 16 species, about or at least about 17 species, about or at least about 18 species, about or at least about 19 species, about or at least about 20 species, or about or at least about 25 species selected from Table 1d.

[0028] In embodiments, the plurality of bacterial isolates and / or species selected from Table 1 d comprise one or more of Alistipes montrealensis, Bacteroides cellulosilyticus, Bacteroides clarus,DBl / 161604598.2 8Atorney Docket No.: 137085-5001 -PCBacteroides intestinigallinarum, Blautia_A faecis, Blautia_A obeum, Blautia_A sp900066145, Blautia_A sp900066335, Blautia_A wexlerae, Blautia_A wexlerae_B, CAG-41 sp900066215, Clostridium_Q symbiosum, Coprococcus eutactus, Dysosmobacter welbionis, Eisenbergiella tayi, Flavonifractor plautii, Intestinimonas butyriciproducens, Mediterraneibacter faecis, Parabacteroides goldsteinii, Parabacteroides johnsonii, Parabacteroides merdae, Phascolarctobacterium sp900544795, Phocaeicola massiliensis, Roseburia inulinivorans, and Ruminococcus_B gnavus.

[0029] In embodiments, the plurality of bacterial species comprises about or at least about 13 isolates, about or at least about 14 isolates, about or at least about 15 isolates, about or at least about 16 isolates, about or at least about 17 isolates, about or at least about 18 isolates, about or at least about 19 isolates, about or at least about 20 isolates, about or at least about 21 isolates, about or at least about 22 isolates, about or at least about 23 isolates, about or at least about 24 isolates, about or at least about 25 isolates, about or at least about 30 isolates, or about or at least about 35 isolates, selected from about or at least about 11 species, about or at least about 12 species, about or at least about 13 species, about or at least about 14 species, about or at least about 15 species, about or at least about 16 species, about or at least about 17 species, about or at least about 18 species, about or at least about 19 species, about or at least about 20 species, or about or at least about 25 species, each having about or at least about 95%, about or at least about 96%, about or at least about 97%, about or at least about 98%, or about or at least about 99% sequence identity to a 16S rRNA sequence of a bacterial species selected from Table 1e and / or Table 1f.

[0030] In embodiments, the plurality of bacterial species comprises about or at least about 13 isolates, about or at least about 14 isolates, about or at least about 15 isolates, about or at least about 16 isolates, about or at least about 17 isolates, about or at least about 18 isolates, about or at least about 19 isolates, about or at least about 20 isolates, about or at least about 21 isolates, about or at least about 22 isolates, about or at least about 23 isolates, about or at least about 24 isolates, about or at least about 25 isolates, about or at least about 30 isolates, or about or at least about 35 isolates, selected from about or at least about 11 species, about or at least about 12 species, about or at least about 13 species, about or at least about 14 species, about or at least about 15 species, about or at least about 16 species, about or at least about 17 species, about or at least about 18 species, about or at least about 19 species, about or at least about 20 species, or about or at least about 25 species selected from Table 1e and / or Table 1f.

[0031] In embodiments, the plurality of bacterial isolates and / or species selected from Table 1e and / or Table 1f comprise one or more of Agathobaculum butyriciproducens, AHstipes communis, AnaerobutyricumDBl / 161604598.2 9Atorney Docket No.: 137085-5001 -PC hallii, Bariatricus comes, Bifidobacterium adolescentis, Bifidobacterium longum, CAG-317 sp000433215, Coprobacter fastidiosus, Coprococcus eutactus, Coprococcus_A catus, Dorea formicigenerans, Faecalibacterium longum, Faecalibacterium prausnitzii, Faecalibacterium prausnitzii_D, Gemmigerformicilis, Oliverpabstia intestinalis, Peptostreptococcus anaerobius, Roseburia hominis, Roseburia intestinalis, Roseburia inulinivorans, and Ruminococcus_E bromii_B.

[0032] In embodiments, the plurality of bacterial species comprises about or at least about 40 isolates, about or at least about 45 isolates, about or at least about 50 isolates, about or at least about 55 isolates, about or at least about 60 isolates, about or at least about 65 isolates, about or at least about 70 isolates, about or at least about 75 isolates, about or at least about 80 isolates, about or at least about 85 isolates, about or at least about 90 isolates, about or at least about 95 isolates, about or at least about 100 isolates, selected from about or at least about 30 species, about or at least about 35 species, about or at least about 40 species, about or at least about 45 species, about or at least about 50 species, about or at least about 55 species, about or at least about 60 species, about or at least about 65 species, about or at least about 70 species, about or at least about 75 species, about or at least about 80 species, or about or at least about 85 species, each species having about or at least about 95%, about or at least about 96%, about or at least about 97%, about or at least about 98%, or about or at least about 99% sequence identity to a 16S rRNA sequence of a bacterial species selected from Table 1 b.

[0033] In embodiments, the plurality of bacterial species comprises about or at least about 40 isolates, about or at least about 45 isolates, about or at least about 50 isolates, about or at least about 55 isolates, about or at least about 60 isolates, about or at least about 65 isolates, about or at least about 70 isolates, about or at least about 75 isolates, about or at least about 80 isolates, about or at least about 85 isolates, about or at least about 90 isolates, about or at least about 95 isolates, about or at least about 100 isolates, selected from about or at least about 30 species, about or at least about 35 species, about or at least about 40 species, about or at least about 45 species, about or at least about 50 species, about or at least about 55 species, about or at least about 60 species, about or at least about 65 species, about or at least about 70 species, about or at least about 75 species, about or at least about 80 species, or about or at least about 85 species selected from Table 1 b.

[0034] In embodiments, the plurality of bacterial isolates and / or species selected from Table 1 b comprise one or more of Acetatifactor sp., Agathobacter faecis, Alistipes finegoldii, Alistipes onderdonkii, Alistipes putredinis, Alistipes senegalensis, Alistipes shahii, Alistipes_A ihumii, Alistipes_A indistinctus,DBl / 161604598.2 10Atorney Docket No.: 137085-5001 -PCAnaerotignum faecicola, Avimicrobium caecorum, Bacteroides eggerthii, Bacteroides finegoldii, Bacteroides fragilis, Bacteroides luhongzhouii, Bacteroides ovatus, Bacteroides stercoris, Bacteroides xylanisolvens, Barnesiella intestinihominis, Bifidobacterium bifidum, Bifidobacteriu sp., Bittarella massiliensis, Blautia_A massiliensis, Blautia_A sp., Blautia_A sp900066505, Butyricicoccus sp900604335, Butyricimonas sp., Catenibacterium sp000437715, Choladousia sp902363665, Christensenella minuta, Clostridium_A leptum, Clostridium_AP sp., Dialister invisus, Diplocloster agilis, Dorea_A sp., Faecalibacillus intestinalis, Faecalibacterium duncaniae, Fusicatenibacter saccharivorans, Harryflintia acetispora, Holdemanella sp., Intestinimonas massiliensis, KLE1615 sp900066985, Lachnoclostridium_B sp900066555, Lachnospira eligens, Lachnospira eligens_A, Lachnospira rogosae, Lachnospira sp000437735, Mediterraneibacter lactaris, Monoglobus pectinilyticus, Muricomes sp000509105, Parabacteroides distasonis, Paraprevotella xylaniphila, Phocaeicola dorei, Prevotella copri_B, Prevotella rara, Ruminococcus_D bicirculans, Ruminococcus_E sp003526955, Ruthenibacterium lactatiformans, Slackia_A isoflavoniconvertens, Tractidigestivibacter sp., Turicibacter sanguinis, UBA3402 sp003478355.

[0035] In embodiments, each bacterial species of the plurality of bacterial species is selected from Table 1 a, Table 1 b, Table 1c, Table 1 d, Table 1e, Table 1f, Table 1g, Table 1 h, Table 1 i, Table 3, Table 5, and / or Table 7; or the plurality of bacterial species is a combination selected from Table 8; or the plurality of bacterial species is a combination selected from Table 12.

[0036] In embodiments, about or at least about 20% of the total bacterial species, about or at least about 25% of the total bacterial species, about or at least about 30% of the total bacterial species, about or at least about 35% of the total bacterial species, about or at least about 40% of the total bacterial species, about or at least about 45% of the total bacterial species, about or at least about 50% of the total bacterial species, about or at least about 55% of the total bacterial species, about or at least about 60% of the total bacterial species, about or at least about 65% of the total bacterial species, about or at least about 70% of the total bacterial species, at least 75% of the total bacterial species, about or at least about 80% of the total bacterial species, at least 85% of the total bacterial species, about or at least about 90% of the total bacterial species, or about or at least about 95% of the total bacterial species of the plurality of bacterial species comprises a butyrate synthesis pathway and / or encodes at least one enzyme suitable for synthesizing butyrate. In embodiments, this equates to about or at least about 25 of the total bacterial species, about or at least about 30 of the total bacterial species, about or at least about 35 of the total bacterial species, about or at least about 40 of the total bacterial species, about or at least about 45 of the total bacterial species, about or at least about 50 of the total bacterial species, about or at least about 55 of the total bacterial species,DBl / 161604598.2 11Atorney Docket No.: 137085-5001 -PC about or at least about 60 of the total bacterial species, about or at least about 65 of the total bacterial species, about or at least about 70 of the total bacterial species, about or at least about 75 of the total bacterial species, about or at least about 80 of the total bacterial species, about or at least about 85 of the total bacterial species, about or at least about 90 of the total bacterial species, about or at least about 95 of the total bacterial species, or about or at least about 100 of the total bacterial species of the plurality of bacterial species comprises a butyrate synthesis pathway and / or encodes at least one enzyme suitable for synthesizing butyrate.

[0037] In embodiments, bacterial consortia herein are designed based on the capacity to produce butyrate, as a whole, using one or more butyrate synthesis pathways. In embodiments, one or more bacterial species / isolates comprises an entire butyrate synthesis pathway. In embodiments, one or more butyrate synthesis pathways are distributed among the plurality of bacterial species / isolates.

[0038] In embodiments, the butyrate synthesis pathway comprises one or more pathways selected from a glutarate pathway, acetyl-CoA pathway, lysine pathway, and 4-aminobutyrate / succinate pathway, optionally wherein the butyrate synthesis pathway comprises each of a glutarate pathway, acetyl-CoA pathway, lysine pathway, and 4-aminobutyrate / succinate pathway. In embodiments, the glutarate pathway comprises one or more genes encoding one or more enzymes selected from 2-hydroxyglutarate dehydrogenase (L2HgdH), glutaconate CoA transferase (comprising a, subunits) (Get), 2-hydroxy-glutaryl- CoA dehydrogenase (comprising a, p, y subunits) (HgCoAd), glutaconyl-CoA decarboxylase (comprising a, P subunits) (Gcd), butyryl-CoA dehydrogenase (comprising electron transfer protein a, subunits) (Bcd-(aP)), and an enzyme having equivalent functionality thereof. In embodiments, the acetyl-CoA pathway comprises one or more genes encoding one or more enzymes selected from thiolase (Thl), p-hydroxybutyryl-CoA dehydrogenase (hbd), crotonase (Cro), butyryl-CoA dehydrogenase (including electron transfer protein a, p subunits) (Bcd-(aP)), butyryl-CoA: acetate CoA transferase (But), phosphate butyryltransferase (Ptb), butyrate kinase (Buk), and an enzyme having equivalent functionality thereof. In embodiments, the lysine pathway comprises one or more genes encoding one or more enzymes selected from lysine-2,3- aminomutase (KamA), p-lysine-5,6-aminomutase (comprising a, p subunits) (KamD,E), 3,5- diaminohexanoate dehydrogenase (Kdd), 3-keto-5-aminohexanoate cleavage enzyme (Kce), 3- aminobutyryl-CoA ammonia lyase (Kai), butyryl-CoA dehydrogenase (including electron transfer protein a, p subunits) (Bcd-(aP)), butyryl-CoA:acetoacetate CoA transferase (comprising a, p subunits) (Ato), and an enzyme having equivalent functionality thereof. In embodiments, the 4-aminobutyrate / succinate pathway comprises one or more genes encoding one or more enzymes selected from 4-hydroxybutyrate dehydrogenase (AbfH), 4-hydroxybutyryl-CoA dehydratase (AbfD), vinylacetyl-CoA 3,2-isomerase (sameDBl / 161604598.2 12Atorney Docket No.: 137085-5001 -PC protein as AbfD), butyryl-CoA:4-hydroxybutyrate CoA transferase (4Hbt), and an enzyme having equivalent functionality thereof. In embodiments, the butyrate synthesis pathway comprises having one or more genes encoding a butyryl-CoA dehydrogenase (Bed) or an enzyme having equivalent functionality thereof.

[0039] In embodiments, the plurality of bacterial species substantially produces butyrate in a gastrointestinal tract.

[0040] In embodiments, about or at least about 20% of the total bacterial species, about or at least about 25% of the total bacterial species, about or at least about 30% of the total bacterial species, about or at least about 35% of the total bacterial species, about or at least about 40% of the total bacterial species, about or at least about 45% of the total bacterial species, about or at least about 50% of the total bacterial species, about or at least about 55% of the total bacterial species, about or at least about 60% of the total bacterial species, about or at least about 65% of the total bacterial species, about or at least about 70% of the total bacterial species, about or at least about 75% of the total bacterial species, about or at least about 80% of the total bacterial species, about or at least about 85% of the total bacterial species, about or at least about 90% of the total bacterial species, or about or at least about 95% of the total bacterial species of the plurality of bacterial species comprises a propionate synthesis pathway and / or encodes at least one enzyme suitable for synthesizing propionate.

[0041] In embodiments, about or at least about 25 of the total bacterial species, about or at least about 30 of the total bacterial species, about or at least about 35 of the total bacterial species, about or at least about 40 of the total bacterial species, about or at least about 45 of the total bacterial species, about or at least about 50 of the total bacterial species, about or at least about 55 of the total bacterial species, about or at least about 60 of the total bacterial species, about or at least about 65 of the total bacterial species, about or at least about 70 of the total bacterial species, about or at least about 75 of the total bacterial species, about or at least about 80 of the total bacterial species, about or at least about 85 of the total bacterial species, about or at least about 90 of the total bacterial species, about or at least about 95 of the total bacterial species, or about or at least about 100 of the total bacterial species of the plurality of bacterial species comprises a propionate synthesis pathway and / or encodes at least one enzyme suitable for synthesizing propionate.

[0042] In embodiments, bacterial consortia herein are designed based on the capacity to produce propionate, as a whole, using one or more propionate synthesis pathways. In embodiments, one or more bacterial species / isolates comprises an entire propionate synthesis pathway. In embodiments, one or more propionate synthesis pathways are distributed among the plurality of bacterial species / isolates.DBl / 161604598.2 13Atorney Docket No.: 137085-5001 -PC

[0043] In embodiments, the propionate synthesis pathway comprises one or more pathways selected from a succinate pathway (mmdA gene cluster), acrylate pathway (LcdA gene cluster), and propanediol pathway (PduP gene cluster), optionally wherein the propionate synthesis pathway comprises each of a succinate pathway, acrylate pathway, and propanediol pathway.

[0044] In embodiments, the plurality of bacterial species substantially produces propionate in a gastrointestinal tract.

[0045] In embodiments, about or at least about 1 % of the total bacterial species, about or at least about 2% of the total bacterial species, about or at least about 3% of the total bacterial species, about or at least about 4% of the total bacterial species, about or at least about 5% of the total bacterial species, about or at least about 6% of the total bacterial species, about or at least about 7% of the total bacterial species, about or at least about 8% of the total bacterial species, about or at least about 9% of the total bacterial species, about or at least about 10% of the total bacterial species, about or at least about 15% of the total bacterial species, or about or at least about 20% of the total bacterial species comprises an IAA synthesis pathway and / or encodes at least one enzyme suitable for synthesizing IAA.

[0046] In embodiments, about or at least about 1 species / isolate produces IAA, about or at least about 2 species / isolates produces IAA, about or at least about 3 species / isolates produces IAA, about or at least about 4 species / isolates produces IAA, about or at least about 5 species / isolates produces IAA, about or at least about 10 species / isolates produces IAA, about or at least about 15 species / isolates produces IAA, or about or at least about 20 species / isolates produces IAA.

[0047] In embodiments, bacterial consortia herein are designed based on the capacity to produce IAA, as a whole, using one or more IAA synthesis pathways. In embodiments, one or more bacterial species / isolates comprises an entire IAA synthesis pathway. In embodiments, one or more IAA synthesis pathways are distributed among the plurality of bacterial species / isolates.

[0048] In embodiments, the IAA synthesis pathway comprises one or more pathways selected from a indole-3-acetonitrile pathway, indole-3-acetamide pathway, indole-3-pyruvate pathway, and tryptamine pathway, optionally wherein the IAA synthesis pathway comprises each of a indole-3-acetonitrile pathway, indole-3-acetamide pathway, indole-3-pyruvate pathway, and tryptamine pathway.

[0049] In embodiments, the plurality of bacterial species substantially produces IAA in a gastrointestinal tract.DBl / 161604598.2 14Atorney Docket No.: 137085-5001 -PC

[0050] In embodiments, about or at least about 1 % of the total bacterial species, about or at least about 2% of the total bacterial species, about or at least about 3% of the total bacterial species, about or at least about 4% of the total bacterial species, about or at least about 5% of the total bacterial species, about or at least about 6% of the total bacterial species, about or at least about 7% of the total bacterial species, about or at least about 8% of the total bacterial species, about or at least about 9% of the total bacterial species, about or at least about 10% of the total bacterial species, about or at least about 15% of the total bacterial species, or about or at least about 20% of the total bacterial species comprises an IPA synthesis pathway and / or encodes at least one enzyme suitable for synthesizing IPA.

[0051] In embodiments, about or at least about 1 species / isolate produces IPA, about or at least about 2 species / isolates produces IPA, about or at least about 3 species / isolates produces IPA, about or at least about 4 species / isolates produces IPA, about or at least about 5 species / isolates produces IPA, about or at least about 10 species / isolates produces IPA, about or at least about 15 species / isolates produces IPA, or about or at least about 20 species / isolates produces IPA.

[0052] In embodiments, bacterial consortia herein are designed based on the capacity to produce IPA using one or more IPA synthesis pathways. In embodiments, one or more bacterial species / isolates comprises an entire IPA synthesis pathway. In embodiments, one or more IPA synthesis pathways are distributed among the plurality of bacterial species / isolates.

[0053] In embodiments, the IPA synthesis pathway comprises one or more enzymes selected from aromatic amino acid aminotransferase (ATT), indolelactate dehydrogenase (ILDH), indolelactate dehydratase (ILD), and acyl-CoA dehydrogenase (ACD), optionally wherein the IPA synthesis pathway comprises each of an aromatic amino acid aminotransferase (ATT), indolelactate dehydrogenase (ILDH), indolelactate dehydratase (ILD), and acyl-CoA dehydrogenase (ACD).

[0054] In embodiments, the plurality of bacterial species substantially produces IPA in a gastrointestinal tract.

[0055] In embodiments, about or at least about 1 % of the total bacterial species, about or at least about 2% of the total bacterial species, about or at least about 3% of the total bacterial species, about or at least about 4% of the total bacterial species, about or at least about 5% of the total bacterial species, about or at least about 6% of the total bacterial species, about or at least about 7% of the total bacterial species, about or at least about 8% of the total bacterial species, about or at least about 9% of the total bacterial species, about or at least about 10% of the total bacterial species, about or at least about 15% of the total bacterialDBl / 161604598.2 15Atorney Docket No.: 137085-5001 -PC species, or about or at least about 20% of the total bacterial species comprises a synthesis pathway for one or more SCFAs and / or encodes at least one enzyme suitable for synthesizing one or more SCFAs.

[0056] In embodiments, about or at least about 1 species / isolate from the consortium produces one or more SCFAs, about or at least about 2 species / isolates produces one or more SCFAs, about or at least about 3 species / isolates produces one or more SCFAs, about or at least about 4 species / isolates produces one or more SCFAs, about or at least about 5 species / isolates produces one or more SCFAs, about or at least about 10 species / isolates produces one or more SCFAs, about or at least about 15 species / isolates produces one or more SCFAs, or about or at least about 20 species / isolates produces one or more SCFAs.

[0057] In embodiments, bacterial consortia herein are designed based on the capacity to produce SCFAs, as a whole, using one or more SCFA synthesis pathways. In embodiments, one or more bacterial species / isolates comprises an entire SCFA synthesis pathway. In embodiments, one or more SCFA synthesis pathways are distributed among the plurality of bacterial species / isolates.

[0058] In embodiments, the plurality of bacterial species comprises the ability to substantially produce short chain fatty acids (SCFAs) in a gastrointestinal tract, optionally selected from one or more of valerate and branched chain SCFAs.

[0059] In embodiments, about or at least about 1 % of the total bacterial species, about or at least about 2% of the total bacterial species, about or at least about 3% of the total bacterial species, about or at least about 4% of the total bacterial species, about or at least about 5% of the total bacterial species, about or at least about 6% of the total bacterial species, about or at least about 7% of the total bacterial species, about or at least about 8% of the total bacterial species, about or at least about 9% of the total bacterial species, about or at least about 10% of the total bacterial species, about or at least about 15% of the total bacterial species, or about or at least about 20% of the total bacterial species comprises a synthesis pathway for bile acid derivatives (BAs) and / or encodes at least one enzyme suitable for synthesizing bile acid derivatives (BAs).

[0060] In embodiments, about or at least about 1 species / isolate produces one or more bile acid derivatives (BAs), about or at least about 2 species / isolates produces one or more bile acid derivatives (BAs), about or at least about 3 species / isolates produces one or more bile acid derivatives (BAs), about or at least about 4 species / isolates produces one or more bile acid derivatives (BAs), about or at least about 5 species / isolates produces one or more bile acid derivatives (BAs), about or at least about 10 species / isolates produces one or more bile acid derivatives (BAs), about or at least about 15 species / isolates produces oneDBl / 161604598.2 16Atorney Docket No.: 137085-5001 -PC or more bile acid derivatives (BAs), or about or at least about 20 species / isolates produces one or more bile acid derivatives (BAs).

[0061] In embodiments, bacterial consortia herein are designed based on the capacity to produce BAs using one or more BA synthesis pathways. In embodiments, one or more bacterial species / isolates comprises an entire BA synthesis pathway. In embodiments, one or more BA synthesis pathways are distributed among the plurality of bacterial species / isolates.

[0062] In embodiments, the plurality of bacterial species substantially produces one or more bile acid derivatives (BAs) in a gastrointestinal tract, optionally comprising one or more of isoalloLCA, deconjugated cBA, secondary bile acid (2BA), tertiary bile acid (3BA), 7-oxoLCA, 7-oxoDCA, and microbially conjugated bile acid (MCBA).

[0063] In embodiments, about or at least about 1 % of the total bacterial species, about or at least about 2% of the total bacterial species, about or at least about 3% of the total bacterial species, about or at least about 4% of the total bacterial species, about or at least about 5% of the total bacterial species, about or at least about 6% of the total bacterial species, about or at least about 7% of the total bacterial species, about or at least about 8% of the total bacterial species, about or at least about 9% of the total bacterial species, about or at least about 10% of the total bacterial species, about or at least about 15% of the total bacterial species, or about or at least about 20% of the total bacterial species comprises an isoalloLCA synthesis pathway and / or encodes at least one enzyme suitable for synthesizing isoalloLCA.

[0064] In embodiments, about or at least about 1 species / isolate produces isoalloLCA, about or at least about 2 species / isolates produces isoalloLCA, about or at least about 3 species / isolates produces isoalloLCA, about or at least about 4 species / isolates produces isoalloLCA, about or at least about 5 species / isolates produces isoalloLCA, about or at least about 10 species / isolates produces isoalloLCA, about or at least about 15 species / isolates produces isoalloLCA, or about or at least about 20 species / isolates isoalloLCA.

[0065] In embodiments, bacterial consortia herein are designed based on the capacity to produce isoalloLCA, as a whole, using one or more isoalloLCA synthesis pathways. In embodiments, one or more bacterial species / isolates comprises an entire isoalloLCA synthesis pathway. In embodiments, one or more isoalloLCA synthesis pathways are distributed among the plurality of bacterial species / isolates.DBl / 161604598.217Atorney Docket No.: 137085-5001 -PC

[0066] In embodiments, the isoallolithocholic acid (isoalloLCA) synthesis pathway comprises one or more pathways selected from a chenodeoxycholic acid (CDCA) to isoalloLCA pathway and a 3-oxoLCA to isoalloLCA pathway.

[0067] In embodiments, the chenodeoxycholic acid (CDCA) to isoalloLCA pathway comprises having one or more genes encoding one or more of 7a-Hydroxysteroid dehydrogenase, 7p-hydroxysteroid dehydrogenase, 3a-hydroxysteroid dehydrogenase, and an enzyme having equivalent functionality thereof.

[0068] In embodiments, the 3-oxoLCA to isoalloLCA pathway comprises having one or more genes encoding one or more of 5|3-reductase, 5a-reductase, 3 -HSDH, and an enzyme having equivalent functionality thereof.

[0069] In embodiments, the plurality of bacterial species substantially produces isoalloLCA in a gastrointestinal tract.

[0070] In embodiments, bacterial consortia herein are designed based on the capacity to produce one or more bacterial metabolites, as a whole, using one or more bacterial metabolite synthesis pathways. In embodiments, one or more bacterial species / isolates comprises an entire bacterial metabolite synthesis pathway. In embodiments, one or more bacterial metabolite synthesis pathways are distributed among the plurality of bacterial species / isolates.

[0071] In embodiments, the plurality of bacterial species comprises the ability to substantially produce one or more bacterial metabolites selected from one or more of cholic acid (CA), threonine-CA, phenylalanine-CA, tyrosine-CA, deoxycholic acid (DCA), glutamic acid-DCA, chenodeoxycholic acid (CDCA), and glutamic acid-CDCA in a gastrointestinal tract.

[0072] In embodiments, the plurality of bacterial species comprises the ability to synthesize at least two bacterial metabolites selected from indole-3-acetic acid (IAA), indole-3-propionic acid (IPA), and bile acid derivatives (BAs) comprising one or more of isoallolithocholic acid (isoalloLCA), deconjugated bile acid (deBA), secondary bile acid (2BA), tertiary bile acid (3BA), 7-oxoLCA, 7-oxoDCA, and microbially conjugated bile acid (MCBA). In embodiments, the plurality of bacterial species is able to synthesize each of IAA, IPA, and one or more BAs.

[0073] In embodiments, the plurality of bacterial species is capable of substantially growing in a gastrointestinal tract, optionally a human gastrointestinal tract.DBl / 161604598.2 18Atorney Docket No.: 137085-5001 -PC

[0074] In embodiments, the plurality of bacterial species (e.g., community-level phenotype) comprises at least 1 characteristic, at least 2 characteristics, at least 3 characteristics, at least 4 characteristics, at least 5 characteristics, at least 6 characteristics, at least 7 characteristics, or all 8 characteristics of the following (a-h):

[0075] (a) ability to substantially decrease one or more metabolites,

[0076] (b) susceptibility to at least 3 antibiotics selected from different antibiotic classes,

[0077] (c) ability to substantially activate one or more endogenous human receptors comprising one or more G protein-coupled receptor (GPCRs) and / or toll-like receptor (TLRs),

[0078] (d) ability to substantially activate or expand one or more immune cells,

[0079] (e) ability to substantially suppress or reduce one or more immune cells,

[0080] (f) ability to re-activate exhausted T cells to a substantially healthy state,

[0081] (g) ability to substantially enhance endogenous immune cell-mediated killing of cancer cells, and

[0082] (h) ability to restore human epithelial barrier function to a substantially healthy state.

[0083] In embodiments, the one or more metabolites comprises phenyl-sulfates and indoxyls, and wherein the reduction is relative to a concentration present in a human gastrointestinal tract lacking one or more of the plurality of bacterial species.

[0084] In embodiments, the different antibiotic classes comprise one or more antibacterial antibiotic classes, optionally selected from bacteriostatic and bactericidal molecules. In embodiments, the one or more antibacterial antibiotic classes comprise aminoglycosides, ansamycins, beta-lactams, carbapenems, cephalosporins, cyclic lipopeptides, fluoroquinolones, glycopeptides, glycylcyclines, lincosamides, macrolides, nitroimidazoles, oxazolidinones, sulfonamides, and / or tetracyclines. In embodiments, the at least 3 antibiotics comprise one or more of amikacin, amoxicillin, azithromycin, cefazolin, cefmetazole, cefotetan, cefoxitin, cefprozil, cefuroxime, cilastatin, ciprofloxacin, clarithromycin, clindamycin, daptomycin, doxycycline, ertapenem, erythromycin, gentamicin, imipenem, levofloxacin, linezolid, meropenem, metronidazole, minocycline, moxifloxacin, penicillin, relebactam, rifampicin, sulfamethoxazole, tebipenem, tigecycline, tobramycin, trimethoprim-sulfamethoxazole, vaborbactam, vancomycin, and analogues and derivatives thereof.DBl / 161604598.2 19Atorney Docket No.: 137085-5001 -PC

[0085] In embodiments, the one or more G protein-coupled receptors (GPCRs) comprises one or more of G protein-coupled receptor 35 (GPR35), G protein-coupled receptor 41 (GPR41), G protein-coupled receptor 43 (GPR43), G protein-coupled receptor 109A (GPR109A), G protein-coupled receptor 119 (GPR119), and G protein-coupled receptor 132 (GPR132).

[0086] In embodiments, the one or more toll-like receptors (TLRs) comprise one or more of toll-like receptor 1 (TLR1), TLR2, TLR5, TLR6, and TLR9.

[0087] In embodiments, the one or more endogenous human receptors comprises one or more of sphingosine-1 -phosphate receptor 4 (S1 PR4), prostaglandin E receptor 4 (PTGER4), prostaglandin I2 receptor (PTGIR), calcium sensor receptor (CasR), peptide transporter 1 (PEPT1), pregnane X receptor (PXR), farnesoid X receptor (FXR), Takeda G protein-receptor-5 (TGR5), aryl hydrocarbon receptor (AhR), and 5-hydroxytryptamine receptors (5-HT3R and 5-HT4R).

[0088] In embodiments, the one or more immune cells are selected from CD4+ T cells, CD8+ T cells, and Natural Killer (NK) cells. In embodiments, the ability to substantially activate or expand one or more immune cells is measured by one or more of activation of CD4+T cells, CD8+ T cells, NK cells, and effector cytokine production (interferon gamma (IFN-y), interleukin 2 (IL-2), interleukin 10 (IL-10), granzyme B (GrB), tumor necrosis factor alpha (TNF-a)).

[0089] In embodiments, the ability to substantially suppress or reduce one or more immune cells comprises immune cells selected from myeloid-derived suppressor cells (MDSCs) and regulatory T cells (Tregs). In embodiments, MDSC and / or Tregsuppression is measured by arginase expression and / or activity.

[0090] In embodiments, the ability to re-activate exhausted T cells to a substantially healthy state is measured by one or more of secretion of interferon gamma (IFN-y), interleukin 2 (IL-2), interleukin 10 (IL- 10), granzyme B (GrB), tumor necrosis factor alpha (TNF-o), and / or granzyme; cytotoxicity; and cell surface expression of one or more of signaling lymphocyte activation molecule 6 (SLAMF6), T cell receptor (TCR), programmed cell death protein 1 (PD-1), cytotoxic T-lymphocyte associated protein 4 (CTLA-4), lymphocyte activation gene-3 (LAG-3, CD223), and T-cell immunoglobulin and mucin-domain containing-3 (TIM-3).

[0091] In embodiments, the ability to substantially enhance endogenous immune cell-mediated killing of cancer cells is measured by one or more of cancer cell death, cell viability, proliferation, growth inhibition, growth rate, cytotoxicity, cell migration, oxidative stress, and anchorage-independent growth (AIG).DBl / 161604598.2 20Atorney Docket No.: 137085-5001 -PC

[0092] In embodiments, the epithelial barrier function comprises gut epithelial barrier, and wherein restoration is measured by one or more of expression and distribution of tight junction proteins, epithelial surface area and / or presence of intestinal villi, mucosal permeability, paracellular permeability, transcellular uptake, electrophysiological parameters (e.g., transepithelial electrical resistance (TEER)), western blotting, mRNA / protein expression, PCR, presence of biomarkers, flow cytometry, immunohistochemistry, fluorescence activated cell sorting (FACS), and enzyme-linked immunosorbent assay (ELISA).

[0093] In embodiments, the plurality of bacterial species are suitable for lyophilization and / or cryopreservation, optionally without a substantial loss in lyorevival and / or cryorevival over a period of about or at least about 1 week, about or at least about 2 weeks, about or at least about 3 weeks, about or at least about 1 months, about or at least about 2 months, about or at least about 4 months, about or at least about 6 months, or about or at least about 1 year.

[0094] In embodiments, the lyorevival and / or cryorevival of the plurality of bacterial species is as measured by fractional viability in liquid culture and / or on agar, is about or at least about 1 %, about or at least about 5%, about or at least about 10%, about or at least about 15%, about or at least about 20%, about or at least about 30%, about or at least about 40%, about or at least about 50%, about or at least about 60%, about or at least about 70%, about or at least about 80%, about or at least about 90%, or about or at least about 99%.

[0095] In embodiments, the composition comprises one or more pharmaceutically acceptable excipients or carriers. In embodiments, the plurality of bacterial species are lyophilized and formulated as a powder, tablet, capsule, or sachet, optionally as a powder encapsulated within a capsule. In embodiments, the composition is suitable for oral administration.

[0096] In embodiments, described herein is a composition comprising at least 50 bacterial species and / or isolates listed in column 3a of Table 3, optionally each of the bacterial species and / or isolates listed in column 3a of Table 3, at least 50 bacterial species and / or isolates listed in column 3b of Table 3, optionally each of the bacterial species and / or isolates listed in column 3b of Table 3, at least 50 bacterial species and / or isolates listed in column 3c of Table 3, optionally each of the bacterial species and / or isolates listed in column 3c of Table 3, or at least 50 bacterial species and / or isolates listed in column 3d of Table 3, optionally each of the bacterial species and / or isolates listed in column 3d of Table 3. In embodiments, the bacterial species / isolates are lyophilized and / or encapsulated.DBl / 161604598.2 21Atorney Docket No.: 137085-5001 -PC

[0097] In embodiments, described herein is a composition comprising at least 50 bacterial species and / or isolates listed in column 8a of Table 8, optionally each of the bacterial species and / or isolates listed in column 8a of Table 8, at least 50 bacterial species and / or isolates listed in column 8b of Table 8, optionally each of the bacterial species and / or isolates listed in column 8b of Table 8, at least 50 bacterial species and / or isolates listed in column 8c of Table 8, optionally each of the bacterial species and / or isolates listed in column 8c of Table 8, or at least 50 bacterial species and / or isolates listed in column 8d of Table 8, each of comprising the bacterial species and / or isolates listed in column 8d of Table 8. In embodiments, the bacterial species / isolates are lyophilized and / or encapsulated.

[0098] In embodiments, the composition comprises an isolated plurality of bacterial species, the plurality of bacterial species comprising the bacterial species and / or isolates listed in column 3a of Table 3; the bacterial species and / or isolates listed in column 3b of Table 3; the bacterial species and / or isolates listed in column 3c of Table 3; the bacterial species and / or isolates listed in column 3d of Table 3; the bacterial species and / or isolates listed in column 8a of Table 8; the bacterial species and / or isolates listed in column 8b of Table 8; the bacterial species and / or isolates listed in column 8c of Table 8; or the bacterial species and / or isolates listed in column 8d of Tabel 8.

[0099] In aspects, described herein are methods of establishing a healthy microbiome and / or treating a disease in a subject in need thereof comprising administering a composition of a plurality of bacterial species, e.g., as described herein. In aspects, described herein are methods of treating cancer.

[0100] In embodiments, the subject is human, and wherein the healthy microbiome is established in at least a portion of the gastrointestinal tract. In embodiments, the subject has, is suspected of having, has been diagnosed with, or is receiving treatment for dysbiosis. In embodiments, the subject has, is suspected of having, has been diagnosed with, or is receiving treatment for one or more types of cancer.

[0101] In embodiments, the disease is cancer. In embodiments, the cancer is or comprises one or more of a carcinoma, sarcoma, myeloma, leukemia, lymphoma, mixed type cancer, and metastatic cancer. In embodiments, the cancer is selected from one or more of acute biphenotypic leukemia, acute eosinophilic leukemia, acute lymphoblastic leukemia, acute lymphocytic leukemia, acute myeloid dendritic cell leukemia, acute myeloid leukemia, adenocarcinoma of the lung, adrenal gland tumors, adrenocortical carcinoma, AIDS- related cancers, AIDS-related lymphoma, alveolar soft part and cardiac sarcoma, amyloidosis, anal cancer, anaplastic large cell lymphoma, angioimmunoblastic T-cell lymphoma, appendix cancer, astrocytoma, ataxiatelangiectasia, attenuated familial adenomatous polyposis, b-cell prolymphocytic leukemia, basal cellDBl / 161604598.2 22Atorney Docket No.: 137085-5001 -PC carcinoma, Beckwith-Wiedemann syndrome, bile duct cancer, Birt-Hogg-Dube syndrome, bladder cancer, bone cancer, brain and nervous system cancer, brain stem glioma, brainstem glioma, brain tumors, breast cancer, bronchial adenomas / carcinoids, Burkitt's lymphoma, carcinoid tumor, carcinoid tumors, Carney complex, central nervous system tumors, cerebellar astrocytoma, cerebral astrocytoma, cervical cancer, childhood desmoplastic ganglioglioma, cholangiocarcinoma, chondrosarcoma, chronic lymphocytic leukemia, chronic myelogenous leukemia, chronic myeloid leukemia, chronic T-cell lymphocytic leukemia, colon cancer, colorectal cancer, Cowden syndrome, craniopharyngioma, cutaneous T-cell lymphoma, dermatofibrosarcoma protuberans, desmoplastic small round cell tumor, diffuse gastric cancer, diffuse large b-cell lymphoma, endocrine system cancer, endocrine tumors, endometrial cancer, eosinophilic leukemia, ependymoma, epithelioid hemangioendothelioma (EHE), esophageal cancer, Ewing sarcoma, extragonadal germ cell tumor, extrahepatic bile duct cancer, eye cancer, eyelid cancer, fallopian tube cancer, familial adenomatous polyposis, familial malignant melanoma, familial clear cell renal cell carcinoma (RCC), follicular lymphoma, gallbladder cancer, Gardner syndrome, gastric (stomach) cancer, gastrointestinal cancer, gastrointestinal carcinoid tumor, gastrointestinal stromal tumor, gastrointestinal stromal tumor (GIST), genitourinary and gynecologic cancer, germ cell tumor, gestational trophoblastic disease, gestational trophoblastic tumor, glioblastoma, glioma, hairy cell leukemia, head and neck cancer, hematopoietic cancer, hepatocellular cancer, hepatosplenic T-cell lymphoma, Hodgkin's lymphoma, hypopharyngeal cancer, inflammatory breast cancer, intravascular large b-cell lymphoma, invasive cribriform carcinoma, invasive lobular carcinoma, islet cell carcinoma (endocrine pancreas), islet cell tumors, juvenile polyposis syndrome, Kaposi Sarcoma, keratoacanthoma, kidney cancer, lacrimal gland tumor, large granular lymphocytic leukemia, laryngeal and hypopharyngeal cancer, leiomyomatosis and renal cell cancer, leiomyosarcoma, Li- Fraumeni syndrome (LFS), liposarcoma, liver cancer, lung cancer, lymphomas of primary cutaneous origin, lymphomatoid granulomatosis, lymphoplasmacytic lymphoma, lynch syndrome, malignant fibrous histiocytoma of bone, mantle cell lymphoma, marginal zone b-cell lymphoma, mast cell leukemia, mastocytosis, mediastinal large b cell lymphoma, medullary carcinoma, medulloblastoma, melanoma, meningioma, Merkel cell carcinoma, mesothelioma, mixed polyposis syndrome, mucosa-associated lymphoid tissue lymphoma, Muir-Torre syndrome (MTS), multiple endocrine neoplasia syndrome, multiple endocrine neoplasia type 1 , multiple endocrine neoplasia type 2, multiple myeloma, multiple myeloma / plasma cell neoplasm, mycosis fungoides, myelodysplastic syndromes, MYH-associated polyposis, myxosarcoma, nasal cavity and paranasal sinus cancer, nephroblastoma, nasopharyngeal cancer, nasopharyngeal carcinoma, neuroblastoma, neuroendocrine tumors, neurofibromatosis type 1 , neurofibromatosis type 2,DBl / 161604598.2 23Atorney Docket No.: 137085-5001 -PC nevoid basal cell carcinoma syndrome, nodal marginal zone b cell lymphoma, non-Hodgkin lymphoma, nonsmall cell lung cancer (NSCLC), non-small cell lung carcinoma, oligodendroglioma, optic nerve glioma, oral and / or oropharyngeal cancer, osteosarcoma, ovarian cancer, ovarian epithelial cancer, ovarian germ cell tumor, pancreatic cancer, papillary renal cell carcinoma, paranasal sinus and nasal cavity cancer, parathyroid cancer, pelvic cancer, penile cancer, Peutz-Jeghers syndrome, pharyngeal cancer, pheochromocytoma, phyllodes tumor, pilocytic astrocytoma, pineal astrocytoma, pituitary adenoma, pituitary gland tumors, plasmablastic lymphoma, pleuropulmonary blastoma, precursor B lymphoblastic leukemia, primary central nervous system lymphoma, primary cutaneous follicular lymphoma, primary cutaneous immunocytoma, primary effusion lymphoma, primitive neuroectodermal tumor, prostate cancer, rectal cancer, renal cancer, renal cell carcinoma (RCC), retinoblastoma, rhabdomyosarcoma, salivary gland cancer, sarcoma, sarcomas of primary cutaneous origin, sebaceous carcinoma, Sezary syndrome, skin adnexal tumors, skin cancer, small bowel cancer, small cell lung cancer, small intestine cancer, splenic marginal zone lymphoma, squamous cell carcinoma of the lung, squamous cell carcinoma, squamous cell skin cancer, stomach cancer, surface epithelial-stromal tumor, T-cell prolymphocytic leukemia, testicular cancer, thoracic and respiratory cancer, thymoma, thymic carcinoma, thyroid cancer, transitional cell cancer, transitional cell cancer adenoid cystic carcinoma, tuberous sclerosis syndrome, tubular carcinoma, Turcot syndrome, unknown primary cancer, unsorted cancer, ureter cancer, urethral cancer, uterine cancer, uterine sarcoma, uveal melanoma, vaginal cancer, visual pathway and hypothalamic glioma, Von Hippel-Li ndau (VHL) syndrome, vulvar cancer, Wilms tumor, and xeroderma pigmentosum.

[0102] In embodiments, the cancer is selected from esophageal cancer, gastric (stomach) cancer, bile duct cancer, small intestine cancer, colorectal cancer, pancreatic cancer, liver cancer, rectal cancer, anal cancer, colon cancer, gallbladder cancer, and stromal tumors.

[0103] In embodiments, the administration is oral, optionally taken with food or beverage. In embodiments, the administration is from about once daily to about once per 3 months.

[0104] In embodiments, the healthy microbiome comprises about or at least about 20% of the total species abundance, about or at least about 25% of the total species abundance, about or at least about 30% of the total species abundance, about or at least about 35% of the total species abundance, about or at least about 40% of the total species abundance, about or at least about 45% of the total species abundance, or about or at least about 50% of the total species abundance of the plurality of bacterial species capable of synthesizing butyrate and / or one or more intermediates of a butyrate synthesis pathway.DBl / 161604598.2 24Atorney Docket No.: 137085-5001 -PC

[0105] In embodiments, the healthy microbiome comprises about or at least about 20% of the total species abundance, about or at least about 25% of the total species abundance, about or at least about 30% of the total species abundance, about or at least about 35% of the total species abundance, about or at least about 40% of the total species abundance, about or at least about 45% of the total species abundance, or about or at least about 50% of the total species abundance of the plurality of bacterial species capable of synthesizing propionate and / or one or more intermediates of a propionate synthesis pathway.

[0106] In embodiments, the healthy microbiome comprises about or at least about 1% of the total species abundance, about or at least about 5% of the total species abundance, about or at least about 10% of the total species abundance, about or at least about 15% of the total species abundance, about or at least about 20% of the total species abundance, about or at least about 30% of the total species abundance, about or at least about 40% of the total species abundance, or about or at least about 50% of the total species abundance of the plurality of bacterial species capable of synthesizing indole-3-acetic acid (IAA) and / or one or more intermediates of an IAA synthesis pathway.

[0107] In embodiments, the healthy microbiome comprises about or at least about 1% of the total species abundance, about or at least about 5% of the total species abundance, about or at least about 10% of the total species abundance, about or at least about 15% of the total species abundance, about or at least about 20% of the total species abundance, about or at least about 30% of the total species abundance, about or at least about 40% of the total species abundance, or about or at least about 50% of the total species abundance of the plurality of bacterial species capable of synthesizing indole-3-propionic acid (IPA) and / or one or more intermediates of an IPA synthesis pathway.

[0108] In embodiments, the healthy microbiome comprises about or at least about 1% of the total species abundance, about or at least about 5% of the total species abundance, about or at least about 10% of the total species abundance, about or at least about 15% of the total species abundance, about or at least about 20% of the total species abundance, about or at least about 30% of the total species abundance, about or at least about 40% of the total species abundance, or about or at least about 50% of the total species abundance of the plurality of bacterial species capable of one or more short chain fatty acid (SCFA) and / or one or more intermediates of a SCFA synthesis pathway.

[0109] In embodiments, the healthy microbiome comprises about or at least about 1% of the total species abundance, about or at least about 5% of the total species abundance, about or at least about 10% of the total species abundance, about or at least about 15% of the total species abundance, about or at leastDBl / 161604598.2 25Atorney Docket No.: 137085-5001 -PC about 20% of the total species abundance, about or at least about 30% of the total species abundance, about or at least about 40% of the total species abundance, or about or at least about 50% of the total species abundance of the plurality of bacterial species capable of one or more bile acid derivative (BA) and / or one or more intermediates of a BA synthesis pathway.

[0110] In embodiments, the administration of the composition of the plurality of bacterial species results in one or more of a decrease of one or more metabolites, e.g., indoxyls and / or phenyl sulfates (e.g., as described herein).

[0111] In embodiments, the administration of the composition of the plurality of bacterial species results in activation of one or more human receptors, e.g., one or more G protein-coupled receptors (GPCRs), tolllike receptors (TLRs), and / or one or more human receptors as described herein.

[0112] In embodiments, the administration of the composition of the plurality of bacterial species results in activation or expansion of one or more immune cells, e.g., CD4+ T cells, CD8+ T cells, and Natural Killer (NK) cells.

[0113] In embodiments, the administration of the composition of the plurality of bacterial species results in suppression or reduction one or more immune cells, e.g., myeloid-derived suppressor cells (MDSCs) and / or regulatory T cells (Tregs).

[0114] In embodiments, the administration of the composition of the plurality of bacterial species results in re-activation of exhausted T cells to a substantially healthy state.

[0115] In embodiments, the administration of the composition of the plurality of bacterial species results in enhancement of endogenous immune cell-mediated killing of cancer cells.

[0116] In embodiments, the administration of the composition of the plurality of bacterial species results in restoration of one or more epithelial barrier function to a substantially healthy state, e.g., selected from expression and distribution of tight junction proteins, epithelial surface area, presence of intestinal villi, mucosal permeability, paracellular permeability, transcellular uptake, and one or more electrophysiological parameters (e.g., transepithelial electrical resistance (TEER)).

[0117] In embodiments, one or more effects of establishing the healthy microbiome and / or treating the disease occurs within about or at least about 1 week, about or at least about 2 weeks, about or at least about 3 weeks, about or at least about 4 weeks, about or at least about 1 month, about or at least about 2 months,DBl / 161604598.2 26Atorney Docket No.: 137085-5001 -PC about or at least about 4 months, about or at least about 6 months, or about or at least about 1 year from administration and / or completion of an administration regimen.

[0118] In embodiments, assessing the subject for the establishment of the healthy microbiome by analyzing a sample obtained from the subject. In embodiments, the sample obtained from the subject is or comprises stool, gastrointestinal biopsy, rectal swab, urine, saliva, blood, sera, and / or plasma.

[0119] In embodiments, methods herein further comprise assessing one or more symptoms of a disease of the subject, optionally selected from a symptom of cancer and / or dysbiosis. In embodiments, methods herein further comprise administering one or more additional therapeutic agents.DESCRIPTION OF THE DRAWINGS

[0120] Figs. 1A-1 B depict non-limiting diagrammatic representations of bacterial species selection processes. Fig. 1A summarizes a bacterial species selection narrows selection from about 1 x 106bacterial strains (species) and 1 x 108bacterial genes to about 150 or fewer bacterial strains (species). Fig. 1B shows an illustrative flowchart for strain decision-making.

[0121] Fig. 2 depicts a non-limiting, illustrative graphical representation of the agreement of bacterial species from next-generation sequencing (NGS) with metagenomic analysis. The algorithm is tunable for sensitivity which alters the limits for detection of false negatives early in bacterial species screening. Each dot is a species detected with some frequency in healthy volunteer (HV) data, x- and y-axes represent two methods.

[0122] Figs. 3A-3D depicts a non-limiting, illustrative graphical representation of bacterial consortia constructed from a 100-target species (left) and 200-target species (right) which have a similar bacterial species community to the populations observed in healthy human individuals. The Figs. 3A-3B output shows the 2D visualization results of a principal coordinate analysis (PCoA) applied to beta diversity method (calculated by Hamming distance). Fig. 3C output shows illustrative 3D visualization results of a principal coordinate analysis (PCoA) applied to beta diversity method (calculated by Hamming distance) from data of healthy bacterial consortia generated from analysis of 3,000 healthy volunteer (HV) metagenomes. Each point is a healthy human’s community projected into reduced dimensional space; shading / color shows the fraction of that community’s biomass included in our synthetic consortia. Fig. 3D shows that a bacterial consortia herein has a similar community structure to that observed in healthy communities. PrincipalDBl / 161604598.2 27Atorney Docket No.: 137085-5001 -PC component analysis using beta diversity method (Hamming distance shown) which shows placement of the bacterial community in a multi-dimensional space, represented in two dimensions for simplicity.

[0123] Figs. 4A-4C depict non-limiting, illustrative graphical representation of the microbiome biomass that is captured by compositions of selected prevalent species. The graphical analysis in Fig. 4A plots the fraction of bacterial community abundance (in terms of number of species / isolates observed) that is captured by a target bacterial consortia. The graphical analysis in Fig. 4B plots the fraction of bacterial community prevalence (in terms of fraction of samples observed in) that is captured by a target bacterial consortia. The graphical analysis in Fig. 4C shows a large fraction of microbiome biomass found in healthy volunteers (HV) is captured by the bacterial consortia described herein, a “core” consortia shared between three exemplary consortia #1 (Fig. 4D), #2 (Fig. 4E), and #3 (Fig. 4F).

[0124] Fig. 5 depicts a non-limiting, illustrative diagrammatic representation of the of “betweennesscentrality” calculation. The nodes (taxa) are presented as a function of their “between-ness” or clustering based on similarity / dissimilarity (e.g., branch points and distance between nodes).

[0125] Fig. 6 depicts a non-limiting, illustrative graphical representation of the distributions of bacterial prevalence based on genetic interrogation (e-value) for the presence / prevalence of metabolic genes and / or operons (hsdh = hydroxysteroid dehydrogenase).

[0126] Figs. 7A-7B depict non-limiting, illustrative phylogenetic model outputs to select bacteria with high confidence of particular metabolism / characteristics based on 8 distinct genetic predictors for a metabolic pathway.

[0127] Fig. 8 depicts a non-limiting, illustrative graphical representation estimating the co-culturability testing of up to 207 bacterial isolates. Growth is analyzed at days 0, 1 , 2, 3, and 7, as measured by optical density (ODeoonm), in various media types (1, 2, 3, and 4). Not all isolates are predicted to grow in any one media.

[0128] Fig. 9 depicts a non-limiting, illustrative graphical representation of the bacterial isolate cryo- revivability as measured by isolate viability after cryopreservation (post-cryo) in both liquid media growth and agar media growth. Results demonstrate that revival of 90%+ bacterial isolates is achievable and that bacterial selection is filterable based on viability after cryopreservation (and / or lyopreservation).

[0129] Fig. 10 depicts a non-limiting, graphical representation of a multi-mechanistic consortium composition design. The dendrogram shown has ~150 leaves, each leaf is a species and the rings show theDBl / 161604598.2 28Atorney Docket No.: 137085-5001 -PC characteristics of that species that make its selection desirable for inclusion in the consortium. The consortia comprise multiple mechanisms to address heterogenous patient populations and functional redundancy to maximize number of shots on goal and size of effect.

[0130] Figs. 11A-11 G depict non-limiting graphical results of a computational screen of bacterial species, strains, and / or isolates for production of bile acid derivatives based on a combination of genomic analysis and metabolic assay data. The isolate (MBSID) identifier relates to the isolates and 16S rRNA sequences listed in Table 12.

[0131] Fig. 12 depicts a non-limiting graphical output from a machine-learning model generated from non-responder (NR) to responder (R) patient data tested for validation of task transferability for overall survival prediction. The model achieved stratification of patients at a log-rank of p=0.0001 .

[0132] Fig. 13 depicts a non-limiting graphical output of out-of-distribution model testing of replicates of clinical results. The model was able to accurately predict positive clinical response for bacterial consortia, as described herein.

[0133] Fig. 14 depicts a non-limiting graphical output of model out-of-distribution testing that further recapitulates clinical results, with positive and dose-dependent response to fecal microbiome transplant (FMT) in multiple types of patient backgrounds. The conditions, from left to right, are donor species among all subjects, responders, non-responders, responder + 1% of donor species, non-responder + 1 % of donor species, responder + 5% of donor species, non-responder + 5% of donor species, responder + 10% of donor species, non-responder + 10% of donor species, responder + 30% of donor species, non-responder + 30% of donor species, responder + 60% of donor species, non-responder + 60% of donor species, responder + 100% of donor species, and non-responder + 100% of donor species.

[0134] Fig. 15 depicts a non-limiting Venn diagram showing the compositional relationship between three exemplary, non-limiting bacterial consortia built of bacterial species, strains, and / or isolates based on co-culturability and fulfillment of consortia characteristics, as described herein. Each consortia (Consortia #1 , #2, and #3) has -150 distinct bacterial species, strains, and / or isolates that were detected at some point during the co-fermentation, sharing a total of 133 bacterial species, strains, and / or isolates between them.

[0135] Figs. 16A-16D depict non-limiting graphical outputs of model screening of bacteria consortia with NR-vs-R model showing prediction of positive clinical response with dose-dependence for use of multiple consortia (“core” consortia in Fig. 16A, Consortia #1 in Fig. 16B, Consortia #2 in Fig. 16C, Consortia #3 inDBl / 161604598.2 29Atorney Docket No.: 137085-5001 -PCFig. 16D) in multiple types of patient backgrounds (responders (R) and non-responders (NR)). The conditions, from left to right, are the full consortia among all subjects, responders, non-responders, responder + 1 % of consortia, non-responder + 1% of consortia, responder + 5% of consortia, non-responder + 5% of consortia, responder + 10% of consortia, non-responder + 10% of consortia, responder + 30% of consortia, non-responder + 30% of consortia, responder + 60% of consortia, non-responder + 60% of consortia, responder + 100% of consortia, and non-responder + 100% of consortia.

[0136] Figs. 17A-17C depict non-limiting graphical summaries of growth curve analyses for co-culturing large numbers of different bacterial species, strains, and isolates to build consortia. Fig. 17A illustrates how co-culturing strains for bacterial consortia herein were classified as a function of their growth as measured by lag time (e.g., lag phase), growth rate (e.g., doubling time, generation time), and max OD (e.g., ODeoonm) to successfully co-culture the plurality of strains in fewer bioreactors. Fig. 17B shows representative growth curves analyzed for “fast” growing co-cultured bacterial strains / isolates, as well as exemplary pre-inoculation growth, seed growth, and fermentor growth incubation times. Fig. 17C shows representative growth curves analyzed for “slow” growing co-cultured bacterial strains / isolates, as well as exemplary pre-inoculation growth, seed growth, and fermentor growth incubation times.

[0137] Figs. 18A-18C depicts non-limiting graphical analyses of viability (Fig. 18A), absolute abundance measured by 16S sequencing (Fig. 18B), and species richness by 16S sequencing (Fig. 18C) for multiple co-culturing fermentation runs, with an illustrative 34-hr. harvest time point.

[0138] Fig. 19 depicts a non-limiting graphical illustration of co-culturing runs of 147 strains (Fermentor run 1) and 116 strains (Fermentor run 2).

[0139] Fig. 20 depicts a non-limiting Venn Diagram showing a summary of bacterial strains that were categorized based on growth rates relative to other co-cultured species. Growth rate variables are useful for bacterial consortia development.

[0140] Figs. 21A-21 B depict non-limiting, illustrative workflows for metabolomics analyses of bacterial consortia described herein, for strain-level determination (Fig. 21 A) and consortia-level analysis (Fig. 22B).

[0141] Figs. 22A-22B depict non-limiting graphical illustrations of the effect of bacterial metabolites on cytokine production of CD4+T cells (Fig. 22A) and CD8+ T cells (Fig. 22B). Fructooligosaccharides (FOS), inulin, and primary bile acids (BA), each showed increased production of cytokines and cytotoxic effectors that are relevant to anti-tumor effects in the tumor microenvironment.DBl / 161604598.2 30Atorney Docket No.: 137085-5001 -PC

[0142] Figs. 23A-23I depict non-limiting graphical illustrations of the effect bacterial consortia have on immune cell stimulation. Figs. 23A, 23D, and 23G shows representative dotplots of T cell activation markers CD25, CD137, CD38, and CD69 stimulated for 7 days of Consortia #1 , #2, and #3, respectively. Figs. 23B, 23E, and 23H shows representative histograms of expanded CD4+ T cell (CD27+CD45RA-, T central memory) expression of INF-y, GrB, and IL-10, for Consortia #1, #2, and #3, respectively. Figs. 23C, 23F, and 23I shows representative histograms of expanded CD8+ T cells (CD27+ CD45RA-, T central memory) expression of INF-y, GrB, and IL-10, for Consortia #1, #2, and #3, respectively. Negative controls for each were unstimulated PBMCs (Unstim.); positive control stimulation with was achieved with phytohemagglutinin (PHA) and potent activating antibody (CytoStim™) to drive cellular activation. Each of the graph inlets in Figs. 23A, 23B, and 23C show log scales on their axes from bottom to top and left to right, ranging from 0 to 103. Each of the graph inlets in Figs. 23B-23C, 23E-23F, and 23H-23I show log scales from left to right, ranging from O to 103.

[0143] Figs. 24A-24E depict non-limiting graphical illustrations of representative quantitative metabolomics of bacterial consortia described herein. Fig. 24A shows the production of a secondary bile acid (BA), deoxycholic acid (DCA), Fig. 24B shows the production butyric acid (butyrate), Fig. 24C shows the production of propanoic acid (propionate), Fig. 24D shows the production of 3-IAA, and Fig. 24E shows the production of 3-IPA. Each metabolite is quantified using liquid chromatography-mass spectrometry (LC- MS) and / or HPLC. Data shown are box and whisker plots with first quartile, median, third quartile, and maximal and minimal values. A statistically significant increase in the production of each metabolite was observed.DETAILED DESCRIPTION

[0144] The present disclosure provides, in part, compositions of bacterial consortia that are selected based on desired characteristics / functionality to substantially recapitulate a microbiome of a heathy human. In embodiments, a “bacterial consortia” refers to a “plurality of bacterial species” and / or a “plurality of bacterial isolates,” which originate from the plurality of species. In embodiments, the “plurality of bacterial species,” refers to a collection (consortia) of multiple bacterial species / strains / isolates. In embodiments, the plurality of bacterial species are “isolated,” referring to their existence in cell banks outside of a human body or sample.

[0145] In embodiments, a bacterial “isolate” refers to a pure microbial culture created by single colony purification (e.g., from healthy human biospecimens). In embodiments, a bacterial “strain” comprises all microbial cells having the same genomic DNA sequence, which is different from the genome of other strains.DBl / 161604598.2 31Atorney Docket No.: 137085-5001 -PCIn embodiments, the “same” genome will be defined by <0.01 % nucleotide divergence, e.g., within the error rates of Whole Genome Shotgun (WGS) Assembly and the possible drift introduced by isolation and culturing. In embodiments, for genomes having 0.01 %-0.1 %, suitable methods with lower limit of detection (LOD) are used to establish genome sequence and uniqueness for strain delineation. In embodiments, a bacterial “species” refers to a phylogenetic group of all strains descended from a common ancestor, operationally defined by >95% average genomic DNA sequence identity to one another, or by >97% 16S rRNA sequence similarity, often designated by a taxonomic name with standing in international nomenclature or from the Genome Taxonomy Database (GTDB) database. In embodiments, a GTDB (or similar) genome identifier or designation is used to identify one or more bacterial species, subspecies (sp.), strains, and / or isolates, for example, as summarized in Table 12 (e.g., SEQ ID NOs: 1-715).

[0146] In embodiments, bacterial compositions herein are in vitro-demed and not fecal-derived, e.g., they do not originate from a donor (fecal sample). In embodiments, the bacterial consortia described herein are synthetic (e.g., non-naturally-occuring) and generated from a series of isolated, pure bacterial isolate stocks that have been genetically characterized (e.g., for one or more of antibiotic susceptibility, presence of harmful phage, metabolic capacity, etc.) used to replicate a total fecal microbiome that might be used for fecal microbiota transplant (FMT). In embodiments, the bacterial consortia herein represent off-the-shelf compositions that are provided without the need to source a suitable donor and manufacture a suitable FMT composition from the donor sample.

[0147] In embodiments, the plurality of bacterial species is useful in methods of establishing a healthy microbiome, e.g., in the gastrointestinal tract of a human subject and / or in an ex vivo or simulated in vitro environment ( .e., simulated gastric acid). In embodiments, the plurality of bacterial species is useful in methods of treating cancer. In embodiments, the plurality of bacterial species is useful in methods of treating and / or ameliorating a disease in a human subject, including addressing one or more symptoms associated with the disease.

[0148] In embodiments, the plurality of bacterial species is capable of substantially growing in a gastrointestinal tract (e.g., a human gastrointestinal tract), where “substantially growing” refers to a range of about or at least about 5% of bacterial species / isolates to about or at least about 90% of bacterial species / isolates in the composition being able to grow in and / or colonize the gut, e.g., as determined by methods of analysis for microbiome of (e.g., fecal analysis). In embodiments, the plurality of bacterial species is far higher in number than traditional probiotic products (e.g., on the order of 1-10 species / isolates) to takeDBl / 161604598.2 32Atorney Docket No.: 137085-5001 -PC advantage of isolation of prevalent organisms from healthy human donors, with good ability to engraft as measured from FMT (fecal microbiome transplant) or similar studies in humans, as well as cross-species synergy in establishing a healthy microbiome (e.g., engraftment), and / or to increase the chances that a wider range of distinct bacterial species survive the growth and / or colonization process. In embodiments, strainspecific engraftment is assessed by measuring each the abundance of each strains’ specific nucleic acid sequences in patient fecal matter, e.g., using PCR, sequencing, or other suitably sensitive and specific nucleic acid detection technologies.

[0149] While there are many isolates that produce, for example, butyrate (among other metabolic functions), the design criteria used herein, inter alia, which guides inclusion or exclusion of bacterial species, isolates, and strains is based on multiple additional inclusion criteria, including co-culturability as well as prevalence and abundance in responder sub-patient populations (e.g., IO therapy response) determined using a combination of in silico analyses (e.g., machine-learning models) and in vitro analyses. In comparison to traditional microbiome product manufacturers, there is little guidance on co-culturability of bacterial consortia or species / isolate selection because traditional microbiome product manufacturing does not translate to producing large bacterial consortia (e.g., having 100+ isolates and 50+ species).Bacterial Consortia

[0150] In aspects, described herein are compositions comprising an isolated plurality of bacterial species. In embodiments, the isolated plurality of bacterial species are a bacteria consortia that is designed to recapitulate a gut microbiome of a healthy human without the need of fecal-derived samples.

[0151] In embodiments, the design criteria of bacterial consortia herein is guided by achieving a consortia of species / isolates that provides a richness of diversity that captures a variety of mechanisms of action (MoAs) that are observed in a healthy human gut microbiome, and achieves a sufficiently large number of different species / isolates to provide redundancy in capturing the MoAs.

[0152] In embodiments, the plurality comprises at least two of the following characteristics (e.g., MoAs), as described herein. In embodiments, these characteristics comprise the ability to substantially decrease one or more metabolites, e.g., such as harmful or disease-related metabolites. In embodiments, these characteristics comprise susceptibility to at least 3 antibiotics selected from different antibiotic classes, e.g., as a regulatory and product control quality that ensures the product cannot be potentially harmful. In embodiments, these characteristics comprise the ability to substantially activate one or more endogenous human receptors, including for example, one or more G protein-coupled receptor (GPCRs) and / or toll-likeDBl / 161604598.2 33Atorney Docket No.: 137085-5001 -PC receptor (TLRs), e.g., to provide benefits to the integrity of the gastrointestinal epithelial lining, response to therapeutics (non-responder to responder), and modulation of gut inflammation and immunological adverse events (AEs). In embodiments, these characteristics comprise the ability to substantially activate or expand one or more immune cells, e.g., cytotoxic T lymphocytes (CTLs), CD4+ T cells, CD8+ T cells, NK cells, etc. In embodiments, these characteristics comprise the ability to substantially suppress or reduce one or more immune cells, e.g., immunosuppressive immune cell subsets such as myeloid-derived suppressor cells (MDSCs) and regulatory T cells (Tregs). In embodiments, these characteristics comprise the ability to reactivate exhausted T cells to a substantially healthy state, e.g., to assist in reactivation of exhausted T cells in a tumor microenvironment. In embodiments, these characteristics comprise the ability to substantially enhance endogenous immune cell-mediated killing of cancer cells. In embodiments, these characteristics comprise the ability to restore human epithelial barrier function to a substantially healthy state.

[0153] In embodiments, the plurality of bacterial species comprises a total of about or at least about 70 isolates (e.g, about or at least about a total of 80 isolates, 90 isolates, 100 isolates, 110 isolates, 120 isolates, 130 isolates, 140 isolates, 150 isolates, 160 isolates, 170 isolates, 180 isolates, 190 isolates, or 200 or more isolates) from at least about 50 bacterial species (e.g, about or at least about 50 species, 55 species, 60 species, 65 species, 70 species, 75 species, 80 species, 85 species, 90 species, 95 species, 100 species, 105 species, 110 species, 115 species, 120 species, 125 species, 130 species, 135 species, 140 species, 145 species, or 150 or more species), including numbers of isolates and species therebetween.

[0154] In embodiments, at least about 7 isolates are selected from at least about 5 species having about or at least about 95% sequence identity to the 16S rRNA sequence of bacterial species selected from Table 1 a. In embodiments, at least about 12 isolates are selected from at least about 8 species having about or at least about 95% sequence identity to the 16S rRNA sequence of bacterial species selected from Table 1c. In embodiments, at least about 12 isolates are selected from at least about 8 species having about or at least about 95% sequence identity to the 16S rRNA sequence of bacterial species selected from Table 1 d. In embodiments, at least about 12 isolates are selected from at least about 8 species having about or at least about 95% sequence identity to the 16S rRNA sequence of bacterial species selected from Table 1e and / or Table 1f. In embodiments, the remaining of the at least about 100 isolates (e.g., not selected from Table 1 a, Table 1c, Table 1 d, Table 1 e, Table 1f, Table 1g, Table 1 h, Table 1 i) from the at least about 50 bacterial species have about or at least about 95% sequence identity to the 16S rRNA sequence of bacterial species selected from Table 1 b.DBl / 161604598.2 34Atorney Docket No.: 137085-5001 -PC

[0155] In embodiments, the plurality of bacterial species / isolates comprises at least about 7 isolates (e.g., about or at least about 8 isolates, 9 isolates, 10 isolates, 11 isolates, 12 isolates, 13 isolates, 14 isolates, 15 isolates, 16 isolates, 17 isolates, 18 isolates, 19 isolates, 20 isolates, 25 isolates, or about or at least about 30 isolates) are selected from about or at least about 5 species (e.g., about or at least about 6 species, 7 species, 8 species, 9 species, 10 species, 11 species, 12 species, 13 species, 14 species, 15 species, 16 species, 17 species, 18 species, 19 species, 20 species, 25 species, or about or at least about 30 species) having at least about 95% 16S rRNA sequence identity (e.g., about or at least about 96%, 97%, 98%, or 99% or more sequence identity) to a bacterial species / isolate selected from Table 1a. In embodiments, the remaining of the at least about 90+ isolates from the at least about 40+ bacterial species has at least about 95% 16S rRNA sequence identity (e.g., about or at least about 96%, 97%, 98%, or 99% or more sequence identity) to a bacterial species selected from Table 1 b. In embodiments, the remaining of the at least about 90+ isolates from the at least about 40+ bacterial species has at least about 95% 168 rRNA sequence identity (e.g., about or at least about 96%, 97%, 98%, or 99% or more sequence identity) to a bacterial species / isolates selected from Table 1 b and / or Table 1c, Table 1 d, Table 1 e, Table 1f, Table 1 g, Table 1 h, Table 1 i, Table 3, Table 5, Table 8, or Table 12.

[0156] In embodiments, about or at least about 25 species (e.g., about or at least about 26 species, 27 species, 28 species, 29 species, 30 species, 35 species, 40 species, 45 species, or about or at least about 50 species) of the plurality of bacterial species comprises a butyrate synthesis pathway and / or encodes at least one enzyme suitable for synthesizing butyrate. In embodiments, about or at least about 25 species (e.g., about or at least about 26 species, 27 species, 28 species, 29 species, 30 species, 35 species, 40 species, 45 species, or about or at least about 50 species) of the plurality of bacterial species comprises a propionate synthesis pathway and / or encodes at least one enzyme suitable for synthesizing propionate.

[0157] In embodiments, the plurality of the bacterial species comprises the ability (e.g., mechanism of action, MoA) to synthesize at least one bacterial metabolite, at least two bacterial metabolites, at least three bacterial metabolites, at least four bacterial metabolites, at least five bacterial metabolites, or at least six or more bacterial metabolites. In embodiments, the one or more bacterial metabolites comprise butyrate, propionate, bile acids (BAs), isoalloLCA, short-chain fatty acids (SCFAs) other than butyrate or propionate, IAA, IPA, and other bacterial metabolites as described herein. In embodiments, the plurality of the bacterial species comprises the ability to synthesize or produce at least two bacterial metabolites selected from indole- 3-acetic acid (IAA), indole-3-propionic acid (IPA), and bile acid derivatives (BAs). In embodiments, the bile acid derivatives (BAs) include one or more of isoallolithocholic acid (isoalloLCA), deconjugated bile acidsDBl / 161604598.2 35Atorney Docket No.: 137085-5001 -PC(deBAs), secondary bile acids (2BAs), tertiary bile acids (3BAs), 7-oxoLCA, 7-oxoDCA, and microbially conjugated bile acids (MCBAs). In embodiments, the plurality of bacterial species / isolates synthesizes and / or produces bacterial metabolites from one or more molecules found in cell media and / or the gastrointestinal environment, for instance in non-limiting examples, production of secondary BAs from primary bile acids / salts.Table 1 a: Illustrative bacterial species / isolates of compositions herein. The MBSID and 16S rRNA / rDNA sequences of (e.q., SEQ ID NOs: 1-715) species, strains, and isolates are listed in Table 12.Table 1 b: Illustrative bacterial species / isolates of compositions herein. The MBSID and 16S rRNA / rDNA sequences (e.q., SEQ ID NOs: 1-715) of species, strains, and isolates are listed in Table 12.DBl / 161604598.2 36Atorney Docket No.: 137085-5001 -PCDB1 / 161604598.2 37Atorney Docket No.: 137085-5001 -PCTable 1c: Illustrative high abundance butyrate producing bacterial species / isolates of compositions herein. The MBSID and 16S rRNA / rDNA seguences (e.q., SEQ ID NOs: 1-715) of species, strains, and isolates are listed in Table 12.Bacterial Genus and / or SpeciesDBl / 161604598.2 38Atorney Docket No.: 137085-5001 -PCTable 1 d: Illustrative high abundance propionate producing bacterial species / isolates of compositions herein. The MBSID and 16S rRNA / rDNA seguences (e.q., SEQ ID NOs: 1-715) of species, strains, and isolates are listed in Table 12.DBl / 161604598.2 39Atorney Docket No.: 137085-5001 -PCTable 1e: Illustrative bacterial species / isolates for immuno-oncoloqy therapy (IO therapy) for compositions herein using species empirically associated with validation from in vivo (e.q., mouse model) effect. The MBSID and 16S rRNA / rDNA sequences (e.q., SEQ ID NOs: 1-715) of species, strains, and isolates are listed in Table 12.Table 1f: Illustrative bacterial species / isolates for immuno-oncoloqy therapy (IO therapy) for compositions herein using species empirically associated with IO response by clinical NGS analyses of high-throughput data. The MBSID and 16S rRNA / rDNA sequences (e.q., SEQ ID NOs: 1-715) of species, strains, and isolates are listed in Table 12.DBl / 161604598.2 40Atorney Docket No.: 137085-5001 -PCTable 1q: Illustrative bacterial species / isolates for IAA producing bacterial species / isolates of compositions herein. The MBSID and 16S rRNA / rDNA sequences (e.g., SEQ ID NOs: 1-715) of species, strains, and isolates are listed in Table 12.Table 1 h: Illustrative bacterial species / isolates for IPA producing bacterial species / isolates of compositions herein. The MBSID and 16S rRNA / rDNA sequences (e.q., SEQ ID NOs: 1-715) of species, strains, and isolates are listed in Table 12.Table 1 i: Illustrative bacterial species / isolates for bile acid (Bai) producing bacterial species / isolates of compositions herein. The MBSID and 16S rRNA / rDNA sequences (e.q., SEQ ID NOs: 1-715) of species, strains, and isolates are listed in Table 12.

[0158] In embodiments, bacterial species selection herein is narrowed from an initial selection from about 1 x 105bacterial species (having about 1 x 108unique bacterial genes) based on the prevalence of bacterial species in the gut microbiome of one or more cohort of healthy humans (e.g., as shown in Fig. 1 A). In embodiments, the selection is guided based on one or more criteria, as described herein, to narrow the number of species / isolates to about 150-250 or fewer bacterial species and / or isolates. In embodiments, the criteria involved metagenomic and genomic screening, metabolic screening and quantitative metabolomics, cell banking experiments, cryorevival and lyorevival analyses, GMP-compliant growth screening (good manufacturing practice), growth curve analyses (e.g., co-culturability), ecological compatibility, in vitroDBl / 161604598.2 41Atorney Docket No.: 137085-5001 -PC antibiotic susceptibility, as well as various cell-based assays, in silico, in vitro, and in vivo functionality screening (e.g., as shown in Fig. 1B).

[0159] In embodiments, bacterial species selection is guided by in vitro co-culturing assessments to determine which bacterial species / isolates are compatible for manufacturing into compositions. A major caveat to the manufacturability of highly diverse microbiome products having live cultures is that it is difficult to co-culture a large number of different bacterial species in a single (or few) bioreactors. Traditionally, this requires numerous bioreactors making the costs of production infeasible or requiring additional sample manipulation to mix higher numbers of individual species. These difficulties can carry over, where species that are incompatible for co-culturing may also be incompatible for coexistent growth and / or colonization within the gastrointestinal tract, resulting in overall poor efficacy of the product, and / or loss of more difficult to culture species during the co-culture process (were added at one point but subsequently out-competed and killed off during co-culturing). In embodiments, the plurality of bacterial species is selected to be suitable for co-culturing in no more than 5 bioreactors, no more than 4 bioreactors, no more than 3 bioreactors, no more than 2 bioreactors, or no more than a single bioreactor (e.g., about or at least about 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 or more distinct bacterial species / isolates selected to be suitable for co-culture).

[0160] In embodiments, bacterial species selection is guided by determining which combinations of bacterial species / isolates are co-culturable. For example, in embodiments and in reference to Fig. 8, an illustrative estimate of the co-culturability of up to 207 bacterial isolates in 4 different media is shown. In embodiments, not all bacterial species grow in a single media type. In embodiments, the growth is analyzed over a range of time points (e.g., at 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 8 days, 9 days, 10 days, 2 weeks, etc.), post inoculation, depending upon the bioreactor volume and starting inoculum. In embodiments, bacterial growth is assessed by measuring the optical density at 600 nm (ODeoonm) of a sample of the culture, although other methods of assessing growth are known in the art, such as spectrophotometric (turbidimetric) analyses, viability counting (e.g., microscopy and staining), serial dilution and plating, etc. In embodiments, bacterial growth is assessed in a variety of standard growth broths and media, including for example, vegetable-based and animal-based media, BHI HIVEG (media with brain-heart infusion and 0.1% agar), GEM universal media (gamete-embryo medium), tryptic soy agar (TSA), Luria broth (LB), and YCFA media (yeast extract, casitone, fatty acid media supplemented with sugar). In embodiments, the growth media used is similar to eukaryotic media to recapitulate the supply of growth factors, vitamins, co-factors, carbon sources, nitrogen sources, etc., that would be available in the human gastrointestinal tract. In embodiments, the compositions herein are prepared from a plurality of bacterial species / isolates that are culturable in liquidDBl / 161604598.2 42Atorney Docket No.: 137085-5001 -PC media and / or solid agar media used for the cultivation of fastidious and non-fastidious microorganisms, including aerobic and anaerobic bacteria, from clinical specimens, food, and environmental samples. In embodiments, bacterial species / isolates are prepared in media that includes simulated gastric acid and / or alike conditions (e.g., to prime bacteria for growth and survival under conditions of the gastrointestinal tract).

[0161] In embodiments, compositions herein comprise about or at least about 50 bacterial species, about or at least about 60 bacterial species, about or at least about 70 bacterial species, about or at least about 80 bacterial species, about or at least about 90 bacterial species, about or at least about 100 bacterial species, about or at least about 110 bacterial species, about or at least about 120 bacterial species, about or at least about 130 bacterial species, about or at least about 140 bacterial species, about or at least about 150 bacterial species, about or at least about 160 bacterial species, about or at least about 170 bacterial species, about or at least about 180 bacterial species, about or at least about 190 bacterial species, or about or at least about 200 bacterial species, including numbers of species therebetween.

[0162] In embodiments, the plurality of bacterial species comprises between about 50 bacterial species and about 100 bacterial species, between about 100 bacterial species and 150 bacterial species, or between about 150 bacterial species and 200 bacterial species. In embodiments, the plurality of bacterial species comprises between about 50 bacterial species and about 60 bacterial species, between about 60 bacterial species and about 70 bacterial species, between about 70 bacterial species and about 80 bacterial species, between about 80 bacterial species and about 90 bacterial species, between about 90 bacterial species and about 100 bacterial species, between about 100 bacterial species and about 110 bacterial species, between about 110 bacterial species and about 120 bacterial species, between about 120 bacterial species and about 130 bacterial species, between about 130 bacterial species and about 140 bacterial species, or between about 140 bacterial species and about 150 bacterial species, including ranges of species therebetween.

[0163] In embodiments, the plurality of bacterial species comprises between about 100 bacterial isolates and about 150 bacterial isolates, between about 150 bacterial isolates and about 200 bacterial isolates, or between about 200 bacterial isolates and about 250 bacterial isolates. In embodiments, the plurality of bacterial species comprises between about 100 bacterial isolates and about 110 bacterial isolates, between about 110 bacterial isolates and about 120 bacterial isolates, between about 120 bacterial isolates and about 130 bacterial isolates, between about 130 bacterial isolates and about 140 bacterial isolates, between about 140 bacterial isolates and about 150 bacterial isolates, between about 150 bacterial isolates and about 160 bacterial isolates, between about 160 bacterial isolates and about 170 bacterial isolates,DBl / 161604598.2 43Atorney Docket No.: 137085-5001 -PC between about 170 bacterial isolates and about 180 bacterial isolates, between about 180 bacterial isolates and about 190 bacterial isolates, or between about 190 bacterial isolates and about 200 bacterial isolates, including ranges of isolates therebetween.

[0164] In embodiments, the plurality of bacterial species comprises up to about 250 to about 200 bacterial isolates, up to about 200 to about 150 bacterial isolates, up to about 150 to about 100 bacterial isolates, or up to about 100 bacterial isolates. In embodiments, the plurality of bacterial species comprises up to about 150 to about 100 bacterial species, up to about 100 to about 50 bacterial species, or up to about 50 bacterial species.

[0165] The taxonomical name of bacterial species, strains, and isolates is constantly changing. The taxonomical name is defined by an annotated bacterial genome deposited in a database, such as the Genome Taxonomy Database (GTDB), Microbial Genome Database for Comparative Analysis (MBGD) or ATCC Microbial Genome Database. In embodiments, a genome identifier (e.g., “MBSID”) is used for identification of bacterial species, strains, and / or isolates used in consortia herein, which provides backwards and forwards compatibility in naming convention. In embodiments, the genome identifier originates from the GTDB. In embodiments, the GTDB representative genome for a taxa represents a genome cluster of approximately 95% DNA identity (called “ANI”) across the genome, i.e., less than about a 5% divergence in genomic DNA identity.

[0166] In embodiments, bacterial species, strains, and / or isolates are defined by percent identity to a 16S sequence (DNA and / or RNA). In embodiments, bacterial species, strains, and / or isolates are considered the same (or functionally equivalent) at about or at least about 95% sequence identity or more to a 16S sequence (i.e., less than about a 5% divergence in 16S sequence). In embodiments, bacterial species, strains, and / or isolates are considered the same (or functionally equivalent) at about or at least about 97% sequence identity or more to a 16S sequence (i.e., less than about a 3% divergence in 16S sequence). In embodiments, one or more bacterial species, strains, and / or isolates is considered substantially the same as a reference bacterial species, strain, and / or isolate herein if it has about or at least about 95% sequence identity, about or at least about 96% sequence identity, about or at least about 97% sequence identity, about or at least about 98% sequence identity, or about or at least about 99% sequence identity to a 16S DNA / RNA sequence of Table 12 (e.g., SEQ ID NOs: 1-715). In embodiments, the one or more bacterial species, strains, and / or isolates comprises about or at least about 97% sequence identity to a 16S DNA / RNA sequence ofDBl / 161604598.2 44Atorney Docket No.: 137085-5001 -PCTable 12 (e.g., SEQ ID NOs: 1-715). In embodiments, the one or more bacterial species, strains, and / or isolates comprises a 16S DNA / RNA sequence of Table 12 (e.g., SEQ ID NOs: 1-715).

[0167] In embodiments, bacterial species selection is guided by in silico analyses. In embodiments, the in silico analyses include analysis of next-generation sequencing (NGS) by integrating results of several methods of metagenomic analysis (e.g., as shown in the illustrative output depicted Fig. 2). In embodiments, the in silico analyses generate outputs (to guide bacterial selection) which are tunable for sensitivity in measuring agreement between the prevalence of species with different methods. In embodiments, the different methods include data repositories, biochemical and in vitro studies, in vivo and clinical data, etc., which may indicate the presence of bacteria species / isolates present in the microbiomes of healthy or non- healthy human cohorts (or responder (R) and non-responder (NR) cohorts), and / or include data to genetic / functional characteristics. In embodiments, tuning the sensitivity of the in silico analyses (e.g., machine-learning model) alters the limits for detection, which alters the number of false negatives / false positive in bacterial species screening (e.g., before in vitro and / or in vivo selection processes). For example, in embodiments and in reference to Fig. 2, each point represents a bacterial species detected with some frequency in healthy volunteer (HV) data, where the x-axis and y-axis represent prevalence measured with two methods. In embodiments, bacterial species are selected based on their calculated prevalence from two or more methods or characteristics, as described herein.

[0168] In embodiments, the plurality of bacterial species belong to one or more bacterial genera of Acetatifactor, Agathobacter, Agathobaculum, Akkermansia, Alistipes, Anaerobutyricum, Anaerostipes, Anaerotignum, Anaerotmncus, Avimicrobium, Bacteroides, Bariatricus, Bamesiella, Bifidobacterium, Bilophila, Bittarella, Blautia, Butyricicoccus, Butyricimonas, Catenibacterium, Candidatus (UBA1417), Choladousia, Christensenella, Clostridium, Clostridiales (KLE1615), Coprobacillus, Coprobacter, Coprococcus, Copromonas, Dialister, Diplocloster, Dorea, Dysosmobacter, Eggerthella, Eisenbergiella, ER4, Eubacterium, Faecalibacillus, Faecalibacterium, Firmicutes (CAG), Fimivivens, Flavonifractor, Fusicatenibacter, Gemmiger, Harryflintia, Holdemanella, Hominisplanchenecus, Hungatella, Intestinimonas, Lachnoclostridium, Lachnospira (UBA3402), Lacrimispora, Ligilactobacillus, Longibaculum, Mediterraneibacter, Monoglobus, Muricomes, Odoribacter, Oliverpabstia, Parabacteroides, Paraprevotella, Peptostreptococcus, Phascolarctobacterium, Phocaeicola, Prevotella, Roseburia, Ruminococcus, Ruthenibacterium, Sarcina, Slackia, Sutterella, Thomasclavelia, Tractidigestivibacter, Turicibacter, and Wujia.DBl / 161604598.2 45Atorney Docket No.: 137085-5001 -PC

[0169] In embodiments, the plurality of bacterial species belong to one or more bacterial genera of Agathobacter, Agathobaculum, Akkermansia, Alistipes, Anaerobutyricum, Anaerostipes, Anaerotignum, Avimicrobium, Bacteroides, Bariatricus, Bamesiella, Bifidobacterium, Bilophila, Bittarella, Blautia_A, Butyricicoccus, Butyricimonas, CAG-317, CAG-41, Christensenella, Clostridium, Coprobacter, Coprococcus_A, Copromonas, Diplocloster, Dorea, Dorea_A, Dysosmobacter, Eisenbergiella, Eubacterium_G, Faecalibacillus, Faecalibacterium, Flavonifractor, Fusicatenibacter, Gemmiger, Harryflintia, Hungatella, Intestinimonas, KLE1615, Lachnoclostridium_B, Lachnospira, Mediterraneibacter, Monoglobus, Muricomes, Odoribacter, Oliverpabstia, Parabacteroides, Peptostreptococcus, Phocaeicola, Prevotella, Roseburia, Ruminococcus_B, Ruminococcus_D, Ruminococcus_E, Ruthenibacterium, Slackia_A, Turicibacter, UBA3402, and Wujia.

[0170] In embodiments, the plurality of bacterial species belong to one or more bacterial genera of Agathobacter, Akkermansia, Anaerobutyricum, Anaerostipes, Bacteroides, Clostridium, Faecalibacterium, Gemmiger, and Phocaeicola.

[0171] In embodiments, the plurality of bacterial species comprises about or at least about 6 genera (e.g., about or at least about 6, 7, 8, 9, 10, 11 , 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, 24, 25, 30, 35, 40, 45, or 50 or more genera), about or at least about 8 species (e.g., about or at least about 8, 9, 10, 11 , 12, 13, 14, 15, 20, 25, 30, 35, 40, 45, or 50 or more species), about or at least about 10 isolates / strains (e.g., about or at least about 10, 11 , 12, 13, 14, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 or more isolates / strains) from one or more of Table 1a, Table 1 b, Table 1c, Table 1 d, Table 1 e, Table 1f, Table 1 g, Table 1 h, and Table 1 i.

[0172] In embodiments, bacterial consortia herein comprise at least about 7 isolates selected from at least about 5 species having about or at least about 96%, about or at least about 97%, about or at least about 98%, or about or at least about 99% sequence identity to the 16S rRNA sequence of bacterial species selected from Table 1a. In embodiments, bacterial consortia herein comprise at least about 12 isolates selected from at least about 10 species having about or at least about 96%, about or at least about 97%, about or at least about 98%, or about or at least about 99% sequence identity to the 16S rRNA sequence of bacterial species selected from Table 1c. In embodiments, bacterial consortia herein comprise at least about 12 isolates selected from at least about 10 species having about or at least about 96%, about or at least about 97%, about or at least about 98%, or about or at least about 99% sequence identity to the 16S rRNA sequence of bacterial species selected from Table 1 d. In embodiments, bacterial consortia herein compriseDBl / 161604598.2 46Atorney Docket No.: 137085-5001 -PC at least about 12 isolates selected from at least about 10 species having about or at least about 96%, about or at least about 97%, about or at least about 98%, or about or at least about 99% sequence identity to the 16S rRNA sequence of bacterial species selected from Table 1e and / or Table 1f. In embodiments, bacterial consortia herein comprise at least about 40 isolates selected from at least about 15 species having about or at least about 96%, about or at least about 97%, about or at least about 98%, or about or at least about 99% sequence identity to the 16S rRNA sequence of bacterial species selected from Table 1 b.

[0173] In embodiments, bacterial consortia herein comprise at least about 7 isolates selected from at least about 5 species, each having the 16S rRNA sequence of bacterial species selected from Table 1a. In embodiments, bacterial consortia herein comprise at least about 12 isolates selected from at least about 10 species, each having the 16S rRNA sequence of bacterial species selected from Table 1c. In embodiments, bacterial consortia herein comprise at least about 12 isolates selected from at least about 10 species, each having the 16S rRNA sequence of bacterial species selected from Table 1 d. In embodiments, bacterial consortia herein comprise at least about 12 isolates selected from at least about 10 species, each having the 16S rRNA sequence of bacterial species selected from Table 1e and / or Table 1f. In embodiments, bacterial consortia herein comprise at least about 40 isolates selected from at least about 15 species, each having the 16S rRNA sequence of bacterial species selected from Table 1 b.

[0174] In embodiments, bacterial consortia herein comprise at least about 7 isolates (e.g. about or at least about 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or 25 or more isolates) selected from at least about 5 species {e.g. about or at least about 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, 15, or 20 or more species) each having about or at least about 96%, about or at least about 97%, about or at least about 98%, or about or at least about 99% sequence identity to the 16S rRNA sequences of bacterial species selected from Table 1 a (e.g., 16S rRNA sequences listed in Table 12 as SEQ ID NOs: 1-715).

[0175] In embodiments, bacterial consortia herein comprise about or at least about 7 isolates, about or at least about 8 isolates, about or at least about 9 isolates, about or at least about 10 isolates, about or at least about 11 isolates, about or at least about 12 isolates, about or at least about 13 isolates, about or at least about 14 isolates, about or at least about 15 isolates, about or at least about 16 isolates, about or at least about 17 isolates, about or at least about 18 isolates, about or at least about 19 isolates, about or at least about 20 isolates, or about or at least about 25 isolates selected from Table 1 a. In embodiments, bacterial consortia herein comprise about or at least about 6 species, about or at least about 7 species, about or at least about 8 species, about or at least about 9 species, about or at least about 10 species, about or atDBl / 161604598.2 47Atorney Docket No.: 137085-5001 -PC least about 11 species, about or at least about 12 species, about or at least about 13 species, about or at least about 14 species, about or at least about 15 species, or about or at least about 20 species selected from Table 1a.

[0176] In non-limiting embodiments, the plurality of bacterial isolates and / or species selected from Table 1 a comprise one or more of Agathobacterrectalis, Akkermansia muciniphila_B, Anaerobutyricum soehngenii, Anaerostipes hadrus, Bacteroides thetaiotaomicron, Bacteroides uniformis, Clostridium _AP scindens, Faecalibacterium prausnitzii_D, Faecalibacterium prausnitziij, and Phocaeicola vulgatus.

[0177] In embodiments, bacterial consortia herein comprise at least about 12 isolates (e.g. about or at least about 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, 24, 25, 30, or 35 or more isolates) selected from at least about 10 species (e.g. about or at least about 10, 11 , 12, 13, 14, 15, 20, or 25 or more species) each having about or at least about 96%, about or at least about 97%, about or at least about 98%, or about or at least about 99% sequence identity to the 16S rRNA sequences of bacterial species selected from Table 1c (e.g., 16S rRNA sequences listed in Table 12 as SEQ ID NOs: 1-715).

[0178] In embodiments, bacterial consortia herein comprise about or at least about 12 isolates, about or at least about 13 isolates, about or at least about 14 isolates, about or at least about 15 isolates, about or at least about 16 isolates, about or at least about 17 isolates, about or at least about 18 isolates, about or at least about 19 isolates, about or at least about 20 isolates, about or at least about 21 isolates, about or at least about 22 isolates, about or at least about 23 isolates, about or at least about 24 isolates, about or at least about 25 isolates, or about or at least about 30, or about or at least about 35 isolates selected from Table 1c. In embodiments, bacterial consortia herein comprise about or at least about 11 species, about or at least about 12 species, about or at least about 13 species, about or at least about 14 species, about or at least about 15 species, about or at least about 16 species, about or at least about 17 species, about or at least about 18 species, about or at least about 19 species, about or at least about 20 species, or about or at least about 25 species selected from Table 1c.

[0179] In non-limiting embodiments, the plurality of bacterial isolates and / or species selected from Table 1c comprise one or more of Bilophila wadsworthia, Butyricimonas virosa, Clostridium cuniculi, Clostridium_Q fessum, Clostridium_Q symbiosum, Copromonas sp900066535, Dysosmobacter sp001916835, Dysosmobacter welbionis, Eisenbergiella sp900066775, ER4 sp900317525, Eubacterium_G sp000432355, Eubacterium_G ventriosum, Flavonifractor plautii, Intestinimonas butyriciproducens, Odoribacter splanchnicus, Wujia chipingensis.DBl / 161604598.2 48Atorney Docket No.: 137085-5001 -PC

[0180] In embodiments, bacterial consortia herein comprise at least about 12 isolates (e.g. about or at least about 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, 24, 25, 30, or 35 or more isolates) selected from at least about 10 species (e.g. about or at least about 10, 11 , 12, 13, 14, 15, 20, or 25 or more species) each having about or at least about 96%, about or at least about 97%, about or at least about 98%, or about or at least about 99% sequence identity to the 16S rRNA sequence of bacterial species selected from Table 1 d (e.g., 16S rRNA sequences listed in Table 12 as SEQ ID NOs: 1-715).

[0181] In embodiments, bacterial consortia herein comprise about or at least about 12 isolates, about or at least about 13 isolates, about or at least about 14 isolates, about or at least about 15 isolates, about or at least about 16 isolates, about or at least about 17 isolates, about or at least about 18 isolates, about or at least about 19 isolates, about or at least about 20 isolates, about or at least about 21 isolates, about or at least about 22 isolates, about or at least about 23 isolates, about or at least about 24 isolates, about or at least about 25 isolates, about or at least about 30 isolates, or about or at least about 35 isolates selected from Table 1d. In embodiments, bacterial consortia herein comprise about or at least about 11 species, about or at least about 12 species, about or at least about 13 species, about or at least about 14 species, about or at least about 15 species, about or at least about 16 species, about or at least about 17 species, about or at least about 18 species, about or at least about 19 species, about or at least about 20 species, or about or at least about 25 species selected from Table 1d.

[0182] In non-limiting embodiments, the plurality of bacterial isolates and / or species selected from Table 1 d comprise one or more of Alistipes montrealensis, Bacteroides cellulosilyticus, Bacteroides clams, Bacteroides intestinigallinarum, Blautia_A faecis, Blautia_A obeum, Blautia_A sp900066145, Blautia_A sp900066335, Blautia_A wexlerae, Blautia_A wexlerae_B, CAG-41 sp900066215, Clostridium_Q symbiosum, Coprococcus eutactus, Dysosmobacter welbionis, Eisenbergiella tayi, Flavonifractor plautii, Intestinimonas butyriciproducens, Mediterraneibacter faecis, Parabacteroides goldsteinii, Parabacteroides johnsonii, Parabacteroides merdae, Phascolarctobacterium sp900544795, Phocaeicola massiliensis, Roseburia inulinivorans, and Ruminococcus_B gnavus.

[0183] In embodiments, bacterial consortia herein comprise at least about 12 isolates (e.g. about or at least about 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, 24, 25, 30, or 35 or more isolates) selected from at least about 10 species (e.g. about or at least about 10, 11 , 12, 13, 14, 15, 20, or 25 or more species) each having about or at least about 96%, about or at least about 97%, about or at least about 98%, or about or at leastDBl / 161604598.2 49Atorney Docket No.: 137085-5001 -PC about 99% sequence identity to the 16S rRNA sequences of bacterial species selected from Table 1e and / or Table 1f (e.g., 16S rRNA sequences listed in Table 12 as SEQ ID NOs: 1-715).

[0184] In embodiments, bacterial consortia herein comprise about or at least about 12 isolates, about or at least about 13 isolates, about or at least about 14 isolates, about or at least about 15 isolates, about or at least about 16 isolates, about or at least about 17 isolates, about or at least about 18 isolates, about or at least about 19 isolates, about or at least about 20 isolates, about or at least about 21 isolates, about or at least about 22 isolates, about or at least about 23 isolates, about or at least about 24 isolates, about or at least about 25 isolates, about or at least about 30 isolates, or about or at least about 35 isolates selected from Table 1e and / or Table 1f. In embodiments, bacterial consortia herein comprise about or at least about11 species, about or at least about 12 species, about or at least about 13 species, about or at least about 14 species, about or at least about 15 species, about or at least about 16 species, about or at least about 17 species, about or at least about 18 species, about or at least about 19 species, about or at least about 20 species, or about or at least about 25 species selected from Table 1e and / or Table 1f.

[0185] In non-limiting embodiments, the plurality of bacterial isolates and / or species selected from Tables 1e and / or Table 1f comprises one or more of Agathobaculum butyriciproducens, Alistipes communis, Anaerobutyricum hallii, Bariatricus comes, Bifidobacterium adolescentis, Bifidobacterium longum, CAG-317 sp000433215, Coprobacter fastidiosus, Coprococcus eutactus, Coprococcus_A catus, Dorea formicigenerans, Faecalibacterium longum, Faecalibacterium prausnitzii, Faecalibacterium prausnitzii_D, Gemmiger formicilis, Oliverpabstia intestinalis, Peptostreptococcus anaerobius, Roseburia hominis, Roseburia intestinalis, Roseburia inulinivorans, and Ruminococcus_E bromii_B.

[0186] In embodiments, bacterial consortia herein comprise at least about 1 isolate (e.g. about or at least about 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, or 15 or more isolates) selected from at least about 1 species (e.g. about or at least about 1 , 2, 3, 4, 5, or 6 or more species) each having about or at least about 96%, about or at least about 97%, about or at least about 98%, or about or at least about 99% sequence identity to the 16S rRNA sequences of bacterial species selected from Table 1 g (e.g., 16S rRNA sequences listed in Table 12 as SEQ ID NOs: 1-715).

[0187] In embodiments, bacterial consortia herein comprise about or at least about 1 isolate, about or at least about 2 isolates, about or at least about 3 isolates, about or at least about 4 isolates, about or at least about 5 isolates, about or at least about 6 isolates, about or at least about 7 isolates, about or at least about 8 isolates, about or at least about 9 isolates, about or at least about 10 isolates, or about or at least about 15DBl / 161604598.2 50Atorney Docket No.: 137085-5001 -PC isolates selected from Table 1 g. In embodiments, bacterial consortia herein comprise about or at least about 1 species, about or at least about 2 species, about or at least about 3 species, about or at least about 4 species, about or at least about 5 species, or about or at least about 6 species selected from T able 1 e and / or Table 1f.

[0188] In non-limiting embodiments, the plurality of bacterial isolates and / or species selected from Table 1 g comprises one or more of Bacteroides eggerthii, Bifidobacterium adolescentis, Bacteroides fragilis, Bacteroides ovatus, Bacteroides thetaiotaomicron, and Parabacteroides distasonis.

[0189] In embodiments, bacterial consortia herein comprise at least about 1 isolate (e.g. about or at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or 15 or more isolates) selected from the 1 species listed in Table 1 h, each having about or at least about 96%, about or at least about 97%, about or at least about 98%, or about or at least about 99% sequence identity to the 16S rRNA sequences of bacterial species selected from Table 1 h (e.g., 16S rRNA sequences listed in Table 12 as SEQ ID NOs: 1-715).

[0190] In embodiments, bacterial consortia herein comprise about or at least about 1 isolate, about or at least about 2 isolates, about or at least about 3 isolates, about or at least about 4 isolates, about or at least about 5 isolates, about or at least about 6 isolates, about or at least about 7 isolates, about or at least about 8 isolates, about or at least about 9 isolates, about or at least about 10 isolates, or about or at least about 15 isolates selected from Table 1 h. In embodiments, bacterial consortia herein comprise the species listed in Table 1 h.

[0191] In non-limiting embodiments, the plurality of bacterial isolates and / or species selected from Table 1 h comprises Peptostreptococcus anaerobius.

[0192] In embodiments, bacterial consortia herein comprise at least about 1 isolate (e.g. about or at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or 15 or more isolates) selected from the 1 or 2 species listed in Table 1 i, each having about or at least about 96%, about or at least about 97%, about or at least about 98%, or about or at least about 99% sequence identity to the 16S rRNA sequences of bacterial species selected from Table 1 i (e.g., 16S rRNA sequences listed in Table 12 as SEQ ID NOs: 1-715).

[0193] In embodiments, bacterial consortia herein comprise about or at least about 1 isolate, about or at least about 2 isolates, about or at least about 3 isolates, about or at least about 4 isolates, about or at least about 5 isolates, about or at least about 6 isolates, about or at least about 7 isolates, about or at least about 8 isolates, about or at least about 9 isolates, about or at least about 10 isolates, or about or at least about 15DBl / 161604598.2 51Atorney Docket No.: 137085-5001 -PC isolates selected from Table 11. In embodiments, bacterial consortia herein comprise the species listed in Table 1i.

[0194] In non-limiting embodiments, the plurality of bacterial isolates and / or species selected from Table 1 h comprises Clostridium_AP sp000509125 and Clostridium_AP scindens.

[0195] In embodiments, bacterial consortia herein comprise at least about 30 isolates (e.g. about or at least about 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 or more isolates) selected from at least about 20 species (e.g. about or at least about 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, or 85 or more species) each having about or at least about 96%, about or at least about 97%, about or at least about 98%, or about or at least about 99% sequence identity to the 16S rRNA sequences of bacterial species selected from Table 1 b (e.g., 16S rRNA sequences listed in Table 12 as SEQ ID NOs: 1-715).

[0196] In embodiments, bacterial consortia herein comprise about or at least about 30 isolates, about or at least about 35 isolates, about or at least about 40 isolates, about or at least about 45 isolates, about or at least about 50 isolates, about or at least about 55 isolates, about or at least about 60 isolates, about or at least about 65 isolates, about or at least about 70 isolates, about or at least about 75, about or at least about 80, about or at least about 85, about or at least about 90, about or at least about 95, about or at least about 100, selected from about or at least about 30 species, about or at least about 35 species, about or at least about 40 species, about or at least about 45 species, about or at least about 50 species, about or at least about 55 species, about or at least about 60 species, about or at least about 65 species, about or at least about 70 species, about or at least about 75 species, about or at least about 80 species, or about or at least about 85 species selected from Table 1 b.

[0197] In non-limiting embodiments, the plurality of bacterial isolates and / or species selected from Table 1 b comprise one or more of Acetatifactor sp., Agathobacter faecis, AHstipes finegoldii, AHstipes onderdonkii, AHstipes putredinis, AHstipes senegalensis, AHstipes shahii, Alistipes_A ihumii, Alistipes_A indistinctus, Anaerotignum faecicola, Avimicrobium caecorum, Bacteroides eggerthii, Bacteroides finegoldii, Bacteroides fragilis, Bacteroides luhongzhouii, Bacteroides ovatus, Bacteroides stercoris, Bacteroides xylanisolvens, Barnesiella intestinihominis, Bifidobacterium bifidum, Bifidobacterium sp., Bittarella massiliensis, Blautia_A massiliensis, Blautia_A sp., Blautia_A sp900066505, Butyricicoccus sp900604335, Butyricimonas sp., Catenibacterium sp000437715, Choladousia sp902363665, Christensenella minuta, Clostridium_A leptum, Clostridium_AP sp., Dialister invisus, Diplocloster agilis, Dorea_A sp., Faecalibacillus intestinalis, Faecalibacterium duncaniae, Fusicatenibacter saccharivorans, Harryflintia acetispora, Holdemanella sp.,DBl / 161604598.2 52Atorney Docket No.: 137085-5001 -PCIntestinimonas massiliensis, KLE1615 sp900066985, Lachnoclostridium_B sp900066555, Lachnospira eligens, Lachnospira eligens_A, Lachnospira rogosae, Lachnospira sp000437735, Mediterraneibacter lactaris, Monoglobus pectinilyticus, Muricomes sp000509105, Parabacteroides distasonis, Paraprevotella xylaniphila, Phocaeicola dorei, Prevotella copri_B, Prevotella rara, Ruminococcus_D bicirculans, Ruminococcus_E sp003526955, Ruthenibacterium lactatiformans, Slackia_A isoflavoniconveriens, Tractidigestivibacter sp., Turicibacter sanguinis, and UBA3402 sp003478355.

[0198] Persons having ordinary skill in the art, with the benefit of this disclosure in its entirety, will understand that the ranges of bacterial species / isolates selected from Table 1 a, Table 1 b, Table 1c, Table 1 d, Table 1 e, Table 1f, Table 1g, Table 1 h, and Table 1i to make the isolated plurality of bacterial species herein can include any number of species / isolates within or between the ranges described herein to satisfy the design criteria described herein. In embodiments, specific ranges or numbers of species / isolates are illustrative.

[0199] In embodiments, about or at least 30%, about or at least 40%, about or at least 50%, about or at least 60%, about or at least 70%, about or at least 80%, or about or at least 90% of the bacterial species / isolates listed in Table 1 a are present in the plurality of bacterial species. In embodiments, the plurality of bacterial species comprises about or at least about 8, about or at least about 9, about or at least about 10, about or at least about 12, about or at least about 14, about or at least about 16, about or at least about 18, about or at least about 20, about or at least about 22, about or at least about 24, about or at least about 28, or about 30 of the bacterial species / isolates listed in Table 1 a.

[0200] In embodiments, about or at least 30%, about or at least 40%, about or at least 50%, about or at least 60%, about or at least 70%, about or at least 80%, or about or at least 90% of the bacterial species / isolates listed in Table 1c are present in the plurality of bacterial species. In embodiments, the plurality of bacterial species comprises about or at least about 8, about or at least about 9, about or at least about 10, about or at least about 12, about or at least about 14, about or at least about 16, about or at least about 18, about or at least about 20, about or at least about 22, about or at least about 24, about or at least about 28, or about 32 of the bacterial species / isolates listed in Table 1c.

[0201] In embodiments, about or at least 30%, about or at least 40%, about or at least 50%, about or at least 60%, about or at least 70%, about or at least 80%, or about or at least 90% of the bacterial species / isolates listed in Table 1 d are present in the plurality of bacterial species. In embodiments, the plurality of bacterial species comprises about or at least about 8, about or at least about 9, about or at leastDBl / 161604598.2 53Atorney Docket No.: 137085-5001 -PC about 10, about or at least about 12, about or at least about 14, about or at least about 16, about or at least about 18, about or at least about 20, about or at least about 22, about or at least about 24, about or at least about 28, or about 32 of the bacterial species / isolates listed in Table 1 d.

[0202] In embodiments, about or at least 30%, about or at least 40%, about or at least 50%, about or at least 60%, about or at least 70%, about or at least 80%, or about or at least 90% of the bacterial species / isolates listed in Table 1e are present in the plurality of bacterial species. In embodiments, the plurality of bacterial species comprises about or at least about 8, about or at least about 9, about or at least about 10, about or at least about 12, about or at least about 14, about or at least about 16, about or at least about 18, about or at least about 20, about or at least about 22, about or at least about 24, about or at least about 28, or about or at least about 32 of the bacterial species / isolates listed in Table 1e.

[0203] In embodiments, about or at least 30%, about or at least 40%, about or at least 50%, about or at least 60%, about or at least 70%, about or at least 80%, or about or at least 90% of the bacterial species / isolates listed in Table 1f are present in the plurality of bacterial species. In embodiments, the plurality of bacterial species comprises about or at least about 1 , about or at least about 2, about or at least about 3, about or at least about 4, about or at least about 5, about or at least about 6, about or at least about 7, about or at least about 8, or about 9 of the bacterial species / isolates listed in Table 1f.

[0204] In embodiments, about or at least about 1 out of 6, 2 out of 6, 3 out of 6, 4 out of 6, 5 out of 6, or all 6 of the bacterial species / isolates listed in Table 1 g are present in the plurality of bacterial species. In embodiments, the plurality of bacterial species comprises about or at least about 1 , about or at least about 2, about or at least about 3, about or at least about 4, about or at least about 5, or about or at least about 6 of the bacterial species listed in Table 1 g.

[0205] In embodiments, about or at least about 1 bacterial species / isolates listed in Table 1 h are present in the plurality of bacterial species.

[0206] In embodiments, about or at least about 1 or about or at least about 2 of the bacterial species / isolates listed in Table 1 i are present in the plurality of bacterial species.

[0207] In embodiments, about or at least 10%, about or at least 20%, about or at least 30%, about or at least 40%, about or at least 50%, about or at least 60%, about or at least 70%, or about or at least about 80% of the bacterial species / isolates listed in Table 1 b are present in the plurality of bacterial species. In embodiments, the plurality of bacterial species comprises about or at least about 20, about or at least aboutDBl / 161604598.2 54Atorney Docket No.: 137085-5001 -PC25, about or at least about 30, about or at least about 35, about or at least about 40, about or at least about 45, about or at least about 50, about or at least about 55, about or at least about 60, about or at least about 65, or about or at least about 70 of the bacterial species / isolates listed in Table 1 b.

[0208] In embodiments, multiple isolates / strains exist for some bacterial species. For example, in nonlimiting embodiments, and in reference to Table 12, for Anaerostipes hadrus, there are three genomic taxa identifiers listed (MBSID) - MBS001 , MBS007, and MBS075 - which, collectively, refer to 19 different 16S rRNA sequences (e.g., SEQ ID NOs: 1-19), or 19 different isolates for that species. In embodiments, the plurality of bacterial species comprise about or at least about 1 isolate per species, about or at least about 2 isolates per species, about or at least about 3 isolates per species, about or at least about 4 isolates per species, about or at least about 5 isolates per species, about or at least about 6 isolates per species, about or at least about 7 isolates per species, about or at least about 8 isolates per species, about or at least about 9 isolates per species, or about or at least about 10 isolates per species. This provides, in embodiments, redundancy in MoAs that ensure the bacterial consortia operates as expected, even if all the isolates of a species or all species from the plurality of species does not adequately grow in the host’s gastrointestinal tract.

[0209] In embodiments, the plurality of bacterial species comprises no more than about 15 individual bacterial species per genera, no more than about 10 individual bacterial species per genera, no more than about 8 individual bacterial species per genera, no more than about 6 individual bacterial species per genera, no more than about 5 individual bacterial species per genera, no more than about 4 individual bacterial species per genera, no more than about 3 individual bacterial species per genera, no more than about 2 individual bacterial species per genera, or no more than a single individual bacterial species per genera.

[0210] In embodiments, the plurality of bacterial species comprises about or at least about 85 distinct bacterial genera, about or at least about 80 distinct bacterial genera, about or at least about 75 distinct bacterial genera, about or at least about 70 distinct bacterial genera, about or at least about 65 distinct bacterial genera, about or at least about 60 distinct bacterial genera, about or at least about 50 distinct bacterial genera, or about or at least about 40 distinct bacterial genera.

[0211] In embodiments, each bacterial species of the plurality of bacterial species has about or at least about 96%, about or at least about 97%, about or at least about 98%, about or at least about 99%, or about 100% 16S rRNA similarity to a bacterial species selected from T able 1 a, T able 1 b, Table 1 c, T able 1 d, T able 1 e, Table 1f, Table 1g, Table 1h, and / or Table 1i, Table 3, Table 5, Table 7, Table 8, or Table 12.DBl / 161604598.2 55Atorney Docket No.: 137085-5001 -PC

[0212] In embodiments, the plurality of bacterial species comprises about or at least about 5 species, about or at least about 6 species, about or at least about 7 species, about or at least about 8 species, about or at least about 9 species, about or at least about 10 species, about or at least about 11 species, about or at least about 12 species, about or at least about 13 species, about or at least about 14 species, about or at least about 15 species, about or at least about 16 species, about or at least about 17 species, about or at least about 18 species, about or at least about 19 species, about or at least about 20 species, or about or at least about 25 species having at least about 95% rRNA similarly to a bacterial species selected from Table 1 a.

[0213] In embodiments, the plurality of bacterial species comprises about or at least about 5 species, about or at least about 6 species, about or at least about 7 species, about or at least about 8 species, about or at least about 9 species, about or at least about 10 species, about or at least about 11 species, about or at least about 12 species, about or at least about 13 species, about or at least about 14 species, about or at least about 15 species, about or at least about 16 species, about or at least about 17 species, about or at least about 18 species, about or at least about 19 species, about or at least about 20 species, or about or at least about 25 species selected from Table 1a.

[0214] In embodiments, the plurality of bacterial species comprises about or at least about 40 species, about or at least about 45 species, about or at least about 50 species, about or at least about 55 species, about or at least about 60 species, about or at least about 65 species, about or at least about 70 species, about or at least about 75 species, about or at least about 80 species, about or at least about 85 species, about or at least about 90 species, about or at least about 95 species, about or at least about 100 species, about or at least about 105 species, about or at least about 110 species, about or at least about 115 species, about or at least about 120 species, about or at least about 125 species, about or at least about 130 species, about or at least about 135 species, about or at least about 140 species having at least about 95% rRNA similarly to a bacterial species selected from Table 1 b.

[0215] In embodiments, the plurality of bacterial species comprises about or at least about 40 species, about or at least about 45 species, about or at least about 50 species, about or at least about 55 species, about or at least about 60 species, about or at least about 65 species, about or at least about 70 species, about or at least about 75 species, about or at least about 80 species, about or at least about 85 species, about or at least about 90 species, about or at least about 95 species, about or at least about 100 species, about or at least about 105 species, about or at least about 110 species, about or at least about 115 species,DBl / 161604598.2 56Atorney Docket No.: 137085-5001 -PC about or at least about 120 species, about or at least about 125 species, about or at least about 130 species, about or at least about 135 species, about or at least about 140 species selected from Table 1 b.

[0216] In embodiments, bacterial species selection is guided by in silico analyses incorporating statistical, computational, and machine-learning modeling to select individual species from a cohort of bacterial species existing in the microbiomes of healthy humans (e.g., as shown in Figs. 3A-3B). For example, in embodiments and in reference to Figs. 3A-3B, illustrative 100-target taxa (Fig. 3A) and 200- target taxa (Fig. 3B) bacterial consortia are arranged based on similarity between bacterial species relative to the bacterial populations observed in healthy humans. For example, in embodiments and in reference to Figs. 3A-3D, illustrative computational prediction of healthy bacterial consortia are generated from 3,000 healthy volunteer (HV) metagenomes. In embodiments, target consortia profiles are generated using outputs, e.g., as shown in Fig. 3A-3D.

[0217] In embodiments, the in silico analyses include the generation of one or more machine-learning models based on the type of analysis that is performed. In embodiments, the machine-learning model is a probabilistic model, including in non-limiting examples, naive Bayes classifiers, Bayesian networks, Gaussian mixture models (GMMs), hidden Markov models (HMMs), neural networks (NNs), probabilistic neural networks (PNNs), radial basis function networks (RBFNs), probabilistic latent semantic analyses (pLSAs), and latent Dirichlet allocations (LDAs). In embodiments, the machine-learning model is a supervised machine-learning model, including in non-limiting examples, linear and polynomial regression models, lasso and ridge regression models, logistic regression, decision trees, random forest, support vector machines (SVMs), K-nearest neighbors (KNN), and some NNs. In embodiments, the machine-learning model is an unsupervised machine-learning model, including in non-limiting examples, K-means and hierarchical clustering, density-based spatial clustering of applications with noise (DBSCAN), principal component analysis (PCA), and t-distributed stochastic neighbor embedding (t-SNE). Persons skilled in the art, upon the benefit of this disclosure in its entirety, will be aware of the various algorithms and machine-learning models that can be used to perform the types of analyses described herein. Additionally, those skilled in the art would understand that several machine-learning models can be used to achieve the same, or similar, functionality, and that many models can be used in one or more different type of machine-learning, for example NNs (e.g., autoencoders) are useful for both supervised and unsupervised machine-learning processes, and likewise, GMMs and HMMs can be used for probabilistic machine-learning modeling and for unsupervised machinelearning processes.DBl / 161604598.2 57Atorney Docket No.: 137085-5001 -PC

[0218] In embodiments, outputs (like that shown in Fig. 3A-3D) are generated to visualize results to aid in selection of bacterial species / isolates using one or more of a principal coordinate analysis (PCoA) and / or beta diversity method (e.g., with Hamming distance shown between points). In embodiments, principal coordinate analysis (PCoA) is a linear dimensionality reduction technique with applications in exploratory data analysis, visualization, and data preprocessing. In embodiments, beta diversity (P-diversity or true beta diversity) is the measure of the difference between two bacterial communities’ composition and is calculated in several ways, some of which reduce the impact of rarer species or less abundant species. In embodiments, beta diversity is also a measure of “nestedness,” which occurs when bacterial species assemblages in species-poor sites are a subset of the assemblages in more species-rich sites. In embodiments, the Hamming distance between two strings or vectors of equal length is the number of positions at which the corresponding symbols are different. In embodiments, the Hamming distance is one of several string metrics for measuring the edit distance (e.g., functional / genetic similarity) between two sequences (e.g., between two bacterial taxa - species, isolates, or strains). In other words, in embodiments, the one or more metrics above measure the minimum number of substitutions required to change one vector of the abundance of bacterial taxa into another, or equivalently, the minimum number of “errors” or “steps” that could transform one into another.

[0219] In embodiments, bacterial species selection is guided by in silica analyses determining the relative levels of microbiome biomass that is capturable by select numbers of prevalent bacterial species. For example, in embodiments and in reference to Figs. 4A-4C, an illustrative graphical representation is shown of an analysis showing the fraction of bacterial community abundance (in terms of number of species / isolates observed) that is captured at various sizes of bacterial consortia (e.g., count). In embodiments, the number of species / isolates selected in the composition is increased or decreased based on the desired level of microbiome biomass capture and based on the desired level of total abundance among microbiomes of healthy humans.

[0220] In embodiments, bacterial species selection is based on sequencing data and / or metagenomic data analyses for the presence of a metabolic gene and / or enzyme (or a functional equivalent). In embodiments, bacterial species selection is based on functional screening for the presence of a metabolic gene and / or enzyme, including detecting the ability for growth from particular starting metabolites and / or detecting the presence of pathway intermediates, in addition to testing for the presence of the end molecule of the pathway(s). In embodiments, the “genetic sequence,” “gene cluster,” or “gene,” of the bacteria may be distributed as one or more DNA sequences (e.g., an operon, open-reading frame (ORF), or a part thereof),DBl / 161604598.2 58Atorney Docket No.: 137085-5001 -PC or may be found in the bacterial chromosome or on a plasmid (e.g., “F plasmid,” “R plasmid,” etc.) maintained by a particular subspecies / isolate.

[0221] In embodiments, “synthesis,” or “production,” or references to bacterial synthesis / production, or references to selection based on the synthesis / production of a molecule herein, refers to the ability of one or more bacterial species / isolates to synthesize a molecule from one or more molecules available in the media and / or human gastrointestinal tract, including any macromolecules and their constituent parts (e.g., amino acids, carbohydrates, lipids, etc.), carbon sources, nitrogen sources, vitamins, minerals, bile acids / salts, or other molecules that are part of a human diet or would otherwise be available in the gut. In embodiments, metabolite quantification is performed with liquid chromatography-mass spectrometry (LC-MS) and / or HPLC- based methods.

[0222] In embodiments, the plurality of bacterial species exhibits a distributed capability to synthesize butyrate, where one or more butyrate synthesis pathway is distributed amongst the collective genomes of the bacterial consortium. In embodiments, about or at least about 20% of the total bacterial species, about or at least about 25% of the total bacterial species, about or at least about 30% of the total bacterial species, about or at least about 35% of the total bacterial species, about or at least about 40% of the total bacterial species, about or at least about 45% of the total bacterial species, about or at least about 50% of the total bacterial species, about or at least about 55% of the total bacterial species, about or at least about 60% of the total bacterial species, about or at least about 65% of the total bacterial species, about or at least about 70% of the total bacterial species, at least 75% of the total bacterial species, about or at least about 80% of the total bacterial species, at least 85% of the total bacterial species, about or at least about 90% of the total bacterial species, or about or at least about 95% of the total bacterial species of the plurality of bacterial species comprises a butyrate synthesis pathway and / or encodes at least one enzyme suitable for synthesizing butyrate.

[0223] In embodiments, an individual bacterial species of the plurality of bacterial species is capable of synthesizing butyrate. In embodiments, about or at least about 25 of the total bacterial species, about or at least about 30 of the total bacterial species, about or at least about 35 of the total bacterial species, about or at least about 40 of the total bacterial species, about or at least about 45 of the total bacterial species, about or at least about 50 of the total bacterial species, about or at least about 55 of the total bacterial species, about or at least about 60 of the total bacterial species, about or at least about 65 of the total bacterial species, about or at least about 70 of the total bacterial species, about or at least about 75 of the total bacterial species,DBl / 161604598.2 59Atorney Docket No.: 137085-5001 -PC about or at least about 80 of the total bacterial species, about or at least about 85 of the total bacterial species, about or at least about 90 of the total bacterial species, about or at least about 95 of the total bacterial species, or about or at least about 100 of the total bacterial species of the plurality of bacterial species comprises a butyrate synthesis pathway and / or encodes at least one enzyme suitable for synthesizing butyrate.

[0224] There are four main butyrate pathways in healthy human gut microbiomes, but different diets and health states can favor efficient production of butyrate through different combinations of these pathways. In embodiments, bacterial consortia herein are designed to have at least one of each of these four pathways present at sufficient abundance post-dosing, to provide robust and efficient butyrate production regardless of the exact diet or patient background microbiome. In embodiments, the four pathways are the glutarate pathway, acetyl-CoA (classical), pathway lysine pathway, and 4-ami nobutyrate (GABA)Zsuccinate pathway.

[0225] In embodiments, the butyrate synthesis pathway comprises one or more pathways selected from the glutarate pathway, acetyl-CoA (classical), pathway lysine pathway, and 4-aminobutyrate (GABA)Zsuccinate pathway. In embodiments, the butyrate synthesis pathway comprises each of a glutarate pathway, acetyl-CoA pathway, lysine pathway, and 4-ami nobutyrate / succinate pathway. In embodiments, the plurality of bacterial species comprises a distributed capability to synthesize butyrate via at least 2 butyrate synthesis pathways, at least 3 butyrate synthesis pathways, or at least 4 butyrate synthesis pathways, e.g., to increase the robustness across patient gut communities, gut environments, and / or dietary inputs.

[0226] In embodiments, the glutarate pathway comprises one or more genes encoding one or more enzymes selected from 2-hydroxyglutarate dehydrogenase (L2HgdH), glutaconate CoA transferase (comprising a, subunits) (Get), 2-hydroxy-glutaryl-CoA dehydrogenase (comprising a, 0, y subunits) (HgCoAd), glutaconyl-CoA decarboxylase (comprising a, 0 subunits) (Gcd), butyryl-CoA dehydrogenase (comprising electron transfer protein a, 0 subunits) (Bcd-(aP)), and an enzyme having equivalent functionality thereof. In embodiments, bacterial species / isolates are selected based on the presence of one or more genetic sequence encoding one or more of L2HgdH, Get, HgCoAd, Gcd, Bcd-(oP), or an enzyme having equivalent functionality thereof. In embodiments, bacterial species / isolates are selected based on functional screening for the presence of one or more of L2HgdH, Get, HgCoAd, Gcd, Bcd-(oP), or an enzyme having equivalent functionality thereof.

[0227] In embodiments, the acetyl-CoA pathway comprises one or more genes encoding one or more enzymes selected from thiolase (Thl), 0-hydroxybutyryl-CoA dehydrogenase (hbd), crotonase (Cro), butyryl- CoA dehydrogenase (including electron transfer protein a, 0 subunits) (Bcd-(aP)), butyryl-CoA:acetate CoADBl / 161604598.2 60Atorney Docket No.: 137085-5001 -PC transferase (But), phosphate butyryltransferase (Ptb), butyrate kinase (Buk), and an enzyme having equivalent functionality thereof. In embodiments, bacterial species / isolates are selected based on the presence of one or more genetic sequence encoding one or more of Thl, hbd, Cro, Bcd-(aP), But, Ptb, Buk, or an enzyme having equivalent functionality thereof. In embodiments, bacterial species / isolates are selected based on functional screening for the presence of one or more of Thl, hbd, Cro, Bcd-(aP), But, Ptb, Buk, or an enzyme having equivalent functionality thereof.

[0228] In embodiments, the lysine pathway comprises one or more genes encoding one or more enzymes selected from lysine-2,3-aminomutase (KamA), p-lysine-5,6-aminomutase (comprising a, p subunits) (KamD,E), 3,5-diaminohexanoate dehydrogenase (Kdd), 3-keto-5-aminohexanoate cleavage enzyme (Kce), 3-aminobutyryl-CoA ammonia lyase (Kai), butyryl-CoA dehydrogenase (including electron transfer protein a, p subunits) (Bcd-(aP)), butyryl-CoA: acetoacetate CoA transferase (comprising a, p subunits) (Ato), and an enzyme having equivalent functionality thereof. In embodiments, bacterial species / isolates are selected based on the presence of one or more genetic sequence encoding one or more KamA, KamD,E, Kdd, Kce, Kai, Bcd-(aP), Ato, or an enzyme having equivalent functionality thereof. In embodiments, bacterial species / isolates are selected based on functional screening for the presence of one or more of KamA, KamD,E, Kdd, Kce, Kai, Bcd-(aP), Ato, or an enzyme having equivalent functionality thereof.

[0229] In embodiments, the 4-aminobutyrate / succinate pathway comprises one or more genes encoding one or more enzymes selected from 4-hydroxybutyrate dehydrogenase (AbfH), 4-hydroxybutyryl- CoA dehydratase (AbfD), vinylacetyl-CoA 3,2-isomerase (same protein as AbfD), butyryl-CoA:4- hydroxybutyrate CoA transferase (4Hbt), and an enzyme having equivalent functionality thereof. In embodiments, bacterial species / isolates are selected based on the presence of one or more genetic sequence encoding one or more of AbfH, AbfD, 4Hbt, or an enzyme having equivalent functionality thereof. In embodiments, bacterial species / isolates are selected based on functional screening for the presence of one or more of AbfH, AbfD, 4Hbt, or an enzyme having equivalent functionality thereof.

[0230] In embodiments, the butyrate synthesis pathway comprises having one or more genes encoding a butyryl-CoA dehydrogenase (Bed) or an enzyme having equivalent functionality thereof.

[0231] In embodiments, the plurality of bacterial species substantially produces butyrate in a gastrointestinal tract (e.g., human gastrointestinal tract, including the stomach, small intestine, large intestine, colon, and rectum). In embodiments, the production is an improvement over a baseline butyrate level byDBl / 161604598.2 61Atorney Docket No.: 137085-5001 -PC about or at least about 20%, about or at least about 40%, about or at least about 60%, about or at least about 80%, or about or at least about 100% relative to the pre-treatment level of butyrate, as measured by one or more of metabolomic measurement of butyrate, butyrate in fecal material, metabolomics of patient serum, enzyme activity, excreted metabolites, and / or blood serum metabolites. Persons skilled in the art, with the benefit of this disclosure in its entirety, will understand the methods used to assess the level of metabolites produced based on stool metabolomics, or an equivalent method thereof.

[0232] In embodiments, the plurality of bacterial species exhibits a distributed capability to synthesize propionate, where one or more propionate synthesis pathway is distributed amongst the collective genomes of the bacterial consortium. In embodiments, about or at least about 20% of the total bacterial species, about or at least about 25% of the total bacterial species, about or at least about 30% of the total bacterial species, about or at least about 35% of the total bacterial species, about or at least about 40% of the total bacterial species, about or at least about 45% of the total bacterial species, about or at least about 50% of the total bacterial species, about or at least about 55% of the total bacterial species, about or at least about 60% of the total bacterial species, about or at least about 65% of the total bacterial species, about or at least about 70% of the total bacterial species, about or at least about 75% of the total bacterial species, about or at least about 80% of the total bacterial species, about or at least about 85% of the total bacterial species, about or at least about 90% of the total bacterial species, or about or at least about 95% of the total bacterial species of the plurality of bacterial species comprises a propionate synthesis pathway and / or encodes at least one enzyme suitable for synthesizing propionate.

[0233] In embodiments, individual bacterial species of the plurality of bacterial species is capable of synthesizing propionate. In embodiments, about or at least about 25 of the total bacterial species, about or at least about 30 of the total bacterial species, about or at least about 35 of the total bacterial species, about or at least about 40 of the total bacterial species, about or at least about 45 of the total bacterial species, about or at least about 50 of the total bacterial species, about or at least about 55 of the total bacterial species, about or at least about 60 of the total bacterial species, about or at least about 65 of the total bacterial species, about or at least about 70 of the total bacterial species, about or at least about 75 of the total bacterial species, about or at least about 80 of the total bacterial species, about or at least about 85 of the total bacterial species, about or at least about 90 of the total bacterial species, about or at least about 95 of the total bacterial species, or about or at least about 100 of the total bacterial species of the plurality of bacterial species comprises a propionate synthesis pathway and / or encodes at least one enzyme suitable for synthesizing propionate.DBl / 161604598.2 62Atorney Docket No.: 137085-5001 -PC

[0234] In embodiments, the propionate synthesis pathway comprises one or more pathways selected from a succinate pathway (mmdA gene cluster), acrylate pathway (LcdA gene cluster), and propanediol pathway (PduP gene cluster). In embodiments, the propionate synthesis pathway comprises each of a succinate pathway, acrylate pathway, and propanediol pathway. In embodiments, the plurality of bacterial species comprises a distributed capability to synthesize butyrate via at least 2 propionate synthesis pathways, or at least 3 propionate synthesis pathways.

[0235] In embodiments, bacterial species / isolates are selected based on the presence of one or more genetic sequence encoding one or more of mmdA gene cluster, or an enzyme having equivalent functionality from one or more genes thereof. In embodiments, bacterial species / isolates are selected based on functional screening for the presence of mmdA gene cluster, or an enzyme having equivalent functionality from one or more genes thereof.

[0236] In embodiments, bacterial species / isolates are selected based on the presence of one or more genetic sequence encoding one or more of LcdA gene cluster, or an enzyme having equivalent functionality from one or more genes thereof. In embodiments, bacterial species / isolates are selected based on functional screening for the presence of LcdA gene cluster, or an enzyme having equivalent functionality from one or more genes thereof.

[0237] In embodiments, bacterial species / isolates are selected based on the presence of one or more genetic sequence encoding one or more of PduP gene cluster, or an enzyme having equivalent functionality from one or more genes thereof. In embodiments, bacterial species / isolates are selected based on functional screening for the presence of PduP gene cluster, or an enzyme having equivalent functionality from one or more genes thereof.

[0238] In embodiments, the plurality of bacterial species substantially produces propionate in a gastrointestinal tract (e.g., human gastrointestinal tract, including the stomach, small intestine, large intestine, colon, and rectum). In embodiments, the production is an improvement over a baseline propionate level by about or at least about 20%, about or at least about 40%, about or at least about 60%, about or at least about 80%, or about or at least about 100% relative to the pre-treatment level of propionate, as measured by one or more of metabolomic measurement of propionate, propionate in fecal material, metabolomics of patient serum, enzyme activity, excreted metabolites, and / or blood serum metabolites.

[0239] In embodiments, the plurality of bacterial species exhibits a distributed capability to synthesize IAA, where one or more IAA synthesis pathway is distributed amongst the collective genomes of the bacterialDBl / 161604598.2 63Atorney Docket No.: 137085-5001 -PC consortium. In embodiments, about or at least about 1% of the total bacterial species, about or at least about 2% of the total bacterial species, about or at least about 3% of the total bacterial species, about or at least about 4% of the total bacterial species, about or at least about 5% of the total bacterial species, about or at least about 6% of the total bacterial species, about or at least about 7% of the total bacterial species, about or at least about 8% of the total bacterial species, about or at least about 9% of the total bacterial species, about or at least about 10% of the total bacterial species, about or at least about 15% of the total bacterial species, or about or at least about 20% of the total bacterial species comprises an IAA synthesis pathway and / or encodes at least one enzyme suitable for synthesizing IAA.

[0240] In embodiments, individual bacterial species of the plurality of bacterial species is capable of synthesizing IAA. In embodiments, about or at least about 1 species / isolate produces IAA, about or at least about 2 species / isolates produces IAA, about or at least about 3 species / isolates produces IAA, about or at least about 4 species / isolates produces IAA, about or at least about 5 species / isolates produces IAA, about or at least about 10 species / isolates produces IAA, about or at least about 15 species / isolates produces IAA, or about or at least about 20 species / isolates produces IAA.

[0241] In embodiments, the IAA synthesis pathway comprises one or more pathways selected from a indole-3-acetonitrile pathway, indole-3-acetamide pathway, indole-3-pyruvate pathway, and tryptamine pathway. In embodiments, the IAA synthesis pathway comprises each of a indole-3-acetonitrile pathway, indole-3-acetamide pathway, indole-3-pyruvate pathway, and tryptamine pathway. In embodiments, the plurality of bacterial species comprises a distributed capability to synthesize IAA via at least 2 propionate synthesis pathways, at least 3 IAA synthesis pathways, or at least 4 IAA synthesis pathways.

[0242] In embodiments, bacterial species / isolates are selected based on the presence of one or more genetic sequence encoding enzyme of an IAA pathway, or an enzyme having equivalent functionality from one or more genes thereof. In embodiments, bacterial species / isolates are selected based on functional screening for the presence of an IAA pathway, or an enzyme having equivalent functionality from one or more genes thereof.

[0243] In embodiments, the plurality of bacterial species substantially produces IAA in a gastrointestinal tract (e.g., human gastrointestinal tract, including the stomach, small intestine, large intestine, colon, and rectum). In embodiments, the production is an improvement over a baseline IAA level by about or at least about 20%, about or at least about 40%, about or at least about 60%, about or at least about 80%, or about or at least about 100% relative to the pre-treatment level of IAA, as measured by one or more of metabolomicDBl / 161604598.2 64Atorney Docket No.: 137085-5001 -PC measurement of IAA, IAA in fecal material, metabolomics of patient serum, enzyme activity, excreted metabolites, and / or blood serum metabolites.

[0244] In embodiments, the plurality of bacterial species exhibits a distributed capability to synthesize IPA, where one or more IPA synthesis pathway is distributed amongst the collective genomes of the bacterial consortium. In embodiments, about or at least about 1% of the total bacterial species, about or at least about 2% of the total bacterial species, about or at least about 3% of the total bacterial species, about or at least about 4% of the total bacterial species, about or at least about 5% of the total bacterial species, about or at least about 6% of the total bacterial species, about or at least about 7% of the total bacterial species, about or at least about 8% of the total bacterial species, about or at least about 9% of the total bacterial species, about or at least about 10% of the total bacterial species, about or at least about 15% of the total bacterial species, or about or at least about 20% of the total bacterial species comprises an IPA synthesis pathway and / or encodes at least one enzyme suitable for synthesizing IPA.

[0245] In embodiments, individual bacterial species of the plurality of bacterial species is capable of synthesizing IPA. In embodiments, about or at least about 1 species / isolate produces IPA, about or at least about 2 species / isolates produces IPA, about or at least about 3 species / isolates produces IPA, about or at least about 4 species / isolates produces IPA, about or at least about 5 species / isolates produces IPA, about or at least about 10 species / isolates produces IPA, about or at least about 15 species / isolates produces IPA, or about or at least about 20 species / isolates produces IPA.

[0246] In embodiments, the IPA synthesis pathway comprises one or more enzymes (or gene sequence encoding one or more enzymes thereof) selected from aromatic amino acid aminotransferase (ATT), indolelactate dehydrogenase (ILDH), indolelactate dehydratase (ILD), and acyl-CoA dehydrogenase (ACD), optionally wherein the IPA synthesis pathway comprises each of an aromatic amino acid aminotransferase (ATT), indolelactate dehydrogenase (ILDH), indolelactate dehydratase (ILD), and acyl-CoA dehydrogenase (ACD). In embodiments, bacterial species / isolates are selected based on functional screening for the presence of one or more of ATT, ILDH, ILD, and ACD, or an enzyme having equivalent functionality thereof. In embodiments, bacterial species / isolates are selected based on the presence of one or more genetic sequence encoding one or more of ATT, ILDH, ILD, and ACD, or an enzyme having equivalent functionality thereof.

[0247] In embodiments, the plurality of bacterial species substantially produces IPA in a gastrointestinal tract (e.g., human gastrointestinal tract, including the stomach, small intestine, large intestine, colon, andDBl / 161604598.2 65Atorney Docket No.: 137085-5001 -PC rectum). In embodiments, the production is an improvement over a baseline IPA level by about or at least about 20%, about or at least about 40%, about or at least about 60%, about or at least about 80%, or about or at least about 100% relative to the pre-treatment level of IPA, as measured by one or more of metabolomic measurement of IPA, IPA in fecal material, metabolomics of patient serum, enzyme activity, excreted metabolites, and / or blood serum metabolites.

[0248] In embodiments, the plurality of bacterial species exhibits a distributed capability to synthesize single chain fatty acids (SCFAs), where one or more SCFA synthesis pathway is distributed amongst the collective genomes of the bacterial consortium. In embodiments, SCFAs refer to single chain fatty acids that are not butyrate or propionate, such as valerate, isovalerate, and branched chain fatty acids. In embodiments, about or at least about 1% of the total bacterial species, about or at least about 2% of the total bacterial species, about or at least about 3% of the total bacterial species, about or at least about 4% of the total bacterial species, about or at least about 5% of the total bacterial species, about or at least about 6% of the total bacterial species, about or at least about 7% of the total bacterial species, about or at least about 8% of the total bacterial species, about or at least about 9% of the total bacterial species, about or at least about 10% of the total bacterial species, about or at least about 15% of the total bacterial species, or about or at least about 20% of the total bacterial species comprises a synthesis pathway for one or more SCFAs and / or encodes at least one enzyme suitable for synthesizing one or more SCFAs.

[0249] In embodiments, individual bacterial species of the plurality of bacterial species is capable of synthesizing SCFAs. In embodiments, about or at least about 1 species / isolate from the consortium produces one or more SCFAs, about or at least about 2 species / isolates produces one or more SCFAs, about or at least about 3 species / isolates produces one or more SCFAs, about or at least about 4 species / isolates produces one or more SCFAs, about or at least about 5 species / isolates produces one or more SCFAs, about or at least about 10 species / isolates produces one or more SCFAs, about or at least about 15 species / isolates produces one or more SCFAs, or about or at least about 20 species / isolates produces one or more SCFAs.

[0250] In embodiments, the plurality of bacterial species substantially produces SCFAs in a gastrointestinal tract (e.g., human gastrointestinal tract, including the stomach, small intestine, large intestine, colon, and rectum). In embodiments, the SCFA is selected from one or more of valerate and branched chain SCFAs. In embodiments, the production is an improvement over a baseline SCFA level by about or at least about 20%, about or at least about 40%, about or at least about 60%, about or at least about 80%, or about or at least about 100% relative to the pre-treatment level of SCFAs, as measured by one or more ofDBl / 161604598.2 66Atorney Docket No.: 137085-5001 -PC metabolomic measurement of SCFAs, SCFAs in fecal material, metabolomics of patient serum, enzyme activity, excreted metabolites, and / or blood serum metabolites.

[0251] In embodiments, the plurality of bacterial species exhibits a distributed capability to synthesize bile acid derivatives (BAs), where one or more BAs synthesis pathway is distributed amongst the collective genomes of the bacterial consortium. In embodiments, “bile acid derivatives (BAs),” refers to both bile acids and derivatives thereof that are synthesized by bacteria and / or humans. In embodiments, about or at least about 1 % of the total bacterial species, about or at least about 2% of the total bacterial species, about or at least about 3% of the total bacterial species, about or at least about 4% of the total bacterial species, about or at least about 5% of the total bacterial species, about or at least about 6% of the total bacterial species, about or at least about 7% of the total bacterial species, about or at least about 8% of the total bacterial species, about or at least about 9% of the total bacterial species, about or at least about 10% of the total bacterial species, about or at least about 15% of the total bacterial species, or about or at least about 20% of the total bacterial species comprises a synthesis pathway for bile acid derivatives (BAs) and / or encodes at least one enzyme suitable for synthesizing bile acid derivatives (BAs).

[0252] In embodiments, individual bacterial species of the plurality of bacterial species is capable of synthesizing bile acid derivatives (BAs). In embodiments, about or at least about 1 species / isolate produces one or more bile acid derivatives (BAs), about or at least about 2 species / isolates produces one or more bile acid derivatives (BAs), about or at least about 3 species / isolates produces one or more bile acid derivatives (BAs), about or at least about 4 species / isolates produces one or more bile acid derivatives (BAs), about or at least about 5 species / isolates produces one or more bile acid derivatives (BAs), about or at least about 10 species / isolates produces one or more bile acid derivatives (BAs), about or at least about 15 species / isolates produces one or more bile acid derivatives (BAs), or about or at least about 20 species / isolates produces one or more bile acid derivatives (BAs).

[0253] In embodiments, the plurality of bacterial species substantially produces one or more bile acid derivatives (BAs) in a gastrointestinal tract (e.g., human gastrointestinal tract, including the stomach, small intestine, large intestine, colon, and rectum). In embodiments, the one or more BAs include isoalloLCA, deconjugated cBA, secondary bile acid (2BA), tertiary bile acid (3BA), 7-oxoLCA, 7-oxoDCA, and / or microbially conjugated bile acid (MCBA). In embodiments, the production is an improvement over a baseline BA level by about or at least about 20%, about or at least about 40%, about or at least about 60%, about or at least about 80%, or about or at least about 100% relative to the pre-treatment level of BAs, as measuredDBl / 161604598.2 67Atorney Docket No.: 137085-5001 -PC by one or more of metabolomic measurement of BAs, BAs in fecal material, metabolomics of patient serum, enzyme activity, excreted metabolites, and / or blood serum metabolites.

[0254] In embodiments, to make immune-active secondary bile acids (such as LCA / DCA, 7-oxo LCA, 7-oxo DCA, and isoalloLCA), several enzymatic reactions are needed. In embodiments, most single isolates only perform a handful of the reactions, so a consortia of bacteria is used to provide a specific combination of the enzymes: bile salt hydrolases, 7a-dehydroxylation, 7a / 7p-HSDHs and 5p-reductase, 5a-reductase, and 3 -HSDH. In embodiments, the consortium is designed to have combinations of organisms to accomplish this community co-metabolism. In embodiments, at least one of each of these pathways is present in the consortium so that the full sequence of enzymatic transformations take place, without relying on any existing microbiome in the subject to supply missing steps.

[0255] In embodiments, the plurality of bacterial species exhibits a distributed capability to synthesize isoalloLCA, where one or more isoalloLCA synthesis pathway is distributed amongst the collective genomes of the bacterial consortium. In embodiments, about or at least about 1 % of the total bacterial species, about or at least about 2% of the total bacterial species, about or at least about 3% of the total bacterial species, about or at least about 4% of the total bacterial species, about or at least about 5% of the total bacterial species, about or at least about 6% of the total bacterial species, about or at least about 7% of the total bacterial species, about or at least about 8% of the total bacterial species, about or at least about 9% of the total bacterial species, about or at least about 10% of the total bacterial species, about or at least about 15% of the total bacterial species, or about or at least about 20% of the total bacterial species comprises an isoalloLCA synthesis pathway and / or encodes at least one enzyme suitable for synthesizing isoalloLCA.

[0256] In embodiments, individual bacterial species of the plurality of bacterial species is capable of synthesizing isoalloLCA. In embodiments, about or at least about 1 species / isolate produces isoalloLCA, about or at least about 2 species / isolates produces isoalloLCA, about or at least about 3 species / isolates produces isoalloLCA, about or at least about 4 species / isolates produces isoalloLCA, about or at least about 5 species / isolates produces isoalloLCA, about or at least about 10 species / isolates produces isoalloLCA, about or at least about 15 species / isolates produces isoalloLCA, or about or at least about 20 species / isolates isoalloLCA.

[0257] In embodiments, the isoalloLCA synthesis pathway comprises one or more pathways selected from a chenodeoxycholic acid (CDCA) to isoalloLCA pathway and a 3-oxoLCA to isoalloLCA pathway. In embodiments, the isoalloLCA synthesis pathway comprises both of a CDCA to isoalloLCA pathway and a 3-DBl / 161604598.2 68Atorney Docket No.: 137085-5001 -PC oxoLCA to isoalloLCA pathway. In embodiments, the plurality of bacterial species comprises a distributed capability to synthesize isoalloLCA via at least 2 isoalloLCA synthesis pathways.

[0258] In embodiments, the CDCA to isoalloLCA pathway comprises having one or more genes encoding one or more of 7a-Hydroxysteroid dehydrogenase, 7p-hydroxysteroid dehydrogenase, 3a- hydroxysteroid dehydrogenase, and an enzyme having equivalent functionality thereof. In embodiments, one or more bacterial species / isolates are selected based on functional screening for the presence of one or more of 7a-Hydroxysteroid dehydrogenase, 7p-hydroxysteroid dehydrogenase, 3a-hydroxysteroid dehydrogenase, or an enzyme having equivalent functionality thereof. In embodiments, bacterial species / isolates are selected based on the presence of one or more genetic sequence encoding one or more of 7a-Hydroxysteroid dehydrogenase, 7p-hydroxysteroid dehydrogenase, 3a-hydroxysteroid dehydrogenase, or an enzyme having equivalent functionality thereof.

[0259] In embodiments, the 3-oxoLCA to isoalloLCA pathway comprises having one or more genes encoding one or more of 5 -reductase, 5a-reductase, 30-HSDH, and an enzyme having equivalent functionality thereof. In embodiments, bacterial species / isolates are selected based on functional screening for the presence of one or more of 5 -reductase, 5a-reductase, 3 -HSDH, or an enzyme having equivalent functionality thereof. In embodiments, bacterial species / isolates are selected based on the presence of one or more genetic sequence encoding one or more of 5 -reductase, 5a-reductase, 30-HSDH (e.g., as shown in Fig. 6).

[0260] In embodiments, the plurality of bacterial species substantially produces isoalloLCA in a gastrointestinal tract (e.g., human gastrointestinal tract, including the stomach, small intestine, large intestine, colon, and rectum). In embodiments, the production is an improvement over a baseline isoalloLCA level by about or at least about 20%, about or at least about 40%, about or at least about 60%, about or at least about 80%, or about or at least about 100% relative to the pre-treatment level of isoalloLCA, as measured by one or more of metabolomic measurement of isoalloLCA, isoalloLCA in fecal material, metabolomics of patient serum, enzyme activity, excreted metabolites, and / or blood serum metabolites.

[0261] In embodiments, the plurality of bacterial species exhibits a distributed capability to synthesize one or more bacterial metabolites selected from cholic acid (CA), threonine-CA, phenylalanine-CA, tyrosine- CA, deoxycholic acid (DCA), glutamic acid-DCA, chenodeoxycholic acid (CDCA), and / or glutamic acid- CDCA, where one or more synthesis pathway or the one or more bacterial metabolites is distributed amongst the collective genomes of the bacterial consortium. In embodiments, individual bacterial species of theDBl / 161604598.2 69Atorney Docket No.: 137085-5001 -PC plurality of bacterial species is capable of synthesizing one or more bacterial metabolites selected from cholic acid (CA), threonine-CA, phenylalanine-CA, tyrosine-CA, deoxycholic acid (DCA), glutamic acid-DCA, chenodeoxycholic acid (CDCA), and / or glutamic acid-CDCA.

[0262] In embodiments, the plurality of bacterial species substantially produces one or more bacterial metabolites selected from cholic acid (CA), threonine-CA, phenylalanine-CA, tyrosine-CA, deoxycholic acid (DCA), glutamic acid-DCA, chenodeoxycholic acid (CDCA), and / or glutamic acid-CDCA in a gastrointestinal tract (e.g., human gastrointestinal tract, including the stomach, small intestine, large intestine, colon, and rectum). In embodiments, the production is an improvement over a baseline bacterial metabolite level by about or at least about 20%, about or at least about 40%, about or at least about 60%, about or at least about 80%, or about or at least about 100% relative to the pre-treatment level of bacterial metabolites, as measured by one or more of metabolomic measurement of bacterial metabolites, bacterial metabolites in fecal material, metabolomics of patient serum, enzyme activity, excreted metabolites, and / or blood serum metabolites.

[0263] In embodiments, bacterial species selection is guided by in silico analyses which determine the coverage of microbiological and biochemical functionality that is desired. For example, in embodiments and in reference to Fig. 5, an illustrative graphical representation depicts clustering of bacterial taxa (represented as nodes) which are presented as a function of their “between-ness” or clustering based on genetic / functional similarity / dissimilarity. In embodiments, the “between-ness,” or clustering, is based on the identification of a genetic and / or functional marker of a butyrate synthesis pathway and / or at least one enzyme suitable for synthesizing butyrate; a propionate synthesis pathway and / or least one enzyme suitable for synthesizing propionate; the ability to synthesize one or more bacterial metabolites (e.g., indole-3-acetic acid (IAA), indole- 3-propionic acid (I PA), short chain fatty acids (SCFAs), bile acid derivatives (BAs) (e.g., comprising one or more of isoallolithocholic acid (isoalloLCA), deconjugated bile acid (deBA), secondary bile acid (2BA), tertiary bile acid (3BA), 7-oxoLCA, 7-oxoDCA, and microbially conjugated bile acid (MCBA)), the ability to substantially decrease one or more metabolites; susceptibility to antibiotics; activation of one or more endogenous human receptors; ability to activate or expand one or more immune cells; ability to re-activate exhausted T cells; ability to substantially enhance endogenous immune cell-mediated killing (e.g., of malignant or transformed cells, tumor cells, etc.) and ability to restore human epithelial barrier function, among other features. In embodiments, the similarity / dissimilarity is represented by branch points and / or by the distance between nodes. In embodiments, clustering is based on genetic data, for example, on the presence of one or more metabolic genes, operons, and / or synthesis pathways to determine coverage of selected bacterial species in the consortia for covering functional aspects of the entire community. ForDBl / 161604598.270Atorney Docket No.: 137085-5001 -PC example, in embodiments, clustering is useful to select a number of bacterial species / isolates with disparate functional, metabolic, and / or biochemical profiles to ensure an appropriate level of biodiversity such that the consortium, as a whole, provides the desired properties when formulated as a composition.

[0264] In embodiments, bacterial species selection is guided by in silica statistical analyses to determine the distributions of bacterial prevalence based on genetic interrogation for the presence / prevalence of functional and / or metabolic genetic sequences. For example, in embodiments and in reference to Fig. 6, an illustrative graphical representation of the distribution of bacterial genomes’ calculated e-values for illustrative metabolic genes of the 3-oxoLCA to isoalloLCA pathway, 5a-reductase (e.g., reductase_5a), 50-reductase (e.g., reductase_5b), and 3 -HSDH (hydroxysteroid dehydrogenase, hsdh) is pictured. In embodiments, the e-value is the expectation value that indicates the number of alignments with a score > S that one can expect to find by chance in a database of size N. Hence, in embodiments, the e-value is dependent on the database size and the query length, where the closer the e-value to 0, the better the alignment. In embodiments, the e-value is a proxy score for probability of the gene sequence (and the metabolic activity) being similar. In embodiments, the e-value is calculated for one or more one or more genetic sequences, enzymes, cell surface markers, secretable factors, and antibiotics resistances. In embodiments, the e-value is calculated using one or more wild-type bacterial genetic sequences encoding one or more enzymes, antibiotics resistance proteins, cell surface markers, secretable factors, etc.

[0265] In embodiments, one or more species / isolates of the plurality of bacterial species are selected based on a calculated statistical likelihood (e.g., probability) and / or e-value for one or more metabolic genes of one or more metabolic pathway related to the synthesis of one or more of butyrate, propionate, IAA, I PA, SCFAs, bile acid derivatives (BAs, including one or more of isoalloLCA, deconjugated bile acids (deBA), secondary bile acids (2BA), tertiary bile acids (3BA), 7-oxoLCA, 7-oxoDCA, and microbially conjugated bile acids (MCBA)), cholic acid (CA), threonine-CA, phenylalanine-CA, tyrosine-CA, deoxycholic acid (DCA), glutamic acid-DCA, chenodeoxycholic acid (CDCA), and glutamic acid-CDCA. In embodiments, the statistical likelihood (e.g., probability) and / or e-value is calculated for the presence of one or more gene sequences (e.g., including mutants), plasmids, and / or enzymes indicative of resistance to an antibiotic (e.g., for selection for antibiotic susceptibility). In embodiments, illustrative genes / enzymes for screening for antibiotic susceptibility / resistance include hydrolases (e.g., beta-lactamases, esterases, epoxide hydrolases), transferases (e.g., acetyltransferases, phosphotransferases, nucleotidyltransferase, glycosyltransferases, ADP-ribosyltransferases, S-transferases), redox enzymes (e.g., monooxygenases, lyases), efflux pumps,DBl / 161604598.2 71Atorney Docket No.: 137085-5001 -PC antibiotic-sequestration proteins, etc. In embodiments, bacterial selection is based on substitutions / variants present in 16S rRNA which may indicate antibiotic susceptibility (or lack thereof).

[0266] In embodiments, antibiotic susceptibility, e.g., of 3+ different antibiotics, provides a regulatory “kill switch” to ensure that the bacterial consortia can be controlled or killed, if needed, after giving to a subject.

[0267] Bacterial species selection was guided by in silico phylogenetic modeling based on an assessment of one or more bacterial characteristics, as described herein. For example, and in reference to Figs. 7A-7B, illustrative phylogenetic models are shown to select bacterial clades with high confidence of a particular metabolic trait (e.g., modeling is shown based on 8 distinct genetic predictions for a metabolic pathway). Clades with high frequencies of these 8 genes’ presence (estimated robustly form a large number of samples) are selected for inclusion in the bacterial consortium. Interrogation of existing bacterial data repositories helped screen isolates in high-throughput where individual genome sequences were not available. Phylogenetic modeling assisted with the selection of bacterial species / isolates to fulfill the desired characteristics / functionality of the entire plurality of bacterial species.Table 2: Illustrative potencies of pluralities of bacterial species for compositions and uses herein. First number represents the minimal potency (number of species), and the second number represents the redundancy (number of strains) for metabolic capabilities of the plurality of bacterial species.Table 3: Illustrative bacterial consortia of four representative compositions based on prevalence in healthy microbiomes.DBl / 161604598.2 72Atorney Docket No.: 137085-5001 -PCDB1 / 161604598.2 73Atorney Docket No.: 137085-5001 -PCDB1 / 161604598.2 74Atorney Docket No.: 137085-5001 -PC

[0268] In embodiments, the composition comprises about or at least about 50 bacterial species / isolates of the bacterial species / isolates listed in column 3d of Table 3. In embodiments, the composition comprises each of the bacterial species / isolates listed in column 3d of Table 3.

[0269] In embodiments, the composition comprises about or at least about 50 bacterial species / isolates (e.g., about or at least about 55, 60, 65, or 70) of the bacterial species / isolates listed in column 3c of Table 3. In embodiments, the composition comprises each of the bacterial species / isolates listed in column 3c of Table 3.

[0270] In embodiments, the composition comprises about or at least about 50 bacterial species / isolates (e.g., about or at least about 55, 60, 65, 70, 75, or 80) of the bacterial species / isolates listed in column 3b of Table 3. In embodiments, the composition comprises each of the bacterial species / isolates listed in column 3b of Table 3.

[0271] In embodiments, the composition comprises about or at least about 50 bacterial species / isolates (e.g., about or at least about 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100) of the bacterial species / isolates listedDBl / 161604598.2 75Atorney Docket No.: 137085-5001 -PC in column 3a of Table 3. In embodiments, the composition comprises each of the bacterial species / isolates listed in column 3a of Table 3.

[0272] In embodiments, the composition comprises about or at least about 50 bacterial species / isolates (e.g., about or at least about 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100) of the bacterial species / isolates listed in column 3a of Table 3. In embodiments, the composition comprises each of the bacterial species / isolates listed in column 3a of Table 3.

[0273] In embodiments, the composition comprises about or at least about 50 bacterial species / isolates (e.g., about or at least about 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, or 130 or more) of the bacterial species / isolates listed in column 8a of Table 8. In embodiments, the composition comprises each of the bacterial species / isolates listed in column 8a of Table 8.

[0274] In embodiments, the composition comprises about or at least about 50 bacterial species / isolates (e.g, about or at least about 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, or 130 or more) of the bacterial species / isolates listed in column 8b of Table 8. In embodiments, the composition comprises each of the bacterial species / isolates listed in column 8b of Table 8.

[0275] In embodiments, the composition comprises about or at least about 50 bacterial species / isolates (e.g, about or at least about 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, or 130 or more) of the bacterial species / isolates listed in column 8c of Table 8. In embodiments, the composition comprises each of the bacterial species / isolates listed in column 8c of Table 8.

[0276] In embodiments, the composition comprises about or at least about 50 bacterial species / isolates (e.g, about or at least about 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, or 130 or more) of the bacterial species / isolates listed in column 8d of Table 8. In embodiments, the composition comprises each of the bacterial species / isolates listed in column 8d of Table 8.

[0277] In embodiments, the composition comprises an isolated plurality of bacterial species, the plurality of bacterial species comprising the bacterial species and / or isolates listed in column 3a of Table 3; the bacterial species and / or isolates listed in column 3b of Table 3; the bacterial species and / or isolates listed in column 3c of Table 3; the bacterial species and / or isolates listed in column 3d of Table 3; the bacterial species and / or isolates listed in column 8a of Table 8; the bacterial species and / or isolates listed in column 8b of Table 8; the bacterial species and / or isolates listed in column 8c of Table 8; or the bacterial species and / or isolates listed in column 8d of Tabel 8. Persons skilled in the art, with the full benefit of this disclosure in itsDBl / 161604598.2 76Atorney Docket No.: 137085-5001 -PC entirety, will understand that each of these are illustrative bacterial consortia and that the application supports the development of other bacterial consortia from the design criteria described herein and / or from the bacterial genus, strains, species, and isolates describes herein.

[0278] In embodiments, and in reference to Fig. 10, depicts a non-limiting, graphical representation of a multi-mechanistic consortium composition design, where the dendrogram shown has -150 leaves, each leaf is a species and the concentric outer rings show the characteristics of that species that make its selection desirable for inclusion in the consortium. In embodiments, the consortia comprise multiple mechanisms to address heterogenous patient populations and functional redundancy to maximize number of “shots on goal” (opportunities to achieve a desired function / outcome) and size of effect. In embodiments, multi-layer characteristic engagement is required for efficacy in a heterogeneous indication.

[0279] In embodiments, the plurality of bacterial species (e.g., community-level phenotype) exhibits at least 1 characteristic, at least 2 characteristics, at least 3 characteristics, at least 4 characteristics, at least 5 characteristics, at least 6 characteristics, at least 7 characteristics, or all 8 characteristics of the following (a- h):

[0280] (a) ability to substantially decrease one or more of indoxyl and phenyl sulfates metabolites,

[0281] (b) susceptibility to at least 3 antibiotics, e.g., selected from different antibiotic classes,

[0282] (c) ability to substantially activate one or more endogenous human receptors comprising one or more G protein-coupled receptor (GPCRs) and / or toll-like receptor (TLRs),

[0283] (d) ability to substantially activate or expand one or more immune cells,

[0284] (e) ability to substantially suppress or reduce one or more immune cells,

[0285] (f) ability to re-activate exhausted T cells to a substantially healthy state,

[0286] (g) ability to substantially enhance endogenous immune cell-mediated killing of cancer cells, and

[0287] (h) ability to restore human epithelial barrier function to a substantially healthy state.

[0288] In embodiments, the one or more endogenous metabolites comprises phenyl-sulfates and indoxyls. In embodiments, the ability to “substantially decrease” one or more metabolites relates to a reduction of about or at least about 5% to 50% or more (e.g., 10%, 20%, 30%, 40%, etc.) in the total amount and / or concentration relative to a total amount and / or concentration present in a human gastrointestinal tract before dosing as measured by metabolomic measurements of patient fecal material pre- and post-treatmentDBl / 161604598.2 77Atorney Docket No.: 137085-5001 -PC(dosing). In embodiments, the one or more metabolites are “endogenous” in that they are synthesized and / or are present in a human host. In embodiments, the plurality of bacterial species reduces the one or more endogenous metabolites (e.g., indoxyls and phenyl sulfates) by metabolizing them, or otherwise detoxifying their effects.

[0289] In embodiments, the synthesis and / or detoxification of metabolites is measured by functional screening, e.g., by culturing bacteria with the metabolites and assaying for their concentration as a function of isolate / species or consortium presence or abundance, where the bacteria use the metabolite in some capacity to diminish its total amount and / or concentration as a function of biomass. In embodiments, screening is performed with liquid and / or agar bacterial culture. In embodiments, the metabolites are labeled with radioisotopes. In embodiments, the metabolites are detected using a metabolite detection assay (e.g., numerous commercially-available detection kits are available). In embodiments, the detection assay includes a fl uorogenic, luminescent, or colorimetric based reagent for measuring or detecting the presence, absence, or concentration of a metabolite, an intermediate, and / or a synthesis pathway. In embodiments, an illustrative metabolite and / or metabolic pathway detection assay includes an ENTEROTUBE, or multi-test bacterial identification based on biochemical tests for detecting certain metabolic capabilities.

[0290] In embodiments, the different antibiotic classes comprise one or more antibacterial antibiotic classes (e.g., including bacteriostatic and bactericidal molecules). In embodiments, the one or more antibacterial antibiotic classes comprise aminoglycosides, ansamycins, beta-lactams, carbapenems, cephalosporins, cyclic lipopeptides, fluoroquinolones, glycopeptides, glycylcyclines, lincosamides, macrolides, nitroimidazoles, oxazolidinones, sulfonamides, and / or tetracyclines. In embodiments, the at least 3 antibiotics comprise one or more of amikacin, amoxicillin, azithromycin, cefazolin, cefmetazole, cefotetan, cefoxitin, cefprozil, cefuroxime, cilastatin, ciprofloxacin, clarithromycin, clindamycin, daptomycin, doxycycline, ertapenem, erythromycin, gentamicin, imipenem, levofloxacin, linezolid, meropenem, metronidazole, minocycline, moxifloxacin, penicillin, relebactam, rifampicin, sulfamethoxazole, tebipenem, tigecycline, tobramycin, trimethoprim-sulfamethoxazole, vaborbactam, vancomycin, and analogues and derivatives thereof. In embodiments, the plurality of bacterial species / isolates is susceptible to at least 3, at least 4, or at least 5 antibiotics suitable for use in humans (e.g., for safety and efficacy of use of the bacterial species / isolates in humans).

[0291] In embodiments, antibiotic susceptibility is measured using a Kirby-Bauer disk diffusion susceptibility test to determine the sensitivity or resistance of each ofthe plurality of bacterial isolates / species,DBl / 161604598.2 78Atorney Docket No.: 137085-5001 -PC where distance of growth is measured relative to the placement of antibiotic substrate and each distance relates to a degree of susceptibility or resistance to the antibiotic. In embodiments, antibiotic susceptibility is measured in liquid and / or agar culture by exposing isolates / strains to individual antibiotics and observing the degree to which they are susceptible by measuring growth curves, doubling time, and / or the presence of growth (e.g., OD or distances of inhibition).

[0292] In embodiments, the one or more G protein-coupled receptors (GPCRs) comprises one or more of G protein-coupled receptor 35 (GPR35), G protein-coupled receptor 41 (GPR41), G protein-coupled receptor 43 (GPR43), G protein-coupled receptor 109A (GPR109A), G protein-coupled receptor 119 (GPR119), and G protein-coupled receptor 132 (GPR132). In embodiments, the ability to “substantially activate” one or more endogenous human GPCRs relates to a level of activation, activity, and / or binding (e.g., an ECso) of one or more GPCRs of about or at least about 10%, about or at least about 20%, about or at least about 30%, about or at least about 40%, about or at least about 50%, about or at least about 60%, about or at least about 70%, about or at least about 80%, about or at least about 90%, about or at least about 100% relative to a level of activation, activity, and / or binding observed from an agonist and / or antagonist of one or more GPCRs (e.g., via a receptor reporter assay). In embodiments, agonists and / or antagonists of GPCRs include physical stimuli and / or chemical ligand such as photons; ions (H+, Zn2+, Ca2+, etc.); odorants; tastants; vitamins (e.g., niacin, vitamin A1 aldehyde, etc.); peptidic and non-peptidergic hormones (e.g., estrogen, angiotensin, etc.); proteins (e.g., chemokines), neurotransmitters (e.g., dopamine, serotonin, etc.); natural products and small molecules (e.g., morphine, salvinorin A, etc.); metabolites (e.g., ATP, ADP, fatty acids, bile acids, etc.); and products from human commensal bacteria. In embodiments, activation of GPCRs is measured using a fluorometric, luminescent, and / or colorimetric based assay, including for example, GPCR assays (e.g., HTRF / reporter assay, calcium influx), SDS-PAGE analysis and / or western blotting of mRNA / protein expression indicative of GPCR signaling, PCR (qPCR, RT-PCR) markers indicative of GPCR signaling, flow cytometry, immunohistochemistry, fluorescence activated cell sorting (FACS), enzyme-linked immunosorbent assay (ELISA), kinetics based assays for measuring GPCR binding, and receptor-reporter cell line assays with fluorometric or bioluminescence based readouts.

[0293] In embodiments, the one or more toll-like receptors (TLRs) comprise one or more of toll-like receptor 1 (TLR), TLR2, TLR5, TLR6, and TLR9. In embodiments, the ability to “substantially activate” one or more endogenous human TLRs relates to a level of activation, activity, and / or binding (e.g., EC50) of one or more TLRs of about or at least about 10%, about or at least about 20%, about or at least about 30%, about or at least about 40%, about or at least about 50%, about or at least about 60%, about or at least about 70%,DBl / 161604598.2 79Atorney Docket No.: 137085-5001 -PC about or at least about 80%, about or at least about 90%, about or at least about 100% relative to a level of activation, activity, and / or binding observed from an agonist and / or antagonist of one or more TLRs. In embodiments, agonists and / or antagonists of TLRs include a variety of pathogen-associated molecular patterns (PAMPs); proteins / peptides such as 0-defensin 2, fibrinogen, fibronectin, HMGB1 , HSPs (e.g., HSP22, HSP60, HSP70, HSP72, endoplasmin, a-crystallin A chain), human cardiac myosin, resistin, S100 proteins, surfactant protein A, tenascin-C; polysaccharides and proteoglycans such as biglycan, CD138, heparan sulphate, oligosaccharides of hyaluronan and hyaluronan breakdown fragments; nucleic acids such as DNA, RNA, (e.g., mRNA and siRNA); phospholipids (e.g., OxPAPC); and small organic molecules (e.g., monosodium urate), etc. In embodiments, activation of TLRs is measured using a fluorometric, luminescent, and / or colorimetric based assay, including for example, SDS-PAGE analysis and / or western blotting of mRNA / protein expression indicative of TLR signaling, PCR (qPCR, RT-PCR) markers indicative of TLR signaling, flow cytometry, immunohistochemistry, FACS, ELISA, and kinetics-based assays for measuring TLR binding.

[0294] In embodiments, the one or more endogenous human receptors comprises one or more of sphingosine-1 -phosphate receptor 4 (S1 PR4), prostaglandin E receptor 4 (PTGER4), prostaglandin I2 receptor (PTGIR), calcium sensor receptor (CasR), peptide transporter 1 (PEPT1), pregnane X receptor (PXR), farnesoid X receptor (FXR), Takeda G protein-receptor-5 (TGR5), aryl hydrocarbon receptor (AhR), and 5-hydroxytryptamine receptors (5-HT3R and 5-HT4R). In embodiments, the ability to “substantially activate” one or more endogenous one or more endogenous human receptors relates to a level of activation, activity, and / or binding (e.g., EC50) of one or more endogenous human receptors of about or at least about 10%, about or at least about 20%, about or at least about 30%, about or at least about 40%, about or at least about 50%, about or at least about 60%, about or at least about 70%, about or at least about 80%, about or at least about 90%, about or at least about 100% relative to a level of activation, activity, and / or binding observed from an agonist and / or antagonist of one or endogenous human receptors. In embodiments, the agonists and / or antagonists of the one or more endogenous human receptors includes sphingosine-1 - phosphate (e.g., for S1 PR4); prostaglandin E (e.g., for PTGER4); prostaglandin I2 (e.g., for PTGIR), Ca2+(e.g., for CasR); dipeptides and tripeptides (e.g., for PEPT1); antibiotics rifampicin, clotrimazole, and ritonavir, the anti neoplastic drugs cyclophosphamide, cyproterone acetate, taxol, tamoxifen, RU486, anti-inflammatory agent dexamethasone, anti-type 2 diabetes drug troglitazone, anti-hypertensive drugs nifedipine and spironolactone, sedatives glutethimide and phenobarbital (e.g., for PXR), bile acids, steroidal and nonsteroidal agents, CA, LCA, OCA, EDP-305, BAR502, CDCA, tropifexor, cilofexor, nidufexor, TERN-101 ,DBl / 161604598.2 80Atorney Docket No.: 137085-5001 -PCDM175, ivermectin, Gly- -MCA, and T3 (e.g., for FXR), bile acids, INT-777, and RO5527239 (e.g., forTGR5), plant flavonoids, polyphenols, indoles, synthetic polycyclic aromatic hydrocarbons, and dioxin-like compounds (e.g., for AhR), serotonin and atypical antipsychotics, such as aripiprazole, asenapine, clozapine, lurasidone, quetiapine, and ziprasidone (e.g., for 5-HT3R and 5-HT4R). In embodiments, activation of endogenous human receptors is measured using a fluorometric, luminescent, and / or colorimetric based assay, including for example, SDS-PAGE analysis and / or western blotting of mRNA / protein expression indicative of receptor signaling, PCR (qPCR, RT-PCR) markers indicative of receptor signaling, flow cytometry, immunohistochemistry, FACS, ELISA, and kinetics-based assays for measuring receptor binding.

[0295] In embodiments, the one or more immune cells are selected from CD4+ T cells, CD8+ T cells, and Natural Killer (NK) cells, or a subset thereof. In embodiments, the ability to “substantially activate or expand” one or more immune cells relates to a level of activation and / or expansion of one or more subsets of CD4+T cells, CD8+ T cells, and / or NK cells, of about or at least about 5%, about or at least about 10%, about or at least about 20%, about or at least about 30%, about or at least about 40%, about or at least about 50%, about or at least about 60%, about or at least about 70%, about or at least about 80%, about or at least about 90%, about or at least about 100% relative to a level of activation and / or expansion observed from antigen-specific immune cell activation (e.g., MHC I or II mediated) and / or CD3 agonism / antagonism of the one or more immune cells. In embodiments, the ability to “substantially activate or expand” one or more immune cells is measured by one or more of activation of CD4+T cells, CD8+ T cells, NK cells, and effector cytokine production (interferon gamma (IFN-y), interleukin 2 (IL-2), interleukin 10 (IL-10), granzyme B (GrB), tumor necrosis factor alpha (TNF-a)). In embodiments, activation and / or expansion of immune cells is measured using a fluorometric, luminescent, and / or colorimetric based assay, including for example, SDS- PAGE analysis and / or western blotting of mRNA / protein expression indicative of activation, PCR (qPCR, RT- PCR) markers indicative of activation, flow cytometry, hemocytometry / cell number, immunohistochemistry, FACS, ELISA, and kinetics based assays for measuring protein activity / level (e.g., of IFN-y, IL-2, IL-10, GrB, TNF-a). In embodiments, activation and / or expansion of the one or more immune cells is measured by flow cytometry with peripheral cells.

[0296] In embodiments, the ability to substantially suppress or reduce one or more immune cells comprises immune cells selected from myeloid-derived suppressor cells (MDSCs) and regulatory T cells (Tregs). In embodiments, the ability to “substantially suppress or reduce” one or more immune cells relates to a level of suppression or reduction of one or more subsets of MDSCs and / or Tregsof about or at least about 10%, about or at least about 20%, about or at least about 30%, about or at least about 40%, about or at leastDBl / 161604598.2 81Atorney Docket No.: 137085-5001 -PC about 50%, about or at least about 60%, about or at least about 70%, about or at least about 80%, about or at least about 90%, about or at least about 100% relative to a level of suppression and / or reduction observed from expression of interferon response genes (e.g., such as interferon alpha and beta receptor subunit 1 (IFNAR) expression / activity / signaling in MDSCs), or expression of Treg-mediated suppressive proteins (e.g., such as interleukin-10 (IL-10), transforming growth factor beta (TGF- ), and interleukin-10 (IL-35) in Legs). In embodiments, the ability to “substantially suppress or reduce” one or more one or more subsets of MDSCs and / or Tregs is measured by one or more of arginase expression and / or activity, interferon response genes (e.g., IFNAR1) expression and / or activity, IL-10, TGF- , and / or IL-35 expression and / or activity. In embodiments, suppression and / or reduction of MDSCs and / or Tregs is measured using a fluorometric, luminescent, and / or colorimetric based assay, including for example, SDS-PAGE analysis and / or western blotting of mRNA / protein expression indicative of activation, PCR (qPCR, RT-PCR) markers indicative of activation, flow cytometry, hemocytometry / cell number, immunohistochemistry, FACS, ELISA, and kinetics based assays for measuring protein activity / level (e.g., of IFNAR1 , IL-10, TGF-0, and / or IL-35).

[0297] In embodiments, the ability to re-activate exhausted T cells relates to a “substantially healthy” state relates to a level of restoration or increase of one or more functions (or dysfunctions) of exhausted T cells of about or at least about 10%, about or at least about 20%, about or at least about 30%, about or at least about 40%, about or at least about 50%, about or at least about 60%, about or at least about 70%, about or at least about 80%, about or at least about 90%, about or at least about 100% relative to a level of level of restoration or increase of one or more functions (or dysfunctions) observed from immune checkpoint blockade, for example, from anti-cytotoxic T lymphocyte antigen 4 (CTLA-4) and / or anti-programmed death 1 (PD-1) antibodies (Abs). In embodiments, the ability to re-activate exhausted T cells to a substantially healthy state is measured by one or more of secretion of interferon gamma (IFN-y), interleukin 2 (IL-2), interleukin 10 (IL-10), granzyme B (GrB), tumor necrosis factor alpha (TNF-a), and / or granzyme; cytotoxicity; mRNA level and / or cell surface expression of one or more of signaling lymphocyte activation molecule 6 (SLAMF6), T cell receptor (TCR), programmed cell death protein 1 (PD-1), cytotoxic T-lymphocyte associated protein 4 (CTLA-4), lymphocyte activation gene-3 (LAG-3, CD223), and T-cell immunoglobulin and mucindomain containing-3 (TIM-3). In embodiments, re-activation of exhausted T cells is measured using a fluorometric, luminescent, and / or colorimetric based assay, including for example, SDS-PAGE analysis and / or western blotting of mRNA / protein expression indicative of restoration of T cell activity, PCR (qPCR, RT-PCR) markers indicative of restoration of T cell activity, flow cytometry, hemocytometry / cell number, cytotoxicity assay, immunohistochemistry, FACS, ELISA, and kinetics based assays for measuring proteinDBl / 161604598.2 82Atorney Docket No.: 137085-5001 -PC activity / level (e.g., of IFN-y, IL-2, IL-10, TNF-a, granzyme, SLAMF6, TCR, PD-1 , CTLA-4, LAG-3 / CD223, and TIM-3).

[0298] In embodiments, the ability to ‘‘substantially enhance” endogenous immune cell-mediated killing of cancer cells relates to a level of cancer cell killing of about or at least about 10%, about or at least about 20%, about or at least about 30%, about or at least about 40%, about or at least about 50%, about or at least about 60%, about or at least about 70%, about or at least about 80%, about or at least about 90%, about or at least about 100% relative to a level of cytotoxicity from an antitumor agent and / or T lymphocyte-mediated cancer cell killing observed with immune checkpoint blockade (e.g., from anti-CTLA-4 and / or anti-PD- 1 Abs), or from anti-CD3 bispecific (which also targets the tumor / cancer cell). In embodiments, the immune cell- mediated killing of cancer cells is measured by one or more of cancer cell death, cell viability (e.g., proliferation, growth inhibition, growth rate, cytotoxicity, etc.), cell migration (e.g., wound healing / migration assay), oxidative stress, and anchorage-independent growth (AIG). In embodiments, enhancement of endogenous immune cell-mediated killing of cancer cells is measured using a fluorometric, luminescent, and / or colorimetric based assay, including for example, SDS-PAGE analysis and / or western blotting of mRNA / protein expression indicative of restoration of T cell activity, PCR (qPCR, RT-PCR) of markers indicative of restoration of T cell activity, flow cytometry, hemocytometry / cell number, cytotoxicity assay, immunohistochemistry, FACS (e.g., T cell / B cell activation and proliferation assay, T cell killing, binding / blocking assay, cell cycle analysis, signaling pathway activation), ELISA (e.g., cytokine release, necroptosis assay), and kinetics based assays for measuring protein activity / level (e.g., of IFN-y, IL-2, IL-10, TNF-a, granzyme, SLAMF6, TCR, PD-1 , CTLA-4, LAG-3 / CD223, and TIM-3). In embodiments, endogenous immune cell-mediated killing of cancer cells is measured using the RECIST criteria, e.g., treatment response defined as complete response (no evidence of tumor); partial response (decrease in tumor size by 30%); stable disease (no change in tumor size); and progressive disease (increase in tumor size by 20%).

[0299] In embodiments, the cancer cell is from one or more of a carcinoma, sarcoma, myeloma, leukemia, lymphoma, mixed type cancer, and / or metastatic cancer.

[0300] In embodiments, the cancer is selected from one or more of acute biphenotypic leukemia, acute eosinophilic leukemia, acute lymphoblastic leukemia, acute lymphocytic leukemia, acute myeloid dendritic cell leukemia, acute myeloid leukemia, adenocarcinoma of the lung, adrenal gland tumors, adrenocortical carcinoma, AIDS-related cancers, AIDS-related lymphoma, alveolar soft part and cardiac sarcoma, amyloidosis, anal cancer, anaplastic large cell lymphoma, angioimmunoblastic T-cell lymphoma, appendixDBl / 161604598.2 83Atorney Docket No.: 137085-5001 -PC cancer, astrocytoma, ataxia-telangiectasia, attenuated familial adenomatous polyposis, b-cell prolymphocytic leukemia, basal cell carcinoma, Beckwith-Wiedemann syndrome, bile duct cancer, Birt-Hogg-Dube syndrome, bladder cancer, bone cancer, brain and nervous system cancer, brain stem glioma, brainstem glioma, brain tumors, breast cancer, bronchial adenomas / carcinoids, Burkitt's lymphoma, carcinoid tumor, carcinoid tumors, Carney complex, central nervous system tumors, cerebellar astrocytoma, cerebral astrocytoma, cervical cancer, childhood desmoplastic ganglioglioma, cholangiocarcinoma, chondrosarcoma, chronic lymphocytic leukemia, chronic myelogenous leukemia, chronic myeloid leukemia, chronic T-cell lymphocytic leukemia, colon cancer, colorectal cancer, Cowden syndrome, craniopharyngioma, cutaneous T-cell lymphoma, dermatofibrosarcoma protuberans, desmoplastic small round cell tumor, diffuse gastric cancer, diffuse large b-cell lymphoma, endocrine system cancer, endocrine tumors, endometrial cancer, eosinophilic leukemia, ependymoma, epithelioid hemangioendothelioma (EHE), esophageal cancer, Ewing sarcoma, extragonadal germ cell tumor, extrahepatic bile duct cancer, eye cancer, eyelid cancer, fallopian tube cancer, familial adenomatous polyposis, familial malignant melanoma, familial clear cell renal cell carcinoma (RCC), follicular lymphoma, gallbladder cancer, Gardner syndrome, gastric (stomach) cancer, gastrointestinal cancer, gastrointestinal carcinoid tumor, gastrointestinal stromal tumor, gastrointestinal stromal tumor (GIST), genitourinary and gynecologic cancer, germ cell tumor, gestational trophoblastic disease, gestational trophoblastic tumor, glioblastoma, glioma, hairy cell leukemia, head and neck cancer, hematopoietic cancer, hepatocellular cancer, hepatosplenic T-cell lymphoma, Hodgkin's lymphoma, hypopharyngeal cancer, inflammatory breast cancer, intravascular large b-cell lymphoma, invasive cribriform carcinoma, invasive lobular carcinoma, islet cell carcinoma (endocrine pancreas), islet cell tumors, juvenile polyposis syndrome, Kaposi Sarcoma, keratoacanthoma, kidney cancer, lacrimal gland tumor, large granular lymphocytic leukemia, laryngeal and hypopharyngeal cancer, leiomyomatosis and renal cell cancer, leiomyosarcoma, Li-Fraumeni syndrome (LFS), liposarcoma, liver cancer, lung cancer, lymphomas of primary cutaneous origin, lymphomatoid granulomatosis, lymphoplasmacytic lymphoma, lynch syndrome, malignant fibrous histiocytoma of bone, mantle cell lymphoma, marginal zone b-cell lymphoma, mast cell leukemia, mastocytosis, mediastinal large b cell lymphoma, medullary carcinoma, medulloblastoma, melanoma, meningioma, Merkel cell carcinoma, mesothelioma, mixed polyposis syndrome, mucosa- associated lymphoid tissue lymphoma, Muir-Torre syndrome (MTS), multiple endocrine neoplasia syndrome, multiple endocrine neoplasia type 1 , multiple endocrine neoplasia type 2, multiple myeloma, multiple myeloma / plasma cell neoplasm, mycosis fungoides, myelodysplastic syndromes, MYH-associated polyposis, myxosarcoma, nasal cavity and paranasal sinus cancer, nephroblastoma, nasopharyngeal cancer,DBl / 161604598.2 84Atorney Docket No.: 137085-5001 -PC nasopharyngeal carcinoma, neuroblastoma, neuroendocrine tumors, neurofibromatosis type 1, neurofibromatosis type 2, nevoid basal cell carcinoma syndrome, nodal marginal zone b cell lymphoma, nonHodgkin lymphoma, non-small cell lung cancer (NSCLC), non-small cell lung carcinoma, oligodendroglioma, optic nerve glioma, oral and / or oropharyngeal cancer, osteosarcoma, ovarian cancer, ovarian epithelial cancer, ovarian germ cell tumor, pancreatic cancer, papillary renal cell carcinoma, paranasal sinus and nasal cavity cancer, parathyroid cancer, pelvic cancer, penile cancer, Peutz-Jeghers syndrome, pharyngeal cancer, pheochromocytoma, phyllodes tumor, pilocytic astrocytoma, pineal astrocytoma, pituitary adenoma, pituitary gland tumors, plasmablastic lymphoma, pleuropulmonary blastoma, precursor B lymphoblastic leukemia, primary central nervous system lymphoma, primary cutaneous follicular lymphoma, primary cutaneous immunocytoma, primary effusion lymphoma, primitive neuroectodermal tumor, prostate cancer, rectal cancer, renal cancer, renal cell carcinoma (RCC), retinoblastoma, rhabdomyosarcoma, salivary gland cancer, sarcoma, sarcomas of primary cutaneous origin, sebaceous carcinoma, Sezary syndrome, skin adnexal tumors, skin cancer, small bowel cancer, small cell lung cancer, small intestine cancer, splenic marginal zone lymphoma, squamous cell carcinoma of the lung, squamous cell carcinoma, squamous cell skin cancer, stomach cancer, surface epithelial-stromal tumor, T-cell prolymphocytic leukemia, testicular cancer, thoracic and respiratory cancer, thymoma, thymic carcinoma, thyroid cancer, transitional cell cancer, transitional cell cancer adenoid cystic carcinoma, tuberous sclerosis syndrome, tubular carcinoma, Turcot syndrome, unknown primary cancer, unsorted cancer, ureter cancer, urethral cancer, uterine cancer, uterine sarcoma, uveal melanoma, vaginal cancer, visual pathway and hypothalamic glioma, Von Hippel-Lindau (VHL) syndrome, vulvar cancer, Wilms tumor, and xeroderma pigmentosum.

[0301] In embodiments, the cancer cell is or comprises a cell from one or more of esophageal cancer, gastric (stomach) cancer, bile duct cancer, small intestine cancer, colorectal cancer, pancreatic cancer, liver cancer, rectal cancer, anal cancer, colon cancer, gallbladder cancer, and stromal tumor cells. In embodiments, the cancer / tumor cell includes a cancer cell line.

[0302] In embodiments, the epithelial barrier function comprises gut epithelial barrier. In embodiments, the ability to restore epithelial barrier function to a “substantially healthy state” relates to a level of epithelial integrity of about or at least about 10%, about or at least about 20%, about or at least about 30%, about or at least about 40%, about or at least about 50%, about or at least about 60%, about or at least about 70%, about or at least about 80%, about or at least about 90%, about or at least about 100% relative to a level of healthy, non-diseased, epithelial barrier function (e.g., relative to an unperturbed in vitro or in vivo model for epithelial barrier). In embodiments, restoration of epithelial barrier function and / or integrity is measured byDBl / 161604598.2 85Atorney Docket No.: 137085-5001 -PC one or more of expression and distribution of tight junction proteins, epithelial surface area and / or presence of intestinal villi, mucosal permeability, paracellular permeability, transcellular uptake, electrophysiological parameters (e.g., measured by transepithelial electrical resistance (TEER)), western blotting, mRNA / protein expression, PCR (qPCR, RT-PCR), presence of biomarkers, flow cytometry, immunohistochemistry, FACS, and ELISA. In embodiments, epithelial barrier function and / or integrity is measured using a fluorometric, luminescent, and / or colorimetric based assay, including for example, SDS-PAGE analysis and / or western blotting of mRNA / protein expression indicative of restoration of epithelial barrier function / integrity, PCR (qPCR, RT-PCR) of markers indicative of epithelial barrier function / integrity, flow cytometry, hemocytometry / cell number, cytotoxicity assay, immunohistochemistry, FACS, ELISA, and kinetics based assays.

[0303] Without wishing to be bound by theory, the plurality of bacterial species assist with maintaining intestinal epithelial regeneration and / or integrity, repairing damaged intestinal mucosa, improving the mechanism of the intestinal barrier by influencing the renewal of intestinal epithelial cells, increasing the production of tight junction proteins, and increasing mucin secretion while promoting the immune system.

[0304] Without wishing to be bound by theory, the plurality of bacterial species herein function to mimic or work synergistically with treatments such as peptide hormones, glucagon, glucagon-like peptides (e.g., GLP-1 / 2), and associated agonists, which function to modulate Hemoglobin A1c (HbA1c) levels, improve nutrient absorption, moderate appetite, assist blood sugar maintenance (e.g., address type II diabetes (adult onset), hypoglycemia, etc.), and bodyweight maintenance (e.g., address obesity). In embodiments, treatments that improve nutrient absorption, intestinal lining integrity, and the like, are used as a comparator, or co-therapeutic with the plurality of bacterial species.

[0305] Without wishing to be bound by theory, the plurality of bacterial species outcompetes pathogenic species (e.g., toxin-secreting bacteria, bacteria that compromise the integrity of the gut epithelial barrier, opportunistic pathogens, parasites, etc.). In embodiments, the presence of pathogenic bacteria is detected using standard bacteria identification methods using fecal samples from the host.

[0306] In embodiments, the plurality of bacterial species are suitable for lyophilization and / or cryopreservation, e.g., without a substantial loss in lyorevival and / or cryorevival over a period of about or at least about 1 week, about or at least about 2 weeks, about or at least about 3 weeks, about or at least about 1 months, about or at least about 2 months, about or at least about 4 months, about or at least about 6 months, or about or at least about 1 year. In embodiments, upon revival from cryopreservation and / orDBl / 161604598.2 86Atorney Docket No.: 137085-5001 -PC lyophilization, the overall viability (total cell count) will decrease by about 1 %, 5%, 10%, 15%, 20%, 25%, 50%, 75%, or 90% or more, but the plurality of bacterial species is able to substantially regain growth capabilities (and cell count) under suitable culturing conditions.

[0307] In embodiments, bacterial species selection is guided by the bacterial species / isolate stability as measured by viability after cryopreservation (post-cryo) or lyophilization (post-lyo). In embodiments, the viability is assessed by liquid media growth and / or on agar. For example, in embodiments and in reference to Fig. 9, an illustrative viability screening result demonstrate at least 90%+ cryo-viability is achievable in pluralities of bacterial isolates described herein. In embodiments, bacterial selection is filterable based on viability after cryopreservation and / or lyopreservation. In embodiments, bacteria that better survive the cryopreservation and / or lyophilization processes are selected for compositions herein.

[0308] In embodiments, the lyorevival and / or cryorevival of the plurality of bacterial species is as measured by fractional viability in liquid culture and / or on agar, is about or at least about 1 %, about or at least about 5%, about or at least about 10%, about or at least about 15%, about or at least about 20%, about or at least about 30%, about or at least about 40%, about or at least about 50%, about or at least about 60%, about or at least about 70%, about or at least about 80%, about or at least about 90%, or about or at least about 99%.

[0309] In embodiments, the composition comprises one or more pharmaceutically acceptable excipients or carriers. In embodiments, the plurality of bacterial species is lyophilized and encapsulated, optionally within a capsule. In embodiments, the composition is suitable for oral administration (e.g., for ingestion by a human subject). In embodiments, the plurality of bacterial species (e.g., consortia) is formulated as a lyophilized powder. In embodiments, the plurality of bacterial species is formulated as one or more of a tablet, capsule (e.g., gelatin and hydroxypropyl methylcellulose (HPMC) capsule), sachet, powder, etc. In embodiments, the plurality of bacterial species is formulated for oral route administration, e.g., to be consumed alone or with food or beverage. In embodiments, the plurality of bacterial species is formulated with a food, beverage, or dietary supplement material, e.g., formulated with one or more of a carbohydrate (e.g., monosaccharide, disaccharide, etc.), amino acid / protein, lipid / fatty acid, flavoring agent, polyol (e.g., polyethylene glycol (PEG), etc.), caking agent, desiccation agent, vitamin, mineral, or other additive that is found in food, beverage, and dietary supplement compositions. In embodiments, the plurality of bacterial species is formulation with a probiotic or other material that is useful to assist in seeding the bacteria into the gastrointestinal tract of a subject.DBl / 161604598.2 87Atorney Docket No.: 137085-5001 -PCBacterial Consortia in Methods of Establishing a Healthy Microbiome, Treating Diseases, and / or Methods of Treating Cancer

[0310] The present disclosure provides, in embodiments, methods utilizing compositions herein comprising a bacterial consortium for establishing a healthy microbiome and / or treating a disease. In embodiments, “treatment” of a disease refers to improvement in a disease, disorder, or condition, and / or an improvement and / or abatement of one or more symptoms, and / or an improvement in the response to a treatment or therapy for the disease (e.g., changing a subject from a “non-responder” to a “responder” to a therapy).

[0311] In embodiments, the subject is human. In embodiments, the healthy microbiome is established in at least a portion of the gastrointestinal tract (e.g, including the esophagus, stomach, small intestine, large intestine, colon, and rectum).

[0312] In embodiments, the subject has, is suspected of having, has been diagnosed with, or is receiving treatment for dysbiosis, or an imbalance within the microbiome (e.g., gastrointestinal microbiome). In embodiments, one or more symptoms of dysbiosis include mucosal inflammation, intestinal barrier derangement (e.g., “leaky” gut), slowed / delayed gut transit, digestion issues, constipation, diarrhea, vomiting, visceral pain, fluctuations in satiety / appetite, fatigue, acid reflux, and / or heartburn. In embodiments, establishing a healthy microbiome is indicated by one or more of an improved gut barrier function, gut homeostasis, microbial colonization resistance, community resilience, host defense, improved food digestion, reduced mucosal inflammation, improved / faster gut transit, and / or reduction or ablation of one or more symptoms of dysbiosis.

[0313] In embodiments, the plurality of bacterial species outcompetes pathogenic bacterial species (e.g., toxin-secreting bacteria, bacteria that compromise the integrity of the gut epithelial barrier, etc.).

[0314] In embodiments, establishing a healthy microbiome is determined by analyzing the presence of one or more biomarkers in a sample obtained from the patient. In embodiments, the assessment is performed by one or more of measuring expression and / or distribution of tight junction proteins; measuring epithelial surface area and / or presence of intestinal villi; measuring mucosal permeability, paracellular permeability, transcellular uptake, electrophysiological parameters (e.g., transepithelial electrical resistance (TEER)); western blotting; measuring mRNA / protein expression; PCR (e.g., to determine gene expression, mRNA expression, and / or protein expression), identification of biomarkers, flow cytometry, immunohistochemistry, fluorescence activated cell sorting (FACS), and enzyme-linked immunosorbent assay (ELISA).DBl / 161604598.2 88Atorney Docket No.: 137085-5001 -PC

[0315] In embodiments, establishment of a healthy microbiome within the gastrointestinal tract, as evidence by colonization by one or more bacterial species / isolates of the plurality of bacterial species / isolates, occurs within about or at least about 1 week, about or at least about 2 weeks, about or at least about 3 weeks, about or at least about 4 weeks, about or at least about 1 month, about or at least about 2 months, about or at least about 4 months, about or at least about 6 months, or about or at least about 1 year from administration and / or completion of an administration regimen.

[0316] In embodiments, the subject has, is suspected of having, has been diagnosed with, or is receiving treatment for one or more type of cancer. In embodiments, the cancer is one or more of a carcinoma, sarcoma, myeloma, leukemia, lymphoma, mixed type cancer, and / or metastatic cancer.

[0317] In embodiments, the cancer is or acute biphenotypic leukemia, acute eosinophilic leukemia, acute lymphoblastic leukemia, acute lymphocytic leukemia, acute myeloid dendritic cell leukemia, acute myeloid leukemia, adenocarcinoma of the lung, adrenal gland tumors, adrenocortical carcinoma, AIDS- related cancers, AIDS-related lymphoma, alveolar soft part and cardiac sarcoma, amyloidosis, anal cancer, anaplastic large cell lymphoma, angioimmunoblastic T-cell lymphoma, appendix cancer, astrocytoma, ataxiatelangiectasia, attenuated familial adenomatous polyposis, b-cell prolymphocytic leukemia, basal cell carcinoma, Beckwith-Wiedemann syndrome, bile duct cancer, Birt-Hogg-Dube syndrome, bladder cancer, bone cancer, brain and nervous system cancer, brain stem glioma, brainstem glioma, brain tumors, breast cancer, bronchial adenomas / carcinoids, Burkitt's lymphoma, carcinoid tumor, carcinoid tumors, Carney complex, central nervous system tumors, cerebellar astrocytoma, cerebral astrocytoma, cervical cancer, childhood desmoplastic ganglioglioma, cholangiocarcinoma, chondrosarcoma, chronic lymphocytic leukemia, chronic myelogenous leukemia, chronic myeloid leukemia, chronic T-cell lymphocytic leukemia, colon cancer, colorectal cancer, Cowden syndrome, craniopharyngioma, cutaneous T-cell lymphoma, dermatofibrosarcoma protuberans, desmoplastic small round cell tumor, diffuse gastric cancer, diffuse large b-cell lymphoma, endocrine system cancer, endocrine tumors, endometrial cancer, eosinophilic leukemia, ependymoma, epithelioid hemangioendothelioma (EHE), esophageal cancer, Ewing sarcoma, extragonadal germ cell tumor, extrahepatic bile duct cancer, eye cancer, eyelid cancer, fallopian tube cancer, familial adenomatous polyposis, familial malignant melanoma, familial clear cell renal cell carcinoma (RCC), follicular lymphoma, gallbladder cancer, Gardner syndrome, gastric (stomach) cancer, gastrointestinal cancer, gastrointestinal carcinoid tumor, gastrointestinal stromal tumor, gastrointestinal stromal tumor (GIST), genitourinary and gynecologic cancer, germ cell tumor, gestational trophoblastic disease, gestational trophoblastic tumor, glioblastoma, glioma, hairy cell leukemia, head and neck cancer, hematopoietic cancer,DBl / 161604598.2 89Atorney Docket No.: 137085-5001 -PC hepatocellular cancer, hepatosplenic T-cell lymphoma, Hodgkin's lymphoma, hypopharyngeal cancer, inflammatory breast cancer, intravascular large b-cell lymphoma, invasive cribriform carcinoma, invasive lobular carcinoma, islet cell carcinoma (endocrine pancreas), islet cell tumors, juvenile polyposis syndrome, Kaposi Sarcoma, keratoacanthoma, kidney cancer, lacrimal gland tumor, large granular lymphocytic leukemia, laryngeal and hypopharyngeal cancer, leiomyomatosis and renal cell cancer, leiomyosarcoma, Li- Fraumeni syndrome (LFS), liposarcoma, liver cancer, lung cancer, lymphomas of primary cutaneous origin, lymphomatoid granulomatosis, lymphoplasmacytic lymphoma, lynch syndrome, malignant fibrous histiocytoma of bone, mantle cell lymphoma, marginal zone b-cell lymphoma, mast cell leukemia, mastocytosis, mediastinal large b cell lymphoma, medullary carcinoma, medulloblastoma, melanoma, meningioma, Merkel cell carcinoma, mesothelioma, mixed polyposis syndrome, mucosa-associated lymphoid tissue lymphoma, Muir-Torre syndrome (MTS), multiple endocrine neoplasia syndrome, multiple endocrine neoplasia type 1 , multiple endocrine neoplasia type 2, multiple myeloma, multiple myeloma / plasma cell neoplasm, mycosis fungoides, myelodysplastic syndromes, MYH-associated polyposis, myxosarcoma, nasal cavity and paranasal sinus cancer, nephroblastoma, nasopharyngeal cancer, nasopharyngeal carcinoma, neuroblastoma, neuroendocrine tumors, neurofibromatosis type 1 , neurofibromatosis type 2, nevoid basal cell carcinoma syndrome, nodal marginal zone b cell lymphoma, non-Hodgkin lymphoma, nonsmall cell lung cancer (NSCLC), non-small cell lung carcinoma, oligodendroglioma, optic nerve glioma, oral and / or oropharyngeal cancer, osteosarcoma, ovarian cancer, ovarian epithelial cancer, ovarian germ cell tumor, pancreatic cancer, papillary renal cell carcinoma, paranasal sinus and nasal cavity cancer, parathyroid cancer, pelvic cancer, penile cancer, Peutz-Jeghers syndrome, pharyngeal cancer, pheochromocytoma, phyllodes tumor, pilocytic astrocytoma, pineal astrocytoma, pituitary adenoma, pituitary gland tumors, plasmablastic lymphoma, pleuropulmonary blastoma, precursor B lymphoblastic leukemia, primary central nervous system lymphoma, primary cutaneous follicular lymphoma, primary cutaneous immunocytoma, primary effusion lymphoma, primitive neuroectodermal tumor, prostate cancer, rectal cancer, renal cancer, renal cell carcinoma (RCC), retinoblastoma, rhabdomyosarcoma, salivary gland cancer, sarcoma, sarcomas of primary cutaneous origin, sebaceous carcinoma, Sezary syndrome, skin adnexal tumors, skin cancer, small bowel cancer, small cell lung cancer, small intestine cancer, splenic marginal zone lymphoma, squamous cell carcinoma of the lung, squamous cell carcinoma, squamous cell skin cancer, stomach cancer, surface epithelial-stromal tumor, T-cell prolymphocytic leukemia, testicular cancer, thoracic and respiratory cancer, thymoma, thymic carcinoma, thyroid cancer, transitional cell cancer, transitional cell cancer adenoid cystic carcinoma, tuberous sclerosis syndrome, tubular carcinoma, Turcot syndrome, unknown primaryDBl / 161604598.2 90Atorney Docket No.: 137085-5001 -PC cancer, unsorted cancer, ureter cancer, urethral cancer, uterine cancer, uterine sarcoma, uveal melanoma, vaginal cancer, visual pathway and hypothalamic glioma, Von Hippel-Li ndau (VHL) syndrome, vulvar cancer, Wilms tumor, and xeroderma pigmentosum.

[0318] In embodiments, the cancer is or comprises esophageal cancer, gastric (stomach) cancer, bile duct cancer, small intestine cancer, colorectal cancer, pancreatic cancer, liver cancer, rectal cancer, anal cancer, colon cancer, gallbladder cancer, and stromal tumors.

[0319] In embodiments, methods of use herein include administration via oral routes (e.g., ingestion), In embodiments, compositions herein are administered with food or beverage or are suitable for being taken with food or beverage, including being admixed with food or beverage before consumption. In embodiments, the administration is from about once daily to about once per 3 months.

[0320] In embodiments, the healthy microbiome establishes a total species prevalence of about or at least about 20% to about or at least about 50%, which relates to the proportion of healthy human microbiomes that contain the bacterial species / isolate.

[0321] In embodiments, the healthy microbiome comprises about or at least about 20% of the total species abundance, about or at least about 25% of the total species abundance, about or at least about 30% of the total species abundance, about or at least about 35% of the total species abundance, about or at least about 40% of the total species abundance, about or at least about 45% of the total species abundance, or about or at least about 50% of the total species abundance of the plurality of bacterial species capable of synthesizing butyrate and / or one or more intermediates of a butyrate synthesis pathway. Without wishing to be bound by theory, in embodiments, a sufficient abundance of bacterial species capable of synthesizing butyrate and / or one or more intermediates of a butyrate synthesis pathway is associated with butyrate levels / concentration supporting anti-cancer immunity via activation of one or more GPCRs, and / or inhibition of histone deacetylases, leading to enhanced anti-cancer effects by improving macrophage activity, dendritic cell activity, cytolytic CD8+ T cell activity, B cell-mediated antibody production, and NK cell activity while inhibiting cancer cell proliferation. Without wishing to be bound by theory, in embodiments, a sufficient abundance of bacterial species capable of synthesizing butyrate and / or one or more intermediates of a butyrate synthesis pathway is associated with butyrate levels supporting an intact mucosal epithelial layer during cancer and / or cancer therapy.

[0322] In embodiments, the healthy microbiome comprises about or at least about 20% of the total species abundance, about or at least about 25% of the total species abundance, about or at least about 30%DBl / 161604598.2 91Atorney Docket No.: 137085-5001 -PC of the total species abundance, about or at least about 35% of the total species abundance, about or at least about 40% of the total species abundance, about or at least about 45% of the total species abundance, or about or at least about 50% of the total species abundance of the plurality of bacterial species capable of synthesizing propionate and / or one or more intermediates of a propionate synthesis pathway. Without wishing to be bound by theory, in embodiments, a sufficient abundance of bacterial species capable of synthesizing propionate and / or one or more intermediates of a propionate synthesis pathway is associated with propionate levels / concentrations leading to enhanced efficacy of anti-cancer effects via activation of GCPRs, and / or activation of peroxisome proliferator-activated receptor-y (PPAR-y), which exerts antiproliferative effects on cancer cells and induces cancer cell apoptosis. Without wishing to be bound by theory, in embodiments, propionate-mediated inhibition of histone deacetylases lead to enhanced anti-cancer efficacy by improving macrophage activity, dendritic cell activity, cytolytic CD8 T cell activity, B cell-mediated antibody production, and NK cell activity. Without wishing to be bound by theory, in embodiments, a sufficient abundance of bacterial species capable of synthesizing propionate and / or one or more intermediates of a propionate synthesis pathway is associated with propionate levels supporting an intact mucosal epithelial layer during cancer and / or cancer therapy.

[0323] In embodiments, the healthy microbiome comprises about or at least about 1% of the total species abundance, about or at least about 5% of the total species abundance, about or at least about 10% of the total species abundance, about or at least about 15% of the total species abundance, about or at least about 20% of the total species abundance, about or at least about 30% of the total species abundance, about or at least about 40% of the total species abundance, or about or at least about 50% of the total species abundance of the plurality of bacterial species capable of synthesizing indole-3-acetic acid (IAA) and / or one or more intermediates of an IAA synthesis pathway. Without wishing to be bound by theory, in embodiments, a sufficient abundance of bacterial species capable of synthesizing indole-3-acetic acid (IAA) and / or one or more intermediates of an IAA synthesis pathway is associated with IAA levels / concentrations associated with enhanced anti-cancer efficacy by increasing reactive oxygen species (ROS) concentration in the tumor microenvironment (TME).

[0324] In embodiments, the healthy microbiome comprises about or at least about 1% of the total species abundance, about or at least about 5% of the total species abundance, about or at least about 10% of the total species abundance, about or at least about 15% of the total species abundance, about or at least about 20% of the total species abundance, about or at least about 30% of the total species abundance, about or at least about 40% of the total species abundance, or about or at least about 50% of the total speciesDBl / 161604598.2 92Atorney Docket No.: 137085-5001 -PC abundance of the plurality of bacterial species capable of synthesizing indole-3-propionic acid (IPA) and / or one or more intermediates of an IPA synthesis pathway. Without wishing to be bound by theory, in embodiments, a sufficient abundance of bacterial species capable of synthesizing IPA and / or one or more intermediates of an IPA synthesis pathway is associated with IAA levels / concentrations associated with enhancing anti-cancer efficacy by improving antitumor CD8+ T cell activity via activation of histone acetylation.

[0325] In embodiments, the healthy microbiome comprises about or at least about 1% of the total species abundance, about or at least about 5% of the total species abundance, about or at least about 10% of the total species abundance, about or at least about 15% of the total species abundance, about or at least about 20% of the total species abundance, about or at least about 30% of the total species abundance, about or at least about 40% of the total species abundance, or about or at least about 50% of the total species abundance of the plurality of bacterial species capable of one or more short chain fatty acid (SCFA) and / or one or more intermediates of a SCFA synthesis pathway.

[0326] In embodiments, the healthy microbiome comprises about or at least about 1% of the total species abundance, about or at least about 5% of the total species abundance, about or at least about 10% of the total species abundance, about or at least about 15% of the total species abundance, about or at least about 20% of the total species abundance, about or at least about 30% of the total species abundance, about or at least about 40% of the total species abundance, or about or at least about 50% of the total species abundance of the plurality of bacterial species capable of one or more bile acid derivative (BA) and / or one or more intermediates of a BA synthesis pathway (e.g., including 3-oxo-LCA). Without wishing to be bound by theory, in embodiments, a sufficient abundance of bacterial species capable of synthesizing one or more bile acid derivatives (BA) and / or one or more intermediates of a BA synthesis pathway (e.g., including 3-oxo- LCA) is associated with BA levels / concentrations associated with enhancing anti-cancer efficacy by inducing apoptosis of cancer cells and / or activating T cells with anti-cancer activity.

[0327] In embodiments, the administration of the composition of the plurality of bacterial species results in one or more of:

[0328] (a) decrease of one or more metabolites, optionally selected from phenyl-sulfates and indoxyls,

[0329] (b) susceptibility to at least 3 antibiotics selected from different antibiotic classes,DBl / 161604598.2 93Atorney Docket No.: 137085-5001 -PC

[0330] (c) activation of one or more endogenous human receptors, optionally comprising one or moreG protein-coupled receptor (GPCRs) and / or toll-like receptor (TLRs),

[0331] (d) activation or expansion of one or more immune cells, optionally selected from CD4+T cells,CD8+T cells, and Natural Killer (NK) cells,

[0332] (e) suppression or reduction one or more immune cells, optionally selected from myeloid-derived suppressor cells (MDSCs) and regulatory T cells (Tregs),

[0333] (f) re-activation of exhausted T cells to a substantially healthy state,

[0334] (g) enhancement of endogenous immune cell-mediated killing of cancer cells, and

[0335] (h) restoration of one or more epithelial barrier function to a substantially healthy state, optionally selected from expression and distribution of tight junction proteins, epithelial surface area, presence of intestinal villi, mucosal permeability, paracellular permeability, transcellular uptake, and one or more electrophysiological parameters (e.g., transepithelial electrical resistance (TEER)).

[0336] In embodiments, one or more effects of establishing the healthy microbiome and / or treating the disease occurs within about or at least about 1 week, about or at least about 2 weeks, about or at least about 3 weeks, about or at least about 4 weeks, about or at least about 1 month, about or at least about 2 months, about or at least about 4 months, about or at least about 6 months, or about or at least about 1 year from administration and / or completion of an administration regimen.

[0337] For example, in embodiments, humans synthesize phenyl-sulfates in the liver, where it contributes to albuminuria and is used as a disease marker in kidney disease (and / or diabetes). In embodiments, dysbiosis in the human gastrointestinal tract leads to the production of phenol from dietary tyrosine (e.g., via bacterial enzymes such as tyrosine phenol-lyase), where the phenol is then converted into phenyl-sulfates in the liver. In embodiments, compositions herein establish healthy microbiome which reduces the levels of phenol and / or phenyl-sulfate production. In embodiments, indoxyls (e.g., indoxyl sulfate) is a uremic toxin that accelerates the progression of chronic kidney disease and is derived from dietary protein. In embodiments, dysbiosis in the human gastrointestinal tract leads to the production of indole by tryptophanase of intestinal bacteria such as E. coli. In embodiments, compositions herein establish healthy microbiome which reduces the levels of indoxyl (e.g., indoxyl sulfate) production.

[0338] In embodiments, diminishment of deleterious metabolites occurs within about or at least about 1 week, about or at least about 2 weeks, about or at least about 3 weeks, about or at least about 4 weeks,DBl / 161604598.2 94Atorney Docket No.: 137085-5001 -PC about or at least about 1 month, about or at least about 2 months, about or at least about 4 months, about or at least about 6 months, or about or at least about 1 year from administration and / or completion of an administration regimen.

[0339] In embodiments, activation of one or more endogenous human receptors, optionally comprising one or more G protein-coupled receptor (GPCRs) and / or toll-like receptor (TLRs) occurs within about or at least about 1 week, about or at least about 2 weeks, about or at least about 3 weeks, about or at least about 4 weeks, about or at least about 1 month, about or at least about 2 months, about or at least about 4 months, about or at least about 6 months, or about or at least about 1 year from administration and / or completion of an administration regimen.

[0340] In embodiments, activation or expansion of one or more immune cells, optionally selected from CD4+T cells, CD8+T cells, and Natural Killer (NK) cells occurs within about or at least about 1 week, about or at least about 2 weeks, about or at least about 3 weeks, about or at least about 4 weeks, about or at least about 1 month, about or at least about 2 months, about or at least about 4 months, about or at least about 6 months, or about or at least about 1 year from administration and / or completion of an administration regimen.

[0341] In embodiments, suppression or reduction one or more immune cells (e.g., selected from myeloid-derived suppressor cells (MDSCs) and regulatory T cells (Tregs)) occurs within about or at least about 1 week, about or at least about 2 weeks, about or at least about 3 weeks, about or at least about 4 weeks, about or at least about 1 month, about or at least about 2 months, about or at least about 4 months, about or at least about 6 months, or about or at least about 1 year from administration and / or completion of an administration regimen.

[0342] In embodiments, re-activation of exhausted T cells to a substantially healthy state occurs within about or at least about 1 week, about or at least about 2 weeks, about or at least about 3 weeks, about or at least about 4 weeks, about or at least about 1 month, about or at least about 2 months, about or at least about 4 months, about or at least about 6 months, or about or at least about 1 year from administration and / or completion of an administration regimen.

[0343] In embodiments, enhancement of endogenous immune cell-mediated killing of cancer cells occurs within about or at least about 1 week, about or at least about 2 weeks, about or at least about 3 weeks, about or at least about 4 weeks, about or at least about 1 month, about or at least about 2 months, about or at least about 4 months, about or at least about 6 months, or about or at least about 1 year from administration and / or completion of an administration regimen.DBl / 161604598.2 95Atorney Docket No.: 137085-5001 -PC

[0344] In embodiments, restoration of one or more epithelial barrier function to a substantially healthy state (e.g., including from expression and distribution of tight junction proteins, epithelial surface area, presence of intestinal villi, mucosal permeability, paracellular permeability, transcellular uptake, and one or more electrophysiological parameters, e.g., transepithelial electrical resistance (TEER)) occurs within about or at least about 1 week, about or at least about 2 weeks, about or at least about 3 weeks, about or at least about 4 weeks, about or at least about 1 month, about or at least about 2 months, about or at least about 4 months, about or at least about 6 months, or about or at least about 1 year from administration and / or completion of an administration regimen.

[0345] In embodiments, methods herein include assessing the subject for the establishment of the healthy microbiome by analyzing a sample obtained from the subject. In embodiments, the sample obtained from the subject is or comprises stool, gastrointestinal biopsy, rectal swab, urine, saliva, blood, sera, and / or plasma.

[0346] In embodiments, methods herein include assessing one or more symptoms of a disease of the subject. In embodiments, the symptoms are selected from a symptom of cancer and / or dysbiosis.

[0347] In embodiments, methods herein include administering one or more additional therapeutic agents.Kits

[0348] In embodiments, compositions of bacterial consortium of the present disclosure are assembled into a kit. In embodiments, the kit comprises capsules, tablets, sachets, powders, vials (e.g., cryovials), tubes, etc., of one or more formulations for use in one or more methods, as described herein. In embodiments, the kit comprises one or more lyophilized or cryopreserved bacterial consortia, as described herein.

[0349] In embodiments, the kit is designed for off-the-shelf bacterial consortium administration. In embodiments, the kit comprises at least one distinct composition of a plurality of bacterial species / isolates, at least two distinct compositions of a plurality of bacterial species / isolates / strains, at least three distinct compositions of a plurality of bacterial species / isolates / strains, at least four distinct compositions of a plurality of bacterial species / isolates / strains, or at least five distinct compositions of a plurality of bacterial species / isolates / strains.

[0350] The kit described herein may include one or more containers housing components for performing the methods described herein and optionally instructions for use. Any of the kits described herein may furtherDBl / 161604598.2 96Atorney Docket No.: 137085-5001 -PC comprise components needed for performing the manufacturing methods described herein. Each component of the kits, where applicable, may be provided in liquid form (e.g., in aqueous solution, cryopreservative, a buffer, or culture media). In embodiments, some of the components are reconstitutable or otherwise processible (e.g, compositions that are lyophilized and are reconstitutable in cell culture, or frozen cell stocks for seeding broth / plates), for example, by the addition of a suitable solvent, media, or other species, which may or may not be provided with the kit.

[0351] The kits may have a variety of forms, such as a blister pouch, a shrink-wrapped pouch, a vacuum sealable pouch, a sealable thermoformed tray, or a similar pouch or tray form, with the accessories loosely packed within the pouch, one or more tubes, containers, a box, or a bag.

[0352] In embodiments, the kits may optionally include instructions and / or promotion for use of the components provided. As used herein, "instructions" can define a component of instruction and / or promotion and typically involve written instructions on or associated with packaging of the disclosure. Instructions also can include any oral or electronic instructions provided in any manner such that a user will clearly recognize that the instructions are to be associated with the kit, for example, audiovisual (e.g, videotape, DVD, etc.), Internet, and / or web-based communications, etc. As used herein, "promoted" includes all methods of doing business including methods of education, engineering instruction, scientific inquiry, discovery or development, academic research, manufacturing, chemical, cosmetic, and pharmaceutical industry activity including sales, and any advertising or other promotional activity including written, oral, and electronic communication of any form, associated with the disclosure. Additionally, the kits may include other components depending on the specific application, as described herein.

[0353] Without further elaboration, it is believed that one skilled in the art can, based on the above description, utilize the present disclosure to its fullest extent. The following specific embodiments are, therefore, to be construed as merely illustrative, and not limiting of the remainder of the disclosure in anyway whatsoever.DEFINITIONS

[0354] The following definitions are used in connection with the disclosure disclosed herein. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood to one of skill in the art to which this disclosure belongs.

[0355] As used herein, “a,” “an,” or “the” can mean one or more than one.DBl / 161604598.2 97Atorney Docket No.: 137085-5001 -PC

[0356] In embodiments, the term “about” in reference to numbers or numerical ranges relates to + / - 10%, e.g., where “about 50,” relates to 45 to 55. In embodiments, where the term “about,” in reference to whole numbers where + / - 10% of the numerical value results in non-whole numbers, the term relates to the next consecutive rounded whole numbers, e.g., where “about 25” refers to 23, 24, 25, 26, 27, or 28, and the like. In embodiments, where the term “about,” in reference to whole numbers where + / - 10% of the numerical value results in non-whole numbers and where rounding does not result in separate whole numbers, the term relates to the next consecutive whole numbers, e.g., where “about 1 ” refers to 0, 1 , or 2, or “about 5” refers to 4, 5, or 6, and the like.

[0357] As referred to herein, all compositional percentages are by weight or amount of the total composition, unless otherwise specified. As used herein, the word “include,” and its variants, is intended to be non-limiting, such that recitation of items in a list is not to the exclusion of other like items that may also be useful in the compositions and methods of this technology. Similarly, the terms “can” and “may” and their variants are intended to be non-limiting, such that recitation that an embodiment can or may comprise certain elements or features does not exclude other embodiments of the present technology that do not contain those elements or features.

[0358] Although the open-ended term “comprising,” as a synonym of terms such as including, containing, or having, is used herein to describe and claim the disclosure, the present disclosure, or embodiments thereof, may alternatively be described using alternative terms such as “consisting of” or “consisting essentially of.”

[0359] In embodiments, as used herein, the words “preferred” and “preferably” refer to embodiments of the technology that afford certain benefits, under certain circumstances. However, other embodiments may also be preferred, under the same or other circumstances. Furthermore, the recitation of one or more preferred embodiments does not imply that other embodiments are not useful and is not intended to exclude other embodiments from the scope of the technology.EXAMPLESExample 1: In silico bacterial species selection for consortium generation.

[0360] A process was utilized for in silico selection of bacterial species for inclusion in a composition to establish a healthy microbiome in humans. In silico bacterial species selection began with an input of about 1 x 106bacterial strains (species) having approximately 1 x 108bacterial genes expected to exist in theDBl / 161604598.2 98Atorney Docket No.: 137085-5001 -PC gastrointestinal microbiome of humans, e.g., as shown in Fig. 1A. The resultant bacterial species was selected based on the prevalence in healthy microbiomes and the characteristics included in Table 4, and as described herein, and the analyses described and shown, for example, in Figs. 2, 3A-3C, 4A-4F, 5-6, 7 A- 7B, 8-10, 11-15, and 16A-16D to result in the bacterial species / isolates depicted in Table 1 a, Table 1 b, Table 1c, Table 1 d, Table 1 e, Table 1f, Table 1 g, Table 1 h, Table 1 i, Table 3, Table 6, Table 7, Table 8, and Table 12.Table 4: Illustrative key to bacterial selection characteristics of Table 5.DBl / 161604598.2 99Atorney Docket No.: 137085-5001 -PCTable 5: Bacterial species / isolate characteristic for consortium selection. Abbreviations for column 16 (most complete butyrate pathway) are: L-qlut = L-qlutamate degradation XI (reductive Stickland reaction); L-qlut 1DB1 / 161604598.2 100Atorney Docket No.: 137085-5001 -PC= L-qlutamate degradation V (via hydroxyqlutarate); 4-amino = 4-aminobutanoate degradation V; pyru = pyruvate fermentation to butanoate; L-lys = L-lysine fermentation to acetate and butanoate; and succ = succinate fermentation to butanoate. Abbreviations for column 17 (most complete propionate pathway) are: acrylate = (R)-lactate fermentation to propanoate II (acrylate pathway); acryl 1 = pyruvate fermentation to propanoate II (acrylate pathway); S-lactate = (S)-lactate fermentation to propanoate, acetate and hydrogen; S-lac 1 = (S)-lactate fermentation to propanoate; and S-prop = (S)-propane-1 ,2-diol degradation.DBl / 161604598.2 101Atorney Docket No.: 137085-5001 -PCDB1 / 161604598.2 102Atorney Docket No.: 137085-5001 -PCDB1 / 161604598.2 103Atorney Docket No.: 137085-5001 -PCDB1 / 161604598.2 104Atorney Docket No.: 137085-5001 -PCDB1 / 161604598.2 105Atorney Docket No.: 137085-5001 -PCDB1 / 161604598.2 106Atorney Docket No.: 137085-5001 -PCDB1 / 161604598.2 107Atorney Docket No.: 137085-5001 -PC

[0361] Lacrimispora sp902363835 has 16s_prevalence = 22.7 and 16s_prev_score = 5.7. Illustrative bacterial species that demonstrated IPA synthesis from literature data and scoring used to infer isolate IPA phenotype include Peptostreptococcus anaerobius. Illustrative bacterial species that demonstrated IAA synthesis from literature data and scoring used to infer isolate IAA phenotype include Bacteroides ovatus, Parabacteroides distasonis, Bacteroides eggerthii, Bacteroides thetaiotaomicron, Bifidobacterium adolescentis, and Bacteroides fragilis. Illustrative species or sub-species associated with responders (versus non-responders) to immuno-oncology therapy (IO therapy) in communities similar to those observed in healthy cancer-free individuals to support healthy immune system function include Peptostreptococcus anaerobius.

[0362] The analysis revealed that 7oxo metabolism is a common, ubiquitous feature between species. Bacterial consortia, as described herein, provide redundancy across species in fulfilling 7oxo metabolism.

[0363] Bacterial species selection was guided by in silico analyses calculating the prevalence of species using data from next-generation sequencing (NGS) and metagenomic analysis with multiple methods. As shown in the output depicted Fig. 2, the in silico analyses generated outputs that were tunable for sensitivity in measuring prevalence of species using multiple methods, which were compared. Tuning the sensitivity altered the limits for detection, which altered the number of false negatives / false positive early in bacterial species screening e.g., before in vitro and / or in vivo selection processes). As shown in Fig. 2, each point represented a bacterial species detected with some frequency in healthy volunteer (HV) data, where the x- axis and y-axis represent prevalence between two methods.

[0364] The in silico analyses incorporated statistical and machine-learning modeling to select species from a cohort of bacterial species existing in the microbiomes of healthy humans (e.g., as shown in Figs. 3A- 3C). As shown in Figs. 3A-3B, an illustrative 100-target taxa (Fig. 3A) and 200-target taxa (Fig. 3B) bacterial consortia were arranged based on similarity between bacterial species relative to the bacterial populations observed in healthy humans, in consideration of characteristics depicted in Table 3. Outputs (like that shown in Fig. 3A-3D) were generated to visualize results to aid in selection of bacterial species using a principal coordinate analysis (PCoA) and beta diversity method (with Hamming distance shown between points. AsDBl / 161604598.2 108Atorney Docket No.: 137085-5001 -PC shown in Fig. 3C, a computational prediction of healthy bacterial consortia was generated from 3,000 healthy volunteer (HV) metagenomes, a representative target “backbone” microbiome was selected, from which the identity of a plurality of bacterial species were identified and interrogated for characteristics to produce compositions herein. As shown in Fig. 3D, bacterial consortia herein are designed to have a community structure that is comparable to that observed in healthy communities. Principal component analysis using beta diversity method (Hamming distance shown) is illustrated with shows placement of the bacterial community in a multi-dimensional space, represented in two dimensions for simplicity.

[0365] The in silico analyses determined the relative levels of microbiome biomass was captured by prevalent bacterial species, e.g., which determined an appropriate number of bacterial species to build the consortia. As shown in Figs. 4A-4F, analyses were performed which determined the fraction of bacterial community abundance (in terms of number of genomes / cells observed) that were captured at various sizes of bacterial consortia (e.g., species count). This information helped determine the potency numbers, e.g., as described in Table 2, as well as the formation of exemplary bacterial consortia #1 , #2, and #3, as well as a “core” bacterial consortia set that are shared between the three exemplary bacterial consortia. Numerous bacterial consortia were created based on the characteristics listed herein and using the bacterial species / isolates described herein. For simplicity, three exemplary bacterial consortia (Consortia #1 , #2, and #3), as well as an exemplary “core” bacterial consortia shared between the three to show that different consortia were generated.

[0366] As described in Tables 6 and 7, and as shown in Figs. 4A-4F, the number of target species with high prevalence (among healthy microbiomes) and the number selected for representative compositions herein was determined. To generate bacterial consortia, bacteria were selected to capture the most common and abundant microbial cells across healthy human variation. As shown in Figs. 4C-4F, the fraction of bacterial community abundance (in terms of number of genomes / cells observed) that is captured by bacterial consortia herein is plotted against successful FMT donors. This was compared to a theoretical maximum (a successful FMT donor community), with 250+ species and perfect engraftment, and to a clinical “best-case” scenario, -60% engraftment from a clinically successful healthy FMT donor.Table 6: Illustrative summary for prevalent species, ordered from “least stringent cutoff” to “most stringent cutoff.” The number of species for the backbone is given for consortia of four representative compositions.DBl / 161604598.2 109Atorney Docket No.: 137085-5001 -PCTable 7: Illustrative bacterial species based for compositions herein.DBl / 161604598.2 110Atorney Docket No.: 137085-5001 -PCDB1 / 161604598.2 111Atorney Docket No.: 137085-5001 -PC

[0367] As shown in Fig. 5, bacterial species selection was guided by in silico analyses utilizing clustering processes which clustered bacterial taxa based on similarities of characteristics, e.g., resulting in pluralities of bacterial species, for example, as listed in Table 1 a, Table 1 b, Table 1c, Table 1 d, Table 1 e, Table 1f, Table 1 g, Table 1 h, Table 1 i, Table 3, Table 6, Table 7, Table 8, and Table 12, and also including the ability of the bacterial species to perform transformation of primary bile acid (BA) to secondary BA, literature data and scoring used to infer isolate IPA phenotype, literature data and scoring used to infer isolate IAA phenotype, and species or sub-species associated with responders (versus non-responders) to IO therapy. The illustrative graphical output shown in Fig. 5 is a correlation analysis of bacterial taxa (represented as nodes) which are presented as a function of their “between-ness” or clustering network analysis based on similarity / dissimilarity of co-occurrence profiles. This clustering was found to aid in selecting bacterial species, e.g., selecting between the species listed in Table 1a, Table 1 b, Table 1c, Table 1 d, Table 1 e, Table 1f, Table 1g, Table 1 h, Table 1 i, Table 3, Table 6, Table 7, Table 8, and Table 12. Data described herein is a combination of in silico analyses from validated in vivo and in vitro analysis, as well as predictive modeling from machine-learning. Data described herein also includes in vitro assessments, such as co-culturing, cryostability, immune cell activation, antibiotic susceptibility, etc.Example 2: Cryostabilitv of bacterial species for consortium generation.

[0368] Bacterial isolates were cultured with samples taken and resuspended in a vegetable-based cryoprotectant ( / .e., glycerol) and frozen to -80°C for several months. The cryopreserved bacteria were then thawed and tested for growth in either liquid media or agar plates. Growth was assessed by ODsoonm measurements and / or colony forming units (CFU) per mL before and after cryostorage. As shown in Fig. 9, an illustrative viability screening result demonstrated at least 90%+ cryo-viability was achievable in the selected pluralities of bacterial isolates described herein. This type of selection is useful for selecting bacterial species for manufacturing purposes.

[0369] While the disclosure has been described in connection with specific embodiments thereof, it will be understood that it is capable of further modifications and this application is intended to cover any variations, uses, or adaptations of the disclosure following, in general, the principles of the disclosure and including such departures from the present disclosure as come within known or customary practice within the art to which the disclosure pertains and as may be applied to the essential features hereinbefore set forth and as follows in the scope of the appended claims.DBl / 161604598.2 112Atorney Docket No.: 137085-5001 -PCExample 3: Co-culturabilitv of bacterial species for consortium generation.

[0370] As shown in the illustrative workflow in Fig. 1 B, strains were isolated from healthy stool and banked to generate pure, isolated stocks that are not fecal matter-based samples. Bacterial identity was determined with full length 16S Sanger sequencing. Purity of isolate cultures was confirmed with deep 16S sequencing, with whole genome sequencing (WGS) used to confirm strain / isolate identity. WGS was used to confirm the absence of any concerning virulence factors or antibiotic resistance genes. The presence of virulent phage induction under manufacturing conditions is a risk to manufacturability of the co-cultures. Therefore, WGS was also used to confirm absence of concerning phage. Final prioritization of isolates with WGS was done to confirm the presence of genes required to produce metabolites of interest for product efficacy. Some strains were included as part of the bacterial consortia are confirmed for prevalence in healthy donors or in other populations of interest (e.g., responders to immune checkpoint inhibitor (ICI) therapy).

[0371] Growth curves are used for categorization of strains / isolates into “fast” and “slow” categories. Then, growth curves were used to predict appropriate culture timings for pre-inoculation, seed bottle growth, and DASGIP fermentation prior to harvest. As shown in Figs. 17A-17C, strains / isolates of interest at this point were characterized for their ability to grow in universal growth media, as well as a small selection of other media types (both in liquid media and on agar plates). This data was used to select growth media for the pre-inoculation culture (small scale culture to be pooled prior to seed bottle inoculation), seed culturing, and fermentor culturing. This step also confirmed viability of the cell stocks. As shown in Fig. 17A, growth curves were also used to categorize isolates into various sub-consortia. Generally, consortia were categorized into two main categories - “fast” and “slow.” As shown in Fig. 17B, the “fast” sub-consortia included strains observed to have a short lag time (e.g., lag phase), fast growth rate (e.g., doubling time, generation time), and / or high max OD (e.g., ODeoonm), while as shown in Fig. 17C, the “slow” sub-consortia included strains observed to have a long lag time, slow growth rate, and / or low max OD. Some strains were not OD responsive, and in these cases, viability was confirmed with colony forming units (CFU) testing, with these strains assigned to the “slow” category. Each sub-consortia described herein are grown in separate seed bottles, which are then inoculated into the DASGIP (parallel bioreactor system) at separate times (e.g., growth curve analysis and bacterial growth classification were used to predict timing of inoculation to achieve co-culture).

[0372] Based on the strain co-culturing analysis and segmentation based on fast and slow growth, the data allowed for the identification of three sets of bacterial growth: A) a set of species that were detected atDBl / 161604598.2 113Atorney Docket No.: 137085-5001 -PC relevant timepoints in co-culture; B) a set of species that were not always detected at relevant timepoints in co-culture; and C) a set of species rarely detected at relevant timepoints in co-culture. To improve the overall richness of species detected in the co-culture harvest timepoints, sets B and C were grown in separate fermenters from set A. All material harvested from fermenters was blended post-lyophilization.

[0373] Each strain in the sets of strains was categorized into “fast” and “slow” strain categories using the co-culturability criteria, as described herein, and also based on the growth curves for those specific cell stocks (e.g., Figs. 17A-17C). The fast and slow categorization was based on the strain composition of each set. For example, a strain that might be categorized as slow in comparison to the majority of isolates, might be categorized as fast in comparison with only other “problem” isolates.

[0374] As shown in Figs. 18A-18C, harvest timing was chosen based on balancing maximum viability of the co-culture and maximum richness of detected species. The absolute abundance analysis informed which species were increasing and decreasing in abundance during fermentation. Chosen harvest timepoints for DASGIPS 11 and 12 (e.g., shown as diamond curves in Figs. 18A-18C) were based on data from two other DASGIPS 9 and 10. Each of the abundance and number of species over time was analyzed using 16S sequencing.

[0375] As shown in Fig. 19, co-culturing was successful in growing approx. 150 strains in 3-5 different fermenters. The co-culturing data identified a core community of bacterial species of approx. 45 distinct species (at least 63 different strains) that were reliably co-cultured, despite any number of additional strains added into the co-culture mix. Of the 168 strains (130 species) that were included in an exemplary final cocultured product, only 13 strains were not detected at any timepoint in the 16 fermentor experiments that were performed. With appropriate harvest timing, 153 strains were grown in co-culture and harvested. As summarized in Fig. 20, of the 13 strains that were not detected in the fermenters at any timepoint, 12 of these were detected in seed bottles. The only strain not detected in the seed bottles or in the fermenters had also not been detected in any inoculum samples. It was concluded that it is likely low or non-viable. Table 8 shows all bacteria that were able to be co-cultured. Numerous combinations of co-culture bacterial isolates were achieved from this illustrative sampling.Table 8. Illustrative bacterial consortia designed from co-culturing data. The -133 “Core” set are shared amongst the three consortia, each consortia having -150 separate species, strains, and isolates. (+) indicates presence of that species, strain, or isolate in the consortia, (-) indicates the absence of that species, strain, or isolate in the consortia.DBl / 161604598.2 114Atorney Docket No.: 137085-5001 -PCDB1 / 161604598.2 115Atorney Docket No.: 137085-5001 -PCDB1 / 161604598.2 116Atorney Docket No.: 137085-5001 -PCDB1 / 161604598.2 117Atorney Docket No.: 137085-5001 -PCDB1 / 161604598.2 118Atorney Docket No.: 137085-5001 -PC

[0376] The successfully co-culturability of large numbers of different types of bacterial species / isolates has long been a hurdle to overcome in the development of complex microbiome products. Overall, these data demonstrated, inter alia, that it is possible to design categories, or culture “buckets,” that grow a full consortium of at least 150 different bacterial strains / isolates in a few bioreactors, which lends feasibility to the manufacturing process - something that has been difficult in the past. Based on the co-culture data, many of the strains outside of the “core” bacterial community were detected at earlier timepoints or in the seed bottle. With appropriate strain composition, media, and / or timing of fermentor inoculation, the data shows that the strategy achieved successful co-culture of at least about 150 strains in about 3 different fermenters. The data also demonstrated, inter alia, that numerous bacterial consortia were generated from permutations of the bacteria described herein with expected behavior based on the in silico analysis and modeling.Example 4: Genetic Analysis for consortia-level metabolic function.

[0377] Bacterial species selection was guided by in silico statistical analyses to determine the distributions of bacterial prevalence based on genetic interrogation for the presence / prevalence of functional and / or metabolic genes and / or operons. As shown in Table 9, an illustrative genetic analysis workflow for isoalloLCA, 7-oxo-LCA and 7-oxo-DCA from LCA and DCA, production of immunomodulatory metabolites LCA and DCA from (deconjugated) primary bile acids, is shown.Table 9: Workflow for genetic analysis of bacterial consortia metabolism.DBl / 161604598.2 119Atorney Docket No.: 137085-5001 -PC

[0378] As shown in Fig. 6, an illustrative graphical model output is shown for calculated e-values for bacterial species relative for illustrative metabolic genes of the 3-oxoLCA to isoalloLCA pathway, 5a- reductase (e.g, reductase_5a), 50-reductase (e.g, reductase_5b), and 30-HSDH (hydroxysteroid dehydrogenase, hsdh). The e-value was a calculated expectation value that indicated the number of alignments with a score > S that one can expect to find by chance in a database of size N. Hence, the e-DB1 / 161604598.2 120Atorney Docket No.: 137085-5001 -PC value was dependent on the database size and the query length, where the closer the e-value to 0, the better the alignment. The e-value was a proxy score for probability of the gene sequence (and the metabolic activity) being similar. The e-value was calculated for one or more one or more enzymes, cell surface markers, secretable factors (relative to one or more wild-type bacterial gene sequences encoding one or more enzymes, cell surface markers, secretable factors, etc.), pictured in Fig. 6 was a representative output for metabolism related to the 3-oxoLCA to isoal Io LCA pathway. The graphical analysis in Fig. 6 shows a bimodal distribution of values for 3 -HSDH, with the majority of values between about 0 and about 50 and about 100 and 150. The graphical analysis in Fig. 6 shows a bimodal distribution of values for 5a-reductase, with the majority of values between about 0 and about 10 and about 100 and 150. The graphical analysis in Fig. 6 shows a bimodal distribution of values for 5 -reductase, with the majority of values between about 0 and about 50 and about 200 and 250. Similar analyses were performed for other bacterial metabolites and pathways.

[0379] As shown in Figs. 7A-7B, illustrative phylogenetic model outputs to select bacterial clades with high confidence of a particular metabolic trait are shown (e.g., modeling is shown based on 8 distinct HMM outputs for 8 genes genetic in a metabolic pathway). Clades with high frequency of gene presence and pathway completeness and a large number of samples were selected for inclusion in the bacterial consortium (e.g., for inclusion in Table 1 a, Table 1 b, Table 1c, Table 1 d, Table 1e, Table 1f, Table 1 g, Table 1 h, and Table 1 i). Interrogation of existing bacterial data repositories helped screen isolates in high-throughput where individual genome sequences were not available. Phylogenetic modeling assisted with the selection of bacterial species / isolates to fulfill the desired characteristics / functionality the entire plurality of bacterial species. The phylogenetic modeling was used to select clades with high confidence of metabolism. Clades with high frequency of gene presence and a large number of samples were shown to provide better results. The data demonstrated, inter alia, that the method provided a use for available genomic data for high- throughput screening of isolates that have no available full genomic sequences.

[0380] As shown in Fig. 10, a non-limiting, graphical representation of a multi-mechanistic consortium composition design is illustrated. The dendrogram shown has -150 leaves, each leaf representing a species / isolate, with the outer concentric rings relating to the characteristics of that species / isolates that make its selection desirable for inclusion in the consortium. Each concentric ring encircling the dendrogram represents a different mechanism of action (MoA), or functional module, modeled onto the bacteria represented in the dendrogram. The innermost ring “Module 0” (grey shaded) refer to species / isolates in the dendrogram that are in Table 1 a or Table 1 b, the next concentric ring “Module 1” is a combined module ofDBl / 161604598.2 121Atorney Docket No.: 137085-5001 -PC the modules listed “1” in the inlet, showing species / isolates that produce butyrate and propionate, butyrate alone, or propionate alone. The next outer concentric ring “Module 2” is a combined module of the modules listed “2” in the inlet, showing species / isolates for producing 7-oxo-LCA, 7-oxo-DCA, and other bile acids (BAs), or isoalloLCA alone, of secondary bile acids (Bai) alone. The next outer concentric ring “Module 3” is a combined module of the modules listed “3” in the inlet, showing species / isolates for producing IPA or IAA. The last, outermost concentric ring “Module 4” shows species / isolates relevant for IO-specific outcomes from in vivo or clinical data. The consortia comprise multiple mechanisms to address heterogenous patient populations and functional redundancy to maximize number of “shots on goal” and size of effect.

[0381] As shown in Figs. 11A-11G, isolate genome sequences were scored with a screening model trained on experimental data for the presence of gene pathways capable of metabolism to create immunomodulatory bile acid metabolites, e.g., isoalloLCA, LCA, DCA, 7-oxo-LCA, or 7-oxo-DCA. The scores were continuous but binarized as positive or negative based on learned cutoffs from training data. The data demonstrate that with a sufficiently large and diverse bacterial consortium, using the criteria as described herein, production of the full suite of metabolites is obtained using community-level metabolism, / .e., multiple isolates in combination.Table 10a: Confirmation of function of metabolic pathways by DNA analyses.

[0382] As shown in Table 10a, the metabolic pathways were detected in isolates that were successfully- co-cultured. The values are reported as either the number of isolates or total projected abundance of isolates. Projected abundance was calculated at the equilibrium abundance in humans for the isolate’s species, and taking the median across people, for each isolate.Example 5: Machine-learning modeling for determining consortia-level IO effect and bacterial selection.

[0383] Model construction. A supervised machine-learning model was constructed to predict, based on gut microbiome species profiles pre-treatment, whether IO patients would be responders or non-responders to immuno-oncology (I) therapy. Typically, this is scored by a standard clinical metric describing whetherDBl / 161604598.2 122Atorney Docket No.: 137085-5001 -PC tumors shrink or grow or how their growth is affected as a function of time in response to treatment. A random forest model was trained on the largest IO dataset with microbiome data (Derosa cohorts from Derosa, et al. “Custom scoring based on ecological topology of gut microbiota associated with cancer immunotherapy outcome,” Cell, Vol. 187, No. 13, P3373-89 (2024), incorporated by reference herein in its entirety). The model parameters were fixed and this was called the R-vs-NR-ML-model, which was an ensemble of dichotomous decision trees that employed a bootstrap aggregating method that takes an input of species’ abundance vectors (patient community at treatment start) and outputs patients’ response (e.g., as responder “R” or non-responder “NR”), often expressed as frequency of the ensemble of models’ predictions of “NR” or “R”.

[0384] Model in-distribution testing. The model screen was validated by showing it was able to distinguish true responders (R) and non-responders (NR) to IO checkpoint inhibitor therapy with accuracy AUC>0.6 (standard supervised learning model stat) on hold-out test samples from patients never seen by the model. There were some patients that were consistently correctly predicted by most models in the ensemble. It was concluded that these patients’ responses were preferentially tied to the microbiome, rather than other unmeasured signals governing IO response. Using this patient subset and a leave-one-out-cross- validation (LOOCV) approach enabled training refined models with mean AUC>0.9.

[0385] Model task transferability. The R-vs-NR-ML-model exhibited task transferability in that it provided accuracy in stratifying overall survival of all patients (a label not provided during training). For example, as shown in Fig. 12, training with leave-one-out-cross-validation (LOOCV) on the largest IO dataset with microbiome data (Derosa et al. 2024 cohorts), resulted in a set of models with mean AUC>0.6 for predicting clinical response on hold-out test samples from patients never seen by the model, and with excellent stratification of all patients by overall survival, p=0.0001 .

[0386] After showing that in-distribution data behaved as expected, the refined R-vs-NR-ML-model was used for out-of-distribution generalization. Samples from a different cohort were used and the model was tested for its ability to replicate the key findings reported from fecal microbiome transplantation (FMT) studies in IO patients, for example as described in Podlesny et al. “Identification of clinical and ecological determinants of strain engraftment after fecal microbiota transplantation using metagenomics,” Cell Reports Medicine, Vol. 3, No. 8, 100711 (2022), the entire contents of which are incorporated by reference herein. The model expressed the output as the “Probability of predicting responder (R)” across model runs, which was normalized to real clinical responders run through the model (e.g., median probability of all clinical RDBl / 161604598.2 123Atorney Docket No.: 137085-5001 -PC across model runs). Next, treatment communities (fecal microbiome transplant, FMT) were added to patient’s pre-treatment communities in various ratios to simulate dosing (and engraftment outcomes) for clinical intervention with a gut microbiome therapy (e.g., a bacterial consortia).

[0387] As shown in Fig. 13, the R-vs-NR-ML-model demonstrated that, assuming different dosing / engraftment models, FMT performs as expected based on using clinically successful FMT data (from a real donor used in London, Ontario clinical study in IO, as described in Routy et al. “Fecal microbiota transplantation plus anti-PD-1 immunotherapy in advanced melanoma: a phase I trial,” Nat Med. (2023) Vol. 29, No. 8, pp: 2121-2132, the entire contents of which are incorp...

Claims

Atorney Docket No.: 137085-5001 -PCCLAIMSWhat is claimed is:1 . A composition comprising an isolated plurality of bacterial species, the plurality of bacterial species comprising a total of at least about 100 isolates from at least about 50 bacterial species, wherein: i. at least about 7 isolates are selected from at least about 5 species having about or at least about95% sequence identity to the 16S rRNA sequence of bacterial species selected from Table 1 a; ii. at least about 12 isolates are selected from at least about 10 species having about or at least about 95% sequence identity to the 16S rRNA sequence of bacterial species selected from Table 1c; ill. at least about 12 isolates are selected from at least about 10 species having about or at least about 95% sequence identity to the 16S rRNA sequence of bacterial species selected from Table 1d; iv. at least about 12 isolates are selected from at least about 10 species having about or at least about 95% sequence identity to the 16S rRNA sequence of bacterial species selected from Table 1e and / or Table 1f; and v. the remaining of the at least about 100 isolates from the at least about 50 bacterial species have about or at least about 95% sequence identity to the 16S rRNA sequence of bacterial species selected from Table 1 b.

2. The composition of claim 1 , wherein the plurality of bacterial species is suitable for co-culturing in no more than 5 bioreactors, no more than 4 bioreactors, no more than 3 bioreactors, no more than 2 bioreactors, or no more than a single bioreactor.

3. The composition of claim 1 or 2, wherein the plurality of bacterial species comprises between about 50 bacterial species and about 100 bacterial species, between about 100 bacterial species and 150 bacterial species, or between about 150 bacterial species and 200 bacterial species, or wherein the plurality of bacterial species comprises between about 50 bacterial species and about 60 bacterial species, between about 60 bacterial species and about 70 bacterial species, between about 70 bacterial species and about 80 bacterial species, between about 80 bacterial species and about 90 bacterial species, between about 90 bacterial species and about 100 bacterial species, betweenDBl / 161604598.2 511Atorney Docket No.: 137085-5001 -PC about 100 bacterial species and about 110 bacterial species, between about 110 bacterial species and about 120 bacterial species, between about 120 bacterial species and about 130 bacterial species, between about 130 bacterial species and about 140 bacterial species, or between about 140 bacterial species and about 150 bacterial species.

4. The composition of any one of claims 1-3, wherein the plurality of bacterial species comprises between about 100 bacterial isolates and about 150 bacterial isolates, between about 150 bacterial isolates and about 200 bacterial isolates, or between about 200 bacterial isolates and about 250 bacterial isolates, or wherein the plurality of bacterial species comprises between about 100 bacterial isolates and about 110 bacterial isolates, between about 110 bacterial isolates and about 120 bacterial isolates, between about 120 bacterial isolates and about 130 bacterial isolates, between about 130 bacterial isolates and about 140 bacterial isolates, between about 140 bacterial isolates and about 150 bacterial isolates, between about 150 bacterial isolates and about 160 bacterial isolates, between about 160 bacterial isolates and about 170 bacterial isolates, between about 170 bacterial isolates and about 180 bacterial isolates, between about 180 bacterial isolates and about 190 bacterial isolates, or between about 190 bacterial isolates and about 200 bacterial isolates.

5. The composition of any one of claims 1 -4, wherein the plurality of bacterial species belong to one or more bacterial genera of Acetatifactor, Agathobacter, Agathobaculum, Akkermansia, Alistipes, Anaerobutyricum, Anaerostipes, Anaerotignum, Anaerotruncus, Avimicrobium, Bacteroides, Bariatricus, Barnesiella, Bifidobacterium, Bilophila, Bittarella, Blautia, Butyricicoccus, Butyricimonas, Catenibacterium, Candidatus (UBA1417), Choladousia, Christensenella, Clostridium, Clostridiales (KLE1615), Coprobacillus, Coprobacter, Coprococcus, Copromonas, Dialister, Diplocloster, Dorea, Dysosmobacter, Eggerthella, Eisenbergiella, ER4, Eubacterium, Faecalibacillus, Faecalibacterium, Firmicutes (CAG), Fimivivens, Flavonifractor, Fusicatenibacter, Gemmiger, Harryflintia, Holdemanella, Hominisplanchenecus, Hungatella, Intestinimonas, Lachnoclostridium, Lachnospira (UBA3402), Lacrimispora, Ligilactobacillus, Longibaculum, Mediterraneibacter, Monoglobus, Muricomes, Odoribacter, Oliverpabstia, Parabacteroides, Paraprevotella, Peptostreptococcus, Phascolarctobacterium, Phocaeicola, Prevotella, Roseburia, Ruminococcus, Ruthenibacterium, Sarcina, Slackia, Sutterella, Thomasclavelia, Tractidigestivibacter, Turicibacter, and Wujia, or optionally wherein the plurality of bacterial species belong to one or more bacterial genera ofDBl / 161604598.2 512Atorney Docket No.: 137085-5001 -PCAgathobacter, Agathobaculum, Akkermansia, Alistipes, Anaerobutyricum, Anaerostipes, Anaerotignum, Avimicrobium, Bacteroides, Bariatricus, Barnesiella, Bifidobacterium, Bilophila, Bittarella, Blautia_A, Butyricicoccus, Butyricimonas, CAG-317, CAG-41, Christensenella, Clostridium, Coprobacter, Coprococcus_A, Copromonas, Diplocloster, Dorea, Dorea_A, Dysosmobacter, Eisenbergiella, Eubacterium_G, Faecalibacillus, Faecalibacterium, Flavonifractor, Fusicatenibacter, Gemmiger, Harryflintia, Hungatella, Intestinimonas, KLE1615, Lachnoclostridium_B, Lachnospira, Mediterraneibacter, Monoglobus, Muricomes, Odoribacter, Oliverpabstia, Parabacteroides, Peptostreptococcus, Phocaeicola, Prevotella, Roseburia, Ruminococcus_B, Ruminococcus_D, Ruminococcus_E, Ruthenibacterium, Slackia_A, Turicibacter, UBA3402, and Wujia, or optionally wherein the plurality of bacterial species belong to one or more bacterial genera of Agathobacter, Akkermansia, Anaerobutyricum, Anaerostipes, Bacteroides, Clostridium, Faecalibacterium, Gemmiger, and Phocaeicola.

6. The composition of any one of claims 1-5, wherein the plurality of bacterial species comprises no more than about 15 individual bacterial species per genera, no more than about 10 individual bacterial species per genera, no more than about 8 individual bacterial species per genera, no more than about 6 individual bacterial species per genera, no more than about 5 individual bacterial species per genera, no more than about 4 individual bacterial species per genera, no more than about 3 individual bacterial species per genera, no more than about 2 individual bacterial species per genera, or no more than a single individual bacterial species per genera, optionally wherein the plurality of bacterial species comprises about or at least about 85 distinct bacterial genera, about or at least about 80 distinct bacterial genera, about or at least about 75 distinct bacterial genera, about or at least about 70 distinct bacterial genera, about or at least about 65 distinct bacterial genera, about or at least about 60 distinct bacterial genera, about or at least about 50 distinct bacterial genera, or about or at least about 40 distinct bacterial genera.

7. The composition of any one of claims 1-6, comprising: i. at least about 7 isolates selected from at least about 5 species having about or at least about 96%, about or at least about 97%, about or at least about 98%, or about or at least about 99% sequence identity to the 16S rRNA sequence of bacterial species selected from Table 1 a,DBl / 161604598.2 513Atorney Docket No.: 137085-5001 -PC optional wherein at least about 7 isolates selected from at least about 5 species, each having the 16S rRNA sequence of bacterial species selected from Table 1a; ii. at least about 12 isolates selected from at least about 8 species having about or at least about 96%, about or at least about 97%, about or at least about 98%, or about or at least about 99% sequence identity to the 16S rRNA sequence of bacterial species selected from Table 1 c, optionally wherein at least about 12 isolates selected from at least about 8 species, each having the 16S rRNA sequence of bacterial species selected from Table 1c; ill. at least about 12 isolates selected from at least about 8 species having about or at least about 96%, about or at least about 97%, about or at least about 98%, or about or at least about 99% sequence identity to the 16S rRNA sequence of bacterial species selected from Table 1 d, optionally wherein at least about 12 isolates selected from at least about 8 species, each having the 16S rRNA sequence of bacterial species selected from Table 1 d; iv. at least about 12 isolates selected from at least about 8 species having about or at least about96%, about or at least about 97%, about or at least about 98%, or about or at least about 99% sequence identity to the 16S rRNA sequence of bacterial species selected from Table 1 e and / or Table 1 f, optionally wherein at least about 12 isolates selected from at least about 8 species, each having the 16S rRNA sequence of bacterial species selected from Table 1e and / or Table 1f; and / or v. at least about 40 isolates selected from at least about 20 species having about or at least about96%, about or at least about 97%, about or at least about 98%, or about or at least about 99% sequence identity to the 16S rRNA sequence of bacterial species selected from Table 1 b, optionally wherein at least about 43 isolates selected from at least about 21 species, each having the 16S rRNA sequence of bacterial species selected from Table 1 b.

8. The composition of any one of claims 1 -7, wherein the plurality of bacterial species comprises: about or at least about 8 isolates, about or at least about 9 isolates, about or at least about 10 isolates, about or at least about 11 isolates, about or at least about 12 isolates, about or at least about 13 isolates, about or at least about 14 isolates, about or at least about 15 isolates, about or at least about 17 isolates, about or at least about 18 isolates, about or at least about 19 isolates, about or at least about 20 isolates, or about or at least about 25 isolates,DBl / 161604598.2 514Atorney Docket No.: 137085-5001 -PC selected from about or at least about 6 species, about or at least about 7 species, about or at least about 8 species, about or at least about 9 species, about or at least about 10 species, about or at least about 11 species, about or at least about 12 species, about or at least about 13 species, about or at least about 14 species, about or at least about 15 species, or about or at least about 20 species, each having about or at least about 95%, about or at least about 96%, about or at least about 97%, about or at least about 98%, or about or at least about 99% sequence identity to a 16S rRNA sequence of a bacterial species selected from Table 1 a, optionally each being selected from Table 1 a, and / or optionally comprising one or more of Agathobacter rectalis, Akkermansia muciniphila_B, Anaerobutyricum soehngenii, Anaerostipes hadnis, Bacteroides thetaiotaomicron, Bacteroides uniformis, Clostridium_AP scindens, Faecalibacterium prausnitzii_D, Faecalibacterium prausnitziij, Phocaeicola vulgatu.

9. The composition of any one of claims 1 -8, wherein the plurality of bacterial species comprises: about or at least about 13 isolates, about or at least about 14 isolates, about or at least about 15 isolates, about or at least about 16 isolates, about or at least about 17 isolates, about or at least about 18 isolates, about or at least about 19 isolates, about or at least about 20 isolates, about or at least about 21 isolates, about or at least about 22 isolates, about or at least about 23 isolates, about or at least about 24 isolates, about or at least about 25 isolates, about or at least about 30 isolates, or about or at least about 35 isolates, selected from about or at least about 11 species, about or at least about 12 species, about or at least about 13 species, about or at least about 14 species, about or at least about 15 species, about or at least about 16 species, about or at least about 17 species, about or at least about 18 species, about or at least about 19 species, about or at least about 20 species, or about or at least about 25 species, each having about or at least about 95%, about or at least about 96%, about or at least about 97%, about or at least about 98%, or about or at least about 99% sequence identity to a 16S rRNA sequence of a bacterial species selected from Table 1c, optionally each being selected from Table 1c, and / or optionally comprising one or more of Bilophila wadsworthia, Butyricimonas virosa, Clostridium cuniculi, Clostridium_Q fessum,DBl / 161604598.2 515Atorney Docket No.: 137085-5001 -PCClostridium_Q symbiosum, Copromonas sp900066535, Dysosmobacter sp001916835, Dysosmobacter welbionis, Eisenbergiella sp900066775, ER4 sp900317525, Eubacterium_G sp000432355, Eubacterium_G ventriosum, Flavonifractor plautii, Intestinimonas butyriciproducens, Odoribacter splanchnicus, Wujia chipingensis.

10. The composition of any one of claims 1 -9, wherein the plurality of bacterial species comprises: about or at least about 13 isolates, about or at least about 14 isolates, about or at least about 15 isolates, about or at least about 16 isolates, about or at least about 17 isolates, about or at least about 18 isolates, about or at least about 19 isolates, about or at least about 20 isolates, about or at least about 21 isolates, about or at least about 22 isolates, about or at least about 23 isolates, about or at least about 24 isolates, about or at least about 25 isolates, about or at least about 30 isolates, or about or at least about 35 isolates, selected from about or at least about 11 species, about or at least about 12 species, about or at least about 13 species, about or at least about 14 species, about or at least about 15 species, about or at least about 16 species, about or at least about 17 species, about or at least about 18 species, about or at least about 19 species, about or at least about 20 species, or about or at least about 25 species, each having about or at least about 95%, about or at least about 96%, about or at least about 97%, about or at least about 98%, or about or at least about 99% sequence identity to a 16S rRNA sequence of a bacterial species selected from Table 1 d, optionally each being selected from Table 1 d, and / or optionally comprising one or more of Alistipes montrealensis, Bacteroides cellulosilyticus, Bacteroides clarus, Bacteroides intestinigallinarum, Blautia_A faecis, Blautia_A obeum, Blautia_A sp900066145, Blautia_A sp900066335, Blautia_A wexlerae, Blautia_A wexlerae_B, CAG-41 sp900066215, Clostridium_Q symbiosum, Coprococcus eutactus, Dysosmobacter welbionis, Eisenbergiella tayi, Flavonifractor plautii, Intestinimonas butyriciproducens, Mediterraneibacter faecis, Parabacteroides goldsteinii, Parabacteroides johnsonii, Parabacteroides merdae, Phascolarctobacterium sp900544795, Phocaeicola massiliensis, Roseburia inulinivorans, and Ruminococcus_B gnavus.

11. The composition of any one of claims 1-10, wherein the plurality of bacterial species comprises:DBl / 161604598.2 516Atorney Docket No.: 137085-5001 -PC about or at least about 13 isolates, about or at least about 14 isolates, about or at least about 15 isolates, about or at least about 16 isolates, about or at least about 17 isolates, about or at least about 18 isolates, about or at least about 19 isolates, about or at least about 20 isolates, about or at least about 21 isolates, about or at least about 22 isolates, about or at least about 23 isolates, about or at least about 24 isolates, about or at least about 25 isolates, about or at least about 30 isolates, or about or at least about 35 isolates, selected from about or at least about 11 species, about or at least about 12 species, about or at least about 13 species, about or at least about 14 species, about or at least about 15 species, about or at least about 16 species, about or at least about 17 species, about or at least about 18 species, about or at least about 19 species, about or at least about 20 species, or about or at least about 25 species, each having about or at least about 95%, about or at least about 96%, about or at least about 97%, about or at least about 98%, or about or at least about 99% sequence identity to a 16S rRNA sequence of a bacterial species selected from Table 1e and / or Table 1f, optionally each being selected from Table 1 d, and / or optionally comprising one or more of Agathobaculum butyriciproducens, AHstipes communis, Anaerobutyricum hallii, Bariatricus comes, Bifidobacterium adolescentis, Bifidobacterium longum, GAG-317 sp000433215, Coprobacter fastidiosus, Coprococcus eutactus, Coprococcus_A catus, Dorea formicigenerans, Faecalibacterium longum, Faecalibacterium prausnitzii, Faecalibacterium prausnitziij), Gemmiger formicilis, Oliverpabstia intestinalis, Peptostreptococcus anaerobius, Roseburia hominis, Roseburia intestinalis, Roseburia inulinivorans, and Ruminococcus_E bromii_B.

12. The composition of any one of claims 1-11, wherein the plurality of bacterial species comprises: about or at least about 40 isolates, about or at least about 45 isolates, about or at least about 50 isolates, about or at least about 55 isolates, about or at least about 60 isolates, about or at least about 65 isolates, about or at least about 70 isolates, about or at least about 75 isolates, about or at least about 80 isolates, about or at least about 85 isolates, about or at least about 90 isolates, about or at least about 95 isolates, about or at least about 100 isolates, selected from about or at least about 30 species, about or at least about 35 species, about or at least about 40 species, about or at least about 45 species, about or at least about 50 species,DBl / 161604598.2 517Atorney Docket No.: 137085-5001 -PC about or at least about 55 species, about or at least about 60 species, about or at least about 65 species, about or at least about 70 species, about or at least about 75 species, about or at least about 80 species, or about or at least about 85 species, each species having about or at least about 95%, about or at least about 96%, about or at least about 97%, about or at least about 98%, or about or at least about 99% sequence identity to a 16S rRNA sequence of a bacterial species selected from Table 1 b, optionally each being selected from Table 1 b, and / or optionally comprising one or more of Acetatif actor sp., Agathobacter faecis, Alistipes finegoldii, Alistipes onderdonkii, Alistipes putredinis, Alistipes senegalensis, Alistipes shahii, Alistipes_A ihumii, Alistipes_A indistinctus, Anaerotignum faecicola, Avimicrobium caecorum, Bacteroides eggerthii, Bacteroides finegoldii, Bacteroides fragilis, Bacteroides luhongzhouii, Bacteroides ovatus, Bacteroides stercoris, Bacteroides xylanisolvens, Barnesiella intestinihominis, Bifidobacterium bifidum, Bifidobacterium sp., Bittarella massiliensis, Blautia_A massiliensis, Blautia_A sp., Blautia_A sp900066505, Butyricicoccus sp900604335, Butyricimonas sp., Catenibacterium sp000437715, Choladousia sp902363665, Christensenella m inuta, Clostridium_A leptum, Clostridium _AP sp., Dialisterinvisus, Diplocloster agilis, Dorea_A sp., Faecalibacillus intestinalis, Faecalibacterium duncaniae, Fusicatenibacter saccharivorans, Harryflintia acetispora, Holdemanella sp., Intestinimonas massiliensis, KLE1615 sp900066985, Lachnoclostridium_B sp900066555, Lachnospira eligens, Lachnospira eligens_A, Lachnospira rogosae, Lachnospira sp000437735, Mediterraneibacter lactaris, Monoglobus pectinilyticus, Muricomes sp000509105, Parabacteroides distasonis, Paraprevotella xylaniphila, Phocaeicola dorei, Prevotella copri_B, Prevotella rara, Ruminococcus_D bicirculans, Ruminococcus_E sp003526955, Ruthenibacterium lactatiformans, Slackia_A isoflavoniconvertens, Tractidigestivibacter sp., Turicibacter sanguinis, UBA3402 sp003478355.

13. The composition of any one of claims 1-12, wherein each bacterial species of the plurality of bacterial species is selected from Table 1a, Table 1 b, Table 1c, Table 1d, Table 1e, Table 1f, Table 1g, Table 1 h, Table 1 i, Table 3, Table 5, and / or Table 7; or wherein the plurality of bacterial species is a combination selected from Table 8; or wherein the plurality of bacterial species is a combination selected from Table 12.DBl / 161604598.2 518Atorney Docket No.: 137085-5001 -PC14. The composition of any one of claims 1-13, wherein about or at least about 20% of the total bacterial species, about or at least about 25% of the total bacterial species, about or at least about 30% of the total bacterial species, about or at least about 35% of the total bacterial species, about or at least about 40% of the total bacterial species, about or at least about 45% of the total bacterial species, about or at least about 50% of the total bacterial species, about or at least about 55% of the total bacterial species, about or at least about 60% of the total bacterial species, about or at least about 65% of the total bacterial species, about or at least about 70% of the total bacterial species, at least 75% of the total bacterial species, about or at least about 80% of the total bacterial species, at least 85% of the total bacterial species, about or at least about 90% of the total bacterial species, or about or at least about 95% of the total bacterial species of the plurality of bacterial species comprises a butyrate synthesis pathway; and / or wherein about or at least about 20% of the total species abundance, about or at least about 25% of the total species abundance, about or at least about 30% of the total species abundance, about or at least about 35% of the total species abundance, about or at least about 40% of the total species abundance, about or at least about 45% of the total species abundance, or about or at least about 50% of the total species abundance of the plurality of bacterial species is capable of producing butyrate and / or one or more intermediates of a butyrate synthesis pathway; and / or wherein about or at least about 25 of the total bacterial species, about or at least about 30 of the total bacterial species, about or at least about 35 of the total bacterial species, about or at least about 40 of the total bacterial species, about or at least about 45 of the total bacterial species, about or at least about 50 of the total bacterial species, about or at least about 55 of the total bacterial species, about or at least about 60 of the total bacterial species, about or at least about 65 of the total bacterial species, about or at least about 70 of the total bacterial species, about or at least about 75 of the total bacterial species, about or at least about 80 of the total bacterial species, about or at least about 85 of the total bacterial species, about or at least about 90 of the total bacterial species, about or at least about 95 of the total bacterial species, or about or at least about 100 of the total bacterial species of the plurality of bacterial species comprises a butyrate synthesis pathway.

15. The composition of any one of claims 1-14, wherein about or at least about 20% of the total bacterial species, about or at least about 25% of the total bacterial species, about or at least about 30% of theDBl / 161604598.2 519Atorney Docket No.: 137085-5001 -PC total bacterial species, about or at least about 35% of the total bacterial species, about or at least about 40% of the total bacterial species, about or at least about 45% of the total bacterial species, about or at least about 50% of the total bacterial species, about or at least about 55% of the total bacterial species, about or at least about 60% of the total bacterial species, about or at least about 65% of the total bacterial species, about or at least about 70% of the total bacterial species, about or at least about 75% of the total bacterial species, about or at least about 80% of the total bacterial species, about or at least about 85% of the total bacterial species, about or at least about 90% of the total bacterial species, or about or at least about 95% of the total bacterial species of the plurality of bacterial species comprises a propionate synthesis pathway; and / or wherein about or at least about 25 of the total bacterial species, about or at least about 30 of the total bacterial species, about or at least about 35 of the total bacterial species, about or at least about 40 of the total bacterial species, about or at least about 45 of the total bacterial species, about or at least about 50 of the total bacterial species, about or at least about 55 of the total bacterial species, about or at least about 60 of the total bacterial species, about or at least about 65 of the total bacterial species, about or at least about 70 of the total bacterial species, about or at least about 75 of the total bacterial species, about or at least about 80 of the total bacterial species, about or at least about 85 of the total bacterial species, about or at least about 90 of the total bacterial species, about or at least about 95 of the total bacterial species, or about or at least about 100 of the total bacterial species of the plurality of bacterial species comprises a propionate synthesis pathway; and / or wherein about or at least about 20% of the total species abundance, about or at least about 25% of the total species abundance, about or at least about 30% of the total species abundance, about or at least about 35% of the total species abundance, about or at least about 40% of the total species abundance, about or at least about 45% of the total species abundance, or about or at least about 50% of the total species abundance of the plurality of bacterial species is capable of producing propionate and / or one or more intermediates of a propionate synthesis pathway.

16. The composition of any one of claims 1 -15, wherein about or at least about 1 % of the total bacterial species, about or at least about 2% of the total bacterial species, about or at least about 3% of the total bacterial species, about or at least about 4% of the total bacterial species, about or at least about 5% of the total bacterial species, about or at least about 6% of the total bacterial species,DBl / 161604598.2 520Atorney Docket No.: 137085-5001 -PC about or at least about 7% of the total bacterial species, about or at least about 8% of the total bacterial species, about or at least about 9% of the total bacterial species, about or at least about 10% of the total bacterial species, about or at least about 15% of the total bacterial species, or about or at least about 20% of the total bacterial species comprises an IAA synthesis pathway; and / or wherein about or at least about 1 species / isolate produces IAA, about or at least about 2 species / isolates produces IAA, about or at least about 3 species / isolates produces IAA, about or at least about 4 species / isolates produces IAA, about or at least about 5 species / isolates produces IAA, about or at least about 10 species / isolates produces IAA, about or at least about 15 species / isolates produces IAA, or about or at least about 20 species / isolates produces IAA; and / or wherein about or at least about 1 % of the total species abundance, about or at least about 5% of the total species abundance, about or at least about 10% of the total species abundance, about or at least about 15% of the total species abundance, about or at least about 20% of the total species abundance, about or at least about 30% of the total species abundance, about or at least about 40% of the total species abundance, or about or at least about 50% of the total species abundance of the plurality of bacterial species is capable of producing indole-3-acetic acid (IAA) and / or one or more intermediates of an IAA synthesis pathway.

17. The composition of any one of claims 1 -16, wherein about or at least about 1 % of the total bacterial species, about or at least about 2% of the total bacterial species, about or at least about 3% of the total bacterial species, about or at least about 4% of the total bacterial species, about or at least about 5% of the total bacterial species, about or at least about 6% of the total bacterial species, about or at least about 7% of the total bacterial species, about or at least about 8% of the total bacterial species, about or at least about 9% of the total bacterial species, about or at least about 10% of the total bacterial species, about or at least about 15% of the total bacterial species, or about or at least about 20% of the total bacterial species comprises an IPA synthesis pathway; and / or wherein about or at least about 1 species / isolate produces IPA, about or at least about 2 species / isolates produces IPA, about or at least about 3 species / isolates produces IPA, about or at least about 4 species / isolates produces IPA, about or at least about 5 species / isolates produces I PA, about or at least about 10 species / isolates produces IPA, about or at least about 15 species / isolates produces IPA, or about or at least about 20 species / isolates produces IPA; and / orDBl / 161604598.2 521Atorney Docket No.: 137085-5001 -PC wherein about or at least about 1 % of the total species abundance, about or at least about 5% of the total species abundance, about or at least about 10% of the total species abundance, about or at least about 15% of the total species abundance, about or at least about 20% of the total species abundance, about or at least about 30% of the total species abundance, about or at least about 40% of the total species abundance, or about or at least about 50% of the total species abundance of the plurality of bacterial species is capable of producing indole-3-propionic acid (I PA) and / or one or more intermediates of an IPA synthesis pathway.

18. The composition of any one of claims 1 -17, wherein about or at least about 1 % of the total bacterial species, about or at least about 2% of the total bacterial species, about or at least about 3% of the total bacterial species, about or at least about 4% of the total bacterial species, about or at least about 5% of the total bacterial species, about or at least about 6% of the total bacterial species, about or at least about 7% of the total bacterial species, about or at least about 8% of the total bacterial species, about or at least about 9% of the total bacterial species, about or at least about 10% of the total bacterial species, about or at least about 15% of the total bacterial species, or about or at least about 20% of the total bacterial species comprises a synthesis pathway for one or more SCFA; and / or wherein about or at least about 1 species / isolate from the consortium produces one or more SCFAs, about or at least about 2 species / isolates produces one or more SCFAs, about or at least about 3 species / isolates produces one or more SCFAs, about or at least about 4 species / isolates produces one or more SCFAs, about or at least about 5 species / isolates produces one or more SCFAs, about or at least about 10 species / isolates produces one or more SCFAs, about or at least about 15 species / isolates produces one or more SCFAs, or about or at least about 20 species / isolates produces one or more SCFAs; and / or wherein the healthy microbiome comprises about or at least about 1 % of the total species abundance, about or at least about 5% of the total species abundance, about or at least about 10% of the total species abundance, about or at least about 15% of the total species abundance, about or at least about 20% of the total species abundance, about or at least about 30% of the total species abundance, about or at least about 40% of the total species abundance, or about or at least about 50% of the total species abundance of the plurality of bacterial species is capable of producing oneDBl / 161604598.2 522Atorney Docket No.: 137085-5001 -PC or more short chain fatty acid (SCFA) and / or one or more intermediates of a SCFA synthesis pathway.

19. The composition of any one of claims 1 -18, wherein about or at least about 1 % of the total bacterial species, about or at least about 2% of the total bacterial species, about or at least about 3% of the total bacterial species, about or at least about 4% of the total bacterial species, about or at least about 5% of the total bacterial species, about or at least about 6% of the total bacterial species, about or at least about 7% of the total bacterial species, about or at least about 8% of the total bacterial species, about or at least about 9% of the total bacterial species, about or at least about 10% of the total bacterial species, about or at least about 15% of the total bacterial species, or about or at least about 20% of the total bacterial species comprises a synthesis pathway for bile acid derivatives (BAs) and / or encodes at least one enzyme suitable for synthesizing bile acid derivatives (BAs); and / or wherein about or at least about 1 species / isolate produces one or more bile acid derivatives (BAs), about or at least about 2 species / isolates produces one or more bile acid derivatives (BAs), about or at least about 3 species / isolates produces one or more bile acid derivatives (BAs), about or at least about 4 species / isolates produces one or more bile acid derivatives (BAs), about or at least about 5 species / isolates produces one or more bile acid derivatives (BAs), about or at least about 10 species / isolates produces one or more bile acid derivatives (BAs), about or at least about 15 species / isolates produces one or more bile acid derivatives (BAs), or about or at least about 20 species / isolates produces one or more bile acid derivatives (BAs); and / or wherein about or at least about 1 % of the total species abundance, about or at least about 5% of the total species abundance, about or at least about 10% of the total species abundance, about or at least about 15% of the total species abundance, about or at least about 20% of the total species abundance, about or at least about 30% of the total species abundance, about or at least about 40% of the total species abundance, or about or at least about 50% of the total species abundance of the plurality of bacterial species is capable of producing one or more bile acid derivative (BA) and / or one or more intermediates of a BA synthesis pathway.

20. The composition of any one of claims 1 -19, wherein about or at least about 1 % of the total bacterial species, about or at least about 2% of the total bacterial species, about or at least about 3% of theDBl / 161604598.2 523Atorney Docket No.: 137085-5001 -PC total bacterial species, about or at least about 4% of the total bacterial species, about or at least about 5% of the total bacterial species, about or at least about 6% of the total bacterial species, about or at least about 7% of the total bacterial species, about or at least about 8% of the total bacterial species, about or at least about 9% of the total bacterial species, about or at least about 10% of the total bacterial species, about or at least about 15% of the total bacterial species, or about or at least about 20% of the total bacterial species comprises an isoalloLCA synthesis pathway; and / or wherein about or at least about 1 species / isolate produces isoalloLCA, about or at least about 2 species / isolates produces isoalloLCA, about or at least about 3 species / isolates produces isoalloLCA, about or at least about 4 species / isolates produces isoalloLCA, about or at least about 5 species / isolates produces isoalloLCA, about or at least about 10 species / isolates produces isoalloLCA, about or at least about 15 species / isolates produces isoalloLCA, or about or at least about 20 species / isolates produces isoalloLCA; and / or wherein about or at least about 1 % of the total species abundance, about or at least about 5% of the total species abundance, about or at least about 10% of the total species abundance, about or at least about 15% of the total species abundance, about or at least about 20% of the total species abundance, about or at least about 30% of the total species abundance, about or at least about 40% of the total species abundance, or about or at least about 50% of the total species abundance of the plurality of bacterial species is capable of producing isoalloLCA and / or one or more intermediates of an isoalloLCA synthesis pathway.

21. The composition of any one of claims 1-20, wherein the plurality of bacterial species substantially produces one or more of butyrate, propionate, indole-3-acetic acid (IAA), indole-3-propionic acid (IPA), short chain fatty acids (SCFAs), bile acid derivatives (BAs), isoalloLCA, cholic acid (CA), threonine-CA, phenylalanine-CA, tyrosine-CA, deoxycholic acid (DCA), glutamic acid-DCA, chenodeoxycholic acid (CDCA), and glutamic acid-CDCA in a gastrointestinal tract, optionally wherein the SCFAs comprise one or more of valerate and branched chain SCFAs, optionally wherein the BAs comprise one or more of isoalloLCA, deconjugated cBA, secondary bile acid (2BA), tertiary bile acid (3BA), 7-oxoLCA, 7-oxoDCA, and microbially conjugated bile acid (MCBA).DBl / 161604598.2 524Atorney Docket No.: 137085-5001 -PC22. The composition of claim 21 , wherein the plurality of bacterial species comprises the ability to synthesize at least two bacterial metabolites selected from indole-3-acetic acid (IAA), indole-3- propionic acid (IPA), and bile acid derivatives (BAs), optionally wherein the BAs comprise one or more of isoallolithocholic acid (isoalloLCA), deconjugated bile acid (deBA), secondary bile acid (2BA), tertiary bile acid (3BA), 7-oxoLCA, 7-oxoDCA, and microbially conjugated bile acid (MCBA).

23. The composition of any one of claims 1-22, wherein the plurality of bacterial species is capable of substantially growing in a gastrointestinal tract, optionally a human gastrointestinal tract.

24. The composition of any one of claims 1-23, wherein the plurality of bacterial species comprises at least two, at least three, at least four, at least five, at least six, at least seven, or all eight of the following characteristics: ability to substantially decrease one or more metabolites; susceptibility to at least 3 antibiotics of different antibiotic classes; ability to substantially activate one or more endogenous human receptors comprising one or more G protein-coupled receptor (GPCRs) and / or toll-like receptor (TLRs); ability to substantially activate or expand one or more immune cells; ability to substantially suppress or reduce one or more immune cells; ability to re-activate exhausted T cells to a substantially healthy state; ability to substantially enhance endogenous immune cell-mediated killing of cancer cells, and ability to restore human epithelial barrier function to a substantially healthy state.

25. The composition of claim 24, wherein: the one or more metabolites comprises phenyl-sulfates and / or indoxyls, and wherein the reduction is relative to a concentration present in a human gastrointestinal tract lacking one or more of the plurality of bacterial species; the different antibiotic classes comprise one or more antibacterial antibiotic classes, optionally selected from bacteriostatic and bactericidal molecules, and / or optionally wherein the one or more antibacterial antibiotic classes comprise aminoglycosides, ansamycins, beta-lactams, carbapenems, cephalosporins, cyclic lipopeptides, fluoroquinolones, glycopeptides, glycylcyclines, lincosamides, macrolides, nitroimidazoles, oxazolidinones, sulfonamides, and / or tetracyclines,DBl / 161604598.2 525Atorney Docket No.: 137085-5001 -PC and / or optionally wherein the at least 3 antibiotics comprise one or more of amikacin, amoxicillin, azithromycin, cefazolin, cefmetazole, cefotetan, cefoxitin, cefprozil, cefuroxime, cilastatin, ciprofloxacin, clarithromycin, clindamycin, daptomycin, doxycycline, ertapenem, erythromycin, gentamicin, imipenem, levofloxacin, linezolid, meropenem, metronidazole, minocycline, moxifloxacin, penicillin, relebactam, rifampicin, sulfamethoxazole, tebipenem, tigecycline, tobramycin, trimethoprim-sulfamethoxazole, vaborbactam, vancomycin, and analogues and derivatives thereof; the one or more G protein-coupled receptors (GPCRs) comprises one or more of G protein- coupled receptor 35 (GPR35), G protein-coupled receptor 41 (GPR41), G protein-coupled receptor 43 (GPR43), G protein-coupled receptor 109A (GPR109A), G protein-coupled receptor 119 (GPR119), and G protein-coupled receptor 132 (GPR132); the one or more toll-like receptors (TLRs) comprise one or more of toll-like receptor 1 (TLR1 ), TLR2, TLR5, TLR6, and TLR9; the one or more endogenous human receptors comprises one or more of sphingosine-1 - phosphate receptor 4 (S1 PR4), prostaglandin E receptor 4 (PTGER4), prostaglandin I2 receptor (PTGIR), calcium sensor receptor (CasR), peptide transporter 1 (PEPT1), pregnane X receptor (PXR), farnesoid X receptor (FXR), Takeda G protein-receptor-5 (TGR5), aryl hydrocarbon receptor (AhR), and 5-hydroxytryptamine receptors (5-HT3R and 5-HT4R); the one or more immune cells are selected from CD4+ T cells, CD8+ T cells, and Natural Killer (NK) cells; the ability to substantially activate or expand one or more immune cells is measured by one or more of activation of CD4+ T cells, CD8+ T cells, NK cells, and effector cytokine production (interferon gamma (IFN-y), interleukin 2 (IL-2), tumor necrosis factor alpha (TNF-o)); the ability to substantially suppress or reduce one or more immune cells comprises immune cells selected from myeloid-derived suppressor cells (MDSCs) and regulatory T cells (Tregs), optionally wherein the MDSC and / or Tregsuppression is measured by arginase expression and / or activity; the ability to re-activate exhausted T cells to a substantially healthy state is measured by one or more of secretion of interferon gamma (IFN-y), interleukin 2 (IL-2), tumor necrosis factor alpha (TNF-a), and / or granzyme; cytotoxicity; and cell surface expression of one or more of signaling lymphocyte activation molecule 6 (SLAMF6), T cell receptor (TCR), programmed cell death proteinDBl / 161604598.2 526Atorney Docket No.: 137085-5001 -PC1 (PD-1), cytotoxic T-lymphocyte associated protein 4 (CTLA-4), lymphocyte activation gene-3 (LAG- 3, CD223), and T-cell immunoglobulin and mucin-domain containing-3 (TIM-3); the ability to substantially enhance endogenous immune cell-mediated killing of cancer cells is measured by one or more of cancer cell death, cell viability, proliferation, growth inhibition, growth rate, cytotoxicity, cell migration, oxidative stress, and anchorage-independent growth (AIG); and / or the epithelial barrier function comprises gut epithelial barrier, and wherein restoration is measured by one or more of expression and distribution of tight junction proteins, epithelial surface area and / or presence of intestinal villi, mucosal permeability, paracellular permeability, transcellular uptake, electrophysiological parameters (transepithelial electrical resistance (TEER)), western blotting, mRNA / protein expression, PCR, presence of biomarkers, flow cytometry, immunohistochemistry, fluorescence activated cell sorting (FACS), and enzyme-linked immunosorbent assay (ELISA).

26. The composition of any one of claims 1-25, wherein the composition comprises one or more pharmaceutically acceptable excipients or carriers.

27. The composition of any one of claims 1 -26, wherein the plurality of bacterial species are lyophilized and formulated as a powder, tablet, capsule, or sachet, optionally as a powder encapsulated within a capsule.

28. The composition of any one of claims 1-27, wherein the composition is suitable for oral administration.

29. The composition of any one of claims 1-28, comprising: at least 50 bacterial species and / or isolates listed in column 3a of Table 3, optionally comprising the bacterial species and / or isolates listed in column 3a of Table 3; at least 50 bacterial species and / or isolates listed in column 3b of Table 3, optionally comprising the bacterial species and / or isolates listed in column 3b of Table 3; at least 50 bacterial species and / or isolates listed in column 3c of Table 3, optionally comprising the bacterial species and / or isolates listed in column 3c of Table 3; orDBl / 161604598.2 527Atorney Docket No.: 137085-5001 -PC at least 50 bacterial species and / or isolates listed in column 3d of Table 3, optionally comprising the bacterial species and / or isolates listed in column 3d of Table 3; optionally wherein the bacterial species / isolates are lyophilized and / or encapsulated.

30. The composition of any one of claims 1-28, comprising: at least 50 bacterial species and / or isolates listed in column 8a of Table 8, optionally comprising the bacterial species and / or isolates listed in column 8a of Table 8; at least 50 bacterial species and / or isolates listed in column 8b of Table 8, optionally comprising the bacterial species and / or isolates listed in column 8b of Table 8; at least 50 bacterial species and / or isolates listed in column 8c of Table 8, optionally comprising the bacterial species and / or isolates listed in column 8c of Table 8, or at least 50 bacterial species and / or isolates listed in column 8d of Table 8, optionally comprising the bacterial species and / or isolates listed in column 8d of Table 8, optionally wherein the bacterial species / isolates are lyophilized and / or encapsulated.

31. A method of establishing a healthy microbiome and / or treating a disease in a subject in need thereof comprising administering a composition of the plurality of bacterial species of any one of claims 1- 30.

32. The method of claim 31 , wherein the subject is human, and wherein the healthy microbiome is established in at least a portion of the gastrointestinal tract.

33. The method of claim 31 or 32, wherein the subject has, is suspected of having, has been diagnosed with, or is receiving treatment for dysbiosis.

34. The method of any one of claims 31-33, wherein the disease is cancer, and / or wherein the subject has, is suspected of having, has been diagnosed with, or is receiving treatment for one or more type of cancer.

35. The method of claim 34, wherein the cancer is or comprises one or more of a carcinoma, sarcoma, myeloma, leukemia, lymphoma, mixed type cancer, and metastatic cancer.DBl / 161604598.2 528Atorney Docket No.: 137085-5001 -PC36. The method of claim 34 or 35, wherein the cancer is selected from esophageal cancer, gastric (stomach) cancer, bile duct cancer, small intestine cancer, colorectal cancer, pancreatic cancer, liver cancer, rectal cancer, anal cancer, colon cancer, gallbladder cancer, and stromal tumors.

37. The method of any one of claims 31 -36, wherein the administration is oral, optionally taken with food or beverage.

38. The method of any one of claims 31 -37, wherein the administration is from about once daily to about once per 3 months.

39. The method of any one of claims 31-38, wherein administering the composition of the plurality of bacterial species results in establishing, in the subject, a total species abundance capable of: synthesizing butyrate and / or one or more intermediates of a butyrate synthesis pathway; synthesizing propionate and / or one or more intermediates of a propionate synthesis pathway; synthesizing indole-3-acetic acid (IAA) and / or one or more intermediates of an IAA synthesis pathway; synthesizing indole-3-propionic acid (IPA) and / or one or more intermediates of an IPA synthesis pathway; synthesizing one or more short chain fatty acid (SCFA) and / or one or more intermediates of a SCFA synthesis pathway; synthesizing one or more bile acid derivative (BA) and / or one or more intermediates of a BA synthesis pathway; and / or synthesizing isoalloLCA and / or one or more intermediates of an isoalloLCA synthesis pathway; decreasing one or more metabolites, optionally selected from phenyl-sulfates and indoxyls; activating one or more endogenous human receptors, optionally comprising one or more G protein-coupled receptor (GPCRs) and / or toll-like receptor (TLRs); activating or expanding one or more immune cell populations, optionally selected from CD4+ T cells, CD8+ T cells, and Natural Killer (NK) cells; suppressing or reducing one or more immune cell populations, optionally selected from myeloid-derived suppressor cells (MDSCs) and regulatory T cells (Legs); re-activating exhausted T cells to a substantially healthy state; enhancing endogenous immune cell-mediated killing of cancer cells; and / orDBl / 161604598.2 529Atorney Docket No.: 137085-5001 -PC restoring one or more epithelial barrier function to a substantially healthy state, optionally wherein the substantially healthy state is measured by expression and / or distribution of tight junction proteins, epithelial surface area, presence of intestinal villi, mucosal permeability, paracellular permeability, transcellular uptake, and one or more electrophysiological parameters (transepithelial electrical resistance (TEER)).

40. The method of any one of claims 31-39, wherein one or more effects of establishing the healthy microbiome and / or treating the disease occurs within about or at least about 1 week, about or at least about 2 weeks, about or at least about 3 weeks, about or at least about 4 weeks, about or at least about 1 month, about or at least about 2 months, about or at least about 4 months, about or at least about 6 months, or about or at least about 1 year from administration and / or completion of an administration regimen.

41. The method of any one of claims 31-40, further comprising assessing the subject for the establishment of the healthy microbiome by analyzing a sample obtained from the subject.

42. The method of claim 41, wherein the sample obtained from the subject is or comprises stool, gastrointestinal biopsy, rectal swab, urine, saliva, blood, sera, and / or plasma.

43. The method of any one of claims 31-42, further comprising assessing one or more symptoms of a disease of the subject, optionally selected from a symptom of cancer and / or dysbiosis.

44. A composition comprising an isolated plurality of bacterial species, the plurality of bacterial species comprising: i. the bacterial species and / or isolates listed in column 3a of Table 3; ii. the bacterial species and / or isolates listed in column 3b of Table 3; ill. the bacterial species and / or isolates listed in column 3c of Table 3; iv. the bacterial species and / or isolates listed in column 3d of Table 3; v. the bacterial species and / or isolates listed in column 8a of Table 8; vi. the bacterial species and / or isolates listed in column 8b of Table 8; vii. the bacterial species and / or isolates listed in column 8c of Table 8; orDBl / 161604598.2 530Atorney Docket No.: 137085-5001 -PC viii. the bacterial species and / or isolates listed in column 8d of Table 8.DBl / 161604598.2 531

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