PROBIOTIC AND PREBIOTIC COMPOSITIONS, AND METHODS OF USE THEREOF FOR TREATMENT AND PREVENTION OF GRAFT VERSUS HOST DISEASE
Probiotic compositions containing non-pathogenic microbial entities, e.g., bacterial or fungal entities, are described herein. The probiotic compositions may optionally contain or be used in conjunction with one or more prebiotics. Uses of the probiotic compositions to treat or prevent transplant disorders, e.g., graft-versus-host disease (GVHD), in a subject are also provided.
1 . A method of increasing the duration of survival of a subject receiving a bone marrow transplant, comprising administering to the subject a probiotic composition comprising an isolated, human-derived bacterial population, such that the duration of survival of the subject is increased.
2 . The method of claim 1 , wherein administration of the probiotic composition reduces the likelihood that the subject will develop sepsis following the bone marrow transplant.
3 . The method of claim 1 , wherein administration of the probiotic composition reduces the likelihood that the subject will develop graft versus host disease (GVHD) following the bone marrow transplant.
4 . A method of increasing the duration of survival of a subject receiving a bone marrow transplant, comprising:
administering to the subject a probiotic composition comprising an isolated bacterial population and a pharmaceutically acceptable excipient, wherein the probiotic composition reduces intestinal permeability in the subject; and
administering to the subject a prebiotic that enhances the activity of the bacterial population,
such that the duration of survival of the subject is increased.
5 . A method of preventing graft versus host disease (GVHD) in a subject receiving a transplant, comprising administering to the subject a probiotic composition comprising an isolated, human-derived bacterial population, such that GVHD is prevented.
6 . The method of claim 5 , wherein the subject is receiving a hematopoietic stem cell transplant.
7 . The method of claim 5 , wherein the subject is receiving a bone marrow transplant.
8 . The method of claim 5 , wherein the subject is receiving a solid organ transplant.
9 . The method of claim 8 , wherein the solid organ transplant is selected from the group consisting of a kidney transplant, a heart transplant, a lung transplant, a skin transplant, a liver transplant, a pancreas transplant, an intestinal transplant, an endocrine gland transplant, a bladder transplant, and a skeletal muscle transplant.
10 . A method of reducing inflammation in the gastrointestinal tract of a subject receiving a transplant, comprising administering to the subject a probiotic composition comprising an isolated, anti-inflammatory bacterial population, such that inflammation in the gastrointestinal tract of the subject receiving the transplant is reduced.
11 . A method of reducing intestinal permeability in a subject receiving a transplant, comprising administering to the subject a probiotic composition comprising an isolated bacterial population, such that the intestinal permeability of the subject receiving the transplant is reduced.
12 . A pharmaceutical composition comprising an isolated anti-inflammatory bacterial population capable of decreasing secretion of a pro-inflammatory cytokine and/or increasing secretion of an anti-inflammatory cytokine by human peripheral blood mononuclear cells (PBMCs), and a pharmaceutically acceptable excipient.
13 . The pharmaceutical composition of claim 12 , further comprising a prebiotic.
14 . The method or of claim 1 , wherein the bacterial population comprises an isolated population of bacteria selected from the group consisting of Acidaminococcus intestine, Acinetobacter baumannii, Acinetobacter lwoffii, Akkermansia muciniphila, Alistipes putredinis, Alistipes shahii, Anaerostipes hadrus, Anaerotruncus colihominis, Bacteroides caccae, Bacteroides cellulosilyticus, Bacteroides dorei, Bacteroides eggerthii, Bacteroides finegoldii, Bacteroides fragilis, Bacteroides massiliensis, Bacteroides ovatus, Bacteroides salanitronis, Bacteroides salyersiae, Bacteroides sp, 1_1_6 , Bacteroides sp, 3_1_23, Bacteroides sp, D20, Bacteroides thetaiotaomicron, Bacteroides uniformis, Bacteroides vulgatus, Bifidobacterium adolescentis, Bifidobacterium bifidum, Bifidobacterium breve, Bifidobacterium faecale, Bifidobacterium kashiwanohense, Bifidobacterium longum subsp, longum, Bifidobacterium pseudocatenulatum, Bifidobacterium stercoris, Blautia ( Ruminococcus ) coccoides, Blautia faecis, Blautia glucerasea, Blautia ( Ruminococcus ) hansenii, Blautia hydrogenotrophica ( Ruminococcus hydrogenotrophicus ), Blautia ( Ruminococcus ) luti, Blautia ( Ruminococcus ) obeum, Blautia producta ( Ruminococcus productus ), Blautia ( Ruminococcus ) schinkii, Blautia stercoris, Blautia uncultured bacterium clone BKLE_a03_2 (GenBank: EU469501.1), Blautia uncultured bacterium clone SJTU_B_14_30 (GenBank: EF402926.1), Blautia uncultured bacterium clone SJTU_C_14_16 (GenBank: EF404657.1), Blautia uncultured bacterium clone S1-5 (GenBank: GQ0898099.1), Blautia uncultured PAC000178_s (www.ezbiocloud.neteztaxon/hierarchy?m=browse&k=PAC000178&d=2), Blautia wexlerae, Candidatus Arthromitus sp. SFB-mouse-Yit, Catenibacterium mitsuokai, Clostridiaceae bacterium ( Dielma fastidiosa ) JC13 , Clostridiales bacterium 1_7_47FAA, Clostridium asparagiforme, Clostridium bolteae, Clostridium clostridioforme, Clostridium glycyrrhizinilyticum, Clostridium ( Hungatella ) hathewayi, Clostridium histolyticum, Clostridium indolis, Clostridium leptum, Clostridium ( Tyzzerella ) nexile, Clostridium perfringens, Clostridium ( Erysipelatoclostridium ) ramosum, Clostridium scindens, Clostridium sp. 14774, Clostridium sp. 7_3_54FAA, Clostridium sp. HGF2, Clostridium symbiosum, Collinsella aerofaciens, Collinsella intestinalis, Coprobacillus sp. D7, Coprococcus catus, Coprococcus comes, Dorea formicigenerans, Dorea longicatena, Enterococcus faecalis, Enterococcus faecium, Erysipelotrichaceae bacterium 3_1_53, Escherichia coli, Escherichia coli 588, Eubacterium eligens, Eubacterium fissicatena, Eubacterium ramulus, Eubacterium rectale, Faecalibacterium prausnitzii, Flavonifractor plautii, Fusobacterium mortiferum, Fusobacterium nucleatum, Holdemania filiformis, Hydrogenoanaerobacterium saccharovorans, Klebsiella oxytoca, Lachnospiraceae bacterium 3_1_57FAA_CT1 , Lachnospiraceae bacterium 7_1_58FAA, Lachnospiraceae bacterium 5_1_57FAA, Lactobacillus casei, Lactobacillus rhamnosus, Lactobacillus ruminis, Lactococcus casei, Odoribacter splanchnicus, Oscillibacter valericigenes, Parabacteroides gordonii, Parabacteroides johnsonii, Parabacteroides merdae, Pediococcus acidilactici, Peptostreptococcus asaccharolyticus, Propionibacterium granulosum, Roseburia intestinalis, Roseburia inulinivorans, Ruminococcus faecis, Ruminococcus gnavus, Ruminococcus sp. ID8 , Ruminococcus torques, Slackia piriformis, Staphylococcus epidermidis, Staphylococcus saprophyticus, Streptococcus cristatus, Streptococcus dysgalactiae subsp, equisimilis, Streptococcus infantis, Streptococcus oralis, Streptococcus sanguinis, Streptococcus viridans, Streptococcus thermophiles, Veillonella dispar , and combinations thereof.
15 - 136 . (canceled)
137 . The method of claim 4 , wherein the bacterial population comprises an isolated population of bacteria selected from the group consisting of Acidaminococcus intestine, Acinetobacter baumannii, Acinetobacter lwoffii, Akkermansia muciniphila, Alistipes putredinis, Alistipes shahii, Anaerostipes hadrus, Anaerotruncus colihominis, Bacteroides caccae, Bacteroides cellulosilyticus, Bacteroides dorei, Bacteroides eggerthii, Bacteroides finegoldii, Bacteroides fragilis, Bacteroides massiliensis, Bacteroides ovatus, Bacteroides salanitronis, Bacteroides salyersiae, Bacteroides sp. 1_1_6, Bacteroides sp. 3_1_23, Bacteroides sp. D20, Bacteroides thetaiotaomicron, Bacteroides uniformis, Bacteroides vulgatus, Bifidobacterium adolescentis, Bifidobacterium bifidum, Bifidobacterium breve, Bifidobacterium faecale, Bifidobacterium kashiwanohense, Bifidobacterium longum subsp. longum, Bifidobacterium pseudocatenulatum, Bifidobacterium stercoris, Blautia ( Ruminococcus ) coccoides, Blautia faecis, Blautia glucerasea, Blautia ( Ruminococcus ) hansenii, Blautia hydrogenotrophica ( Ruminococcus hydrogenotrophicus ), Blautia ( Ruminococcus ) luti, Blautia ( Ruminococcus ) obeum, Blautia producta ( Ruminococcus productus ), Blautia ( Ruminococcus ) schinkii, Blautia stercoris, Blautia uncultured bacterium clone BKLE_a03_2 (GenBank: EU469501.1), Blautia uncultured bacterium clone SJTU_B_14_30 (GenBank: EF402926.1), Blautia uncultured bacterium clone SJTU_C_14_16 (GenBank: EF404657.1), Blautia uncultured bacterium clone S1-5 (GenBank: GQ898099.1), Blautia uncultured PAC000178_s (www.ezbiocloud.net/eztaxon/hierarchy?m=browse&k=PAC000178&d=2), Blautia wexlerae, Candidatus Arthromitus sp. SFB-mouse-Yit, Catenibacterium mitsuokai, Clostridiaceae bacterium ( Dielma fastidiosa ) JC13 , Clostridiales bacterium 1_7_47FAA, Clostridium asparagiforme, Clostridium bolteae, Clostridium clostridioforme, Clostridium glycyrrhizinilyticum, Clostridium ( Hungatella ) hathewayi, Clostridium histolyticum, Clostridium indolis, Clostridium leptum, Clostridium ( Tyzzerella ) nexile, Clostridium perfringens, Clostridium ( Erysipelatoclostridium ) ramosum, Clostridium scindens, Clostridium sp. 14774, Clostridium sp. 7_3_54FAA, Clostridium sp. HGF2, Clostridium symbiosum, Collinsella aerofaciens, Collinsella intestinalis, Coprobacillus sp. D7, Coprococcus catus, Coprococcus comes, Dorea formicigenerans, Dorea longicatena, Enterococcus faecalis, Enterococcus faecium, Erysipelotrichaceae bacterium 3_1_53, Escherichia coli, Escherichia coli S88, Eubacterium eligens, Eubacterium fissicatena, Eubacterium ramulus, Eubacterium rectale, Faecalibacterium prausnitzii, Flavonifractor plautii, Fusobacterium mortiferum, Fusobacterium nucleatum, Holdemania filiformis, Hydrogenoanaerobacterium saccharovorans, Klebsiella oxytoca, Lachnospiraceae bacterium 3_1_57FAA_CT1 , Lachnospiraceae bacterium 7_1_58FAA, Lachnospiraceae bacterium 5_1_57FAA, Lactobacillus casei, Lactobacillus rhamnosus, Lactobacillus ruminis, Lactococcus casei, Odoribacter splanchnicus, Oscillibacter valericigenes, Parabacteroides gordonii, Parabacteroides johnsonii, Parabacteroides merdae, Pediococcus acidilactici, Peptostreptococcus asaccharolyticus, Propionibacterium granulosum, Roseburia intestinalis, Roseburia inulinivorans, Ruminococcus faecis, Ruminococcus gnavus, Ruminococcus sp. ID8 , Ruminococcus torques, Slackia piriformis, Staphylococcus epidermidis, Staphylococcus saprophyticus, Streptococcus cristatus, Streptococcus dysgalactiae subsp. equisimilis, Streptococcus infantis, Streptococcus oralis, Streptococcus sanguinis, Streptococcus viridans, Streptococcus thermophiles, Veillonella dispar , and combinations thereof.
138 . The method of claim 5 , wherein the bacterial population comprises an isolated population of bacteria selected from the group consisting of Acidaminococcus intestine, Acinetobacter baumannii, Acinetobacter lwoffii, Akkermansia muciniphila, Alistipes putredinis, Alistipes shahii, Anaerostipes hadrus, Anaerotruncus colihominis, Bacteroides caccae, Bacteroides cellulosilyticus, Bacteroides dorei, Bacteroides eggerthii, Bacteroides finegoldii, Bacteroides fragilis, Bacteroides massiliensis, Bacteroides ovatus, Bacteroides salanitronis, Bacteroides salyersiae, Bacteroides sp. 1_1_6, Bacteroides sp. 3_1_23, Bacteroides sp. D20, Bacteroides thetaiotaomicron, Bacteroides uniformis, Bacteroides vulgatus, Bifidobacterium adolescentis, Bifidobacterium bifidum, Bifidobacterium breve, Bifidobacterium faecale, Bifidobacterium kashiwanohense, Bifidobacterium longum subsp. longum, Bifidobacterium pseudocatenulatum, Bifidobacterium stercoris, Blautia ( Ruminococcus ) coccoides, Blautia faecis, Blautia glucerasea, Blautia ( Ruminococcus ) hansenii, Blautia hydrogenotrophica ( Ruminococcus hydrogenotrophicus ), Blautia ( Ruminococcus ) luti, Blautia ( Ruminococcus ) obeum, Blautia producta ( Ruminococcus productus ), Blautia ( Ruminococcus ) schinkii, Blautia stercoris, Blautia uncultured bacterium clone BKLE_a03_2 (GenBank: EU469501.1), Blautia uncultured bacterium clone SJTU_B_14_30 (GenBank: EF402926.1), Blautia uncultured bacterium clone SJTU_C_14_16 (GenBank: EF404657.1), Blautia uncultured bacterium clone S1-5 (GenBank: GQ898099.1), Blautia uncultured PAC000178_s (www.ezbiocloud.net/eztaxon/hierarchy?m=browse&k=PAC000178&d=2), Blautia wexlerae, Candidatus Arthromitus sp. SFB-mouse-Yit, Catenibacterium mitsuokai, Clostridiaceae bacterium ( Dielma fastidiosa ) JC13 , Clostridiales bacterium 1_7_47FAA, Clostridium asparagiforme, Clostridium bolteae, Clostridium clostridioforme, Clostridium glycyrrhizinilyticum, Clostridium ( Hungatella ) hathewayi, Clostridium histolyticum, Clostridium indolis, Clostridium leptum, Clostridium ( Tyzzerella ) nexile, Clostridium perfringens, Clostridium ( Erysipelatoclostridium ) ramosum, Clostridium scindens, Clostridium sp. 14774, Clostridium sp. 7_3_54FAA, Clostridium sp. HGF2, Clostridium symbiosum, Collinsella aerofaciens, Collinsella intestinalis, Coprobacillus sp. D7, Coprococcus catus, Coprococcus comes, Dorea formicigenerans, Dorea longicatena, Enterococcus faecalis, Enterococcus faecium, Erysipelotrichaceae bacterium 3_1_53, Escherichia coli, Escherichia coli S88, Eubacterium eligens, Eubacterium fissicatena, Eubacterium ramulus, Eubacterium rectale, Faecalibacterium prausnitzii, Flavonifractor plautii, Fusobacterium mortiferum, Fusobacterium nucleatum, Holdemania filiformis, Hydrogenoanaerobacterium saccharovorans, Klebsiella oxytoca, Lachnospiraceae bacterium 3_1_57FAA_CT1 , Lachnospiraceae bacterium 7_1_58FAA, Lachnospiraceae bacterium 5_1_57FAA, Lactobacillus casei, Lactobacillus rhamnosus, Lactobacillus ruminis, Lactococcus casei, Odoribacter splanchnicus, Oscillibacter valericigenes, Parabacteroides gordonii, Parabacteroides johnsonii, Parabacteroides merdae, Pediococcus acidilactici, Peptostreptococcus asaccharolyticus, Propionibacterium granulosum, Roseburia intestinalis, Roseburia inulinivorans, Ruminococcus faecis, Ruminococcus gnavus, Ruminococcus sp. ID8 , Ruminococcus torques, Slackia piriformis, Staphylococcus epidermidis, Staphylococcus saprophyticus, Streptococcus cristatus, Streptococcus dysgalactiae subsp. equisimilis, Streptococcus infantis, Streptococcus oralis, Streptococcus sanguinis, Streptococcus viridans, Streptococcus thermophiles, Veillonella dispar , and combinations thereof.
139 . The method of claim 10 , wherein the bacterial population comprises an isolated population of bacteria selected from the group consisting of Acidaminococcus intestine, Acinetobacter baumannii, Acinetobacter lwoffii, Akkermansia muciniphila, Alistipes putredinis, Alistipes shahii, Anaerostipes hadrus, Anaerotruncus colihominis, Bacteroides caccae, Bacteroides cellulosilyticus, Bacteroides dorei, Bacteroides eggerthii, Bacteroides finegoldii, Bacteroides fragilis, Bacteroides massiliensis, Bacteroides ovatus, Bacteroides salanitronis, Bacteroides salyersiae, Bacteroides sp. 1_1_6, Bacteroides sp. 3_1_23, Bacteroides sp. D20, Bacteroides thetaiotaomicron, Bacteroides uniformis, Bacteroides vulgatus, Bifidobacterium adolescentis, Bifidobacterium bifidum, Bifidobacterium breve, Bifidobacterium faecale, Bifidobacterium kashiwanohense, Bifidobacterium longum subsp. longum, Bifidobacterium pseudocatenulatum, Bifidobacterium stercoris, Blautia ( Ruminococcus ) coccoides, Blautia faecis, Blautia glucerasea, Blautia ( Ruminococcus ) hansenii, Blautia hydrogenotrophica ( Ruminococcus hydrogenotrophicus ), Blautia ( Ruminococcus ) luti, Blautia ( Ruminococcus ) obeum, Blautia producta ( Ruminococcus productus ), Blautia ( Ruminococcus ) schinkii, Blautia stercoris, Blautia uncultured bacterium clone BKLE_a03_2 (GenBank: EU469501.1), Blautia uncultured bacterium clone SJTU_B_14_30 (GenBank: EF402926.1), Blautia uncultured bacterium clone SJTU_C_14_16 (GenBank: EF404657.1), Blautia uncultured bacterium clone S1-5 (GenBank: GQ898099.1), Blautia uncultured PAC000178_s (www.ezbiocloud.net/eztaxon/hierarchy?m=browse&k=PAC000178&d=2), Blautia wexlerae, Candidatus Arthromitus sp. SFB-mouse-Yit, Catenibacterium mitsuokai, Clostridiaceae bacterium ( Dielma fastidiosa ) JC13 , Clostridiales bacterium 1_7_47FAA, Clostridium asparagiforme, Clostridium bolteae, Clostridium clostridioforme, Clostridium glycyrrhizinilyticum, Clostridium ( Hungatella ) hathewayi, Clostridium histolyticum, Clostridium indolis, Clostridium leptum, Clostridium ( Tyzzerella ) nexile, Clostridium perfringens, Clostridium ( Erysipelatoclostridium ) ramosum, Clostridium scindens, Clostridium sp. 14774, Clostridium sp. 7_3_54FAA, Clostridium sp. HGF2, Clostridium symbiosum, Collinsella aerofaciens, Collinsella intestinalis, Coprobacillus sp. D7, Coprococcus catus, Coprococcus comes, Dorea formicigenerans, Dorea longicatena, Enterococcus faecalis, Enterococcus faecium, Erysipelotrichaceae bacterium 3_1_53, Escherichia coli, Escherichia coli S88, Eubacterium eligens, Eubacterium fissicatena, Eubacterium ramulus, Eubacterium rectale, Faecalibacterium prausnitzii, Flavonifractor plautii, Fusobacterium mortiferum, Fusobacterium nucleatum, Holdemania filiformis, Hydrogenoanaerobacterium saccharovorans, Klebsiella oxytoca, Lachnospiraceae bacterium 3_1_57FAA_CT1 , Lachnospiraceae bacterium 7_1_58FAA, Lachnospiraceae bacterium 5_1_57FAA, Lactobacillus casei, Lactobacillus rhamnosus, Lactobacillus ruminis, Lactococcus casei, Odoribacter splanchnicus, Oscillibacter valericigenes, Parabacteroides gordonii, Parabacteroides johnsonii, Parabacteroides merdae, Pediococcus acidilactici, Peptostreptococcus asaccharolyticus, Propionibacterium granulosum, Roseburia intestinalis, Roseburia inulinivorans, Ruminococcus faecis, Ruminococcus gnavus, Ruminococcus sp. ID8 , Ruminococcus torques, Slackia piriformis, Staphylococcus epidermidis, Staphylococcus saprophyticus, Streptococcus cristatus, Streptococcus dysgalactiae subsp. equisimilis, Streptococcus infantis, Streptococcus oralis, Streptococcus sanguinis, Streptococcus viridans, Streptococcus thermophiles, Veillonella dispar , and combinations thereof.
140 . The method of claim 11 , wherein the bacterial population comprises an isolated population of bacteria selected from the group consisting of Acidaminococcus intestine, Acinetobacter baumannii, Acinetobacter lwoffii, Akkermansia muciniphila, Alistipes putredinis, Alistipes shahii, Anaerostipes hadrus, Anaerotruncus colihominis, Bacteroides caccae, Bacteroides cellulosilyticus, Bacteroides dorei, Bacteroides eggerthii, Bacteroides finegoldii, Bacteroides fragilis, Bacteroides massiliensis, Bacteroides ovatus, Bacteroides salanitronis, Bacteroides salyersiae, Bacteroides sp. 1_1_6, Bacteroides sp. 3_1_23, Bacteroides sp. D20, Bacteroides thetaiotaomicron, Bacteroides uniformis, Bacteroides vulgatus, Bifidobacterium adolescentis, Bifidobacterium bifidum, Bifidobacterium breve, Bifidobacterium faecale, Bifidobacterium kashiwanohense, Bifidobacterium longum subsp. longum, Bifidobacterium pseudocatenulatum, Bifidobacterium stercoris, Blautia ( Ruminococcus ) coccoides, Blautia faecis, Blautia glucerasea, Blautia ( Ruminococcus ) hansenii, Blautia hydrogenotrophica ( Ruminococcus hydrogenotrophicus ), Blautia ( Ruminococcus ) luti, Blautia ( Ruminococcus ) obeum, Blautia producta ( Ruminococcus productus ), Blautia ( Ruminococcus ) schinkii, Blautia stercoris, Blautia uncultured bacterium clone BKLE_a03_2 (GenBank: EU469501.1), Blautia uncultured bacterium clone SJTU_B_14_30 (GenBank: EF402926.1), Blautia uncultured bacterium clone SJTU_C_14_16 (GenBank: EF404657.1), Blautia uncultured bacterium clone S1-5 (GenBank: GQ898099.1), Blautia uncultured PAC000178_s (www.ezbiocloud.net/eztaxon/hierarchy?m=browse&k=PAC000178&d=2), Blautia wexlerae, Candidatus Arthromitus sp. SFB-mouse-Yit, Catenibacterium mitsuokai, Clostridiaceae bacterium ( Dielma fastidiosa ) JC13 , Clostridiales bacterium 1_7_47FAA, Clostridium asparagiforme, Clostridium bolteae, Clostridium clostridioforme, Clostridium glycyrrhizinilyticum, Clostridium ( Hungatella ) hathewayi, Clostridium histolyticum, Clostridium indolis, Clostridium leptum, Clostridium ( Tyzzerella ) nexile, Clostridium perfringens, Clostridium ( Erysipelatoclostridium ) ramosum, Clostridium scindens, Clostridium sp. 14774, Clostridium sp. 7_3_54FAA, Clostridium sp. HGF2, Clostridium symbiosum, Collinsella aerofaciens, Collinsella intestinalis, Coprobacillus sp. D7, Coprococcus catus, Coprococcus comes, Dorea formicigenerans, Dorea longicatena, Enterococcus faecalis, Enterococcus faecium, Erysipelotrichaceae bacterium 3_1_53, Escherichia coli, Escherichia coli S88, Eubacterium eligens, Eubacterium fissicatena, Eubacterium ramulus, Eubacterium rectale, Faecalibacterium prausnitzii, Flavonifractor plautii, Fusobacterium mortiferum, Fusobacterium nucleatum, Holdemania filiformis, Hydrogenoanaerobacterium saccharovorans, Klebsiella oxytoca, Lachnospiraceae bacterium 3_1_57FAA_CT1 , Lachnospiraceae bacterium 7_1_58FAA, Lachnospiraceae bacterium 5_1_57FAA, Lactobacillus casei, Lactobacillus rhamnosus, Lactobacillus ruminis, Lactococcus casei, Odoribacter splanchnicus, Oscillibacter valericigenes, Parabacteroides gordonii, Parabacteroides johnsonii, Parabacteroides merdae, Pediococcus acidilactici, Peptostreptococcus asaccharolyticus, Propionibacterium granulosum, Roseburia intestinalis, Roseburia inulinivorans, Ruminococcus faecis, Ruminococcus gnavus, Ruminococcus sp. ID8 , Ruminococcus torques, Slackia piriformis, Staphylococcus epidermidis, Staphylococcus saprophyticus, Streptococcus cristatus, Streptococcus dysgalactiae subsp. equisimilis, Streptococcus infantis, Streptococcus oralis, Streptococcus sanguinis, Streptococcus viridans, Streptococcus thermophiles, Veillonella dispar , and combinations thereof.
141 . The pharmaceutical composition of claim 12 , wherein the bacterial population comprises an isolated population of bacteria selected from the group consisting of Acidaminococcus intestine, Acinetobacter baumannii, Acinetobacter lwoffii, Akkermansia muciniphila, Alistipes putredinis, Alistipes shahii, Anaerostipes hadrus, Anaerotruncus colihominis, Bacteroides caccae, Bacteroides cellulosilyticus, Bacteroides dorei, Bacteroides eggerthii, Bacteroides finegoldii, Bacteroides fragilis, Bacteroides massiliensis, Bacteroides ovatus, Bacteroides salanitronis, Bacteroides salyersiae, Bacteroides sp. 1_1_6, Bacteroides sp. 3_1_23, Bacteroides sp. D20, Bacteroides thetaiotaomicron, Bacteroides uniformis, Bacteroides vulgatus, Bifidobacterium adolescentis, Bifidobacterium bifidum, Bifidobacterium breve, Bifidobacterium faecale, Bifidobacterium kashiwanohense, Bifidobacterium longum subsp. longum, Bifidobacterium pseudocatenulatum, Bifidobacterium stercoris, Blautia ( Ruminococcus ) coccoides, Blautia faecis, Blautia glucerasea, Blautia ( Ruminococcus ) hansenii, Blautia hydrogenotrophica ( Ruminococcus hydrogenotrophicus ), Blautia ( Ruminococcus ) luti, Blautia ( Ruminococcus ) obeum, Blautia producta ( Ruminococcus productus ), Blautia ( Ruminococcus ) schinkii, Blautia stercoris, Blautia uncultured bacterium clone BKLE_a03_2 (GenBank: EU469501.1), Blautia uncultured bacterium clone SJTU_B_14_30 (GenBank: EF402926.1), Blautia uncultured bacterium clone SJTU_C_14_16 (GenBank: EF404657.1), Blautia uncultured bacterium clone S1-5 (GenBank: GQ898099.1), Blautia uncultured PAC000178_s (www.ezbiocloud.net/eztaxon/hierarchy?m=browse&k=PAC000178&d=2), Blautia wexlerae, Candidatus Arthromitus sp. SFB-mouse-Yit, Catenibacterium mitsuokai, Clostridiaceae bacterium ( Dielma fastidiosa ) JC13 , Clostridiales bacterium 1_7_47FAA, Clostridium asparagiforme, Clostridium bolteae, Clostridium clostridioforme, Clostridium glycyrrhizinilyticum, Clostridium ( Hungatella ) hathewayi, Clostridium histolyticum, Clostridium indolis, Clostridium leptum, Clostridium ( Tyzzerella ) nexile, Clostridium perfringens, Clostridium ( Erysipelatoclostridium ) ramosum, Clostridium scindens, Clostridium sp. 14774, Clostridium sp. 7_3_54FAA, Clostridium sp. HGF2, Clostridium symbiosum, Collinsella aerofaciens, Collinsella intestinalis, Coprobacillus sp. D7, Coprococcus catus, Coprococcus comes, Dorea formicigenerans, Dorea longicatena, Enterococcus faecalis, Enterococcus faecium, Erysipelotrichaceae bacterium 3_1_53, Escherichia coli, Escherichia coli S88, Eubacterium eligens, Eubacterium fissicatena, Eubacterium ramulus, Eubacterium rectale, Faecalibacterium prausnitzii, Flavonifractor plautii, Fusobacterium mortiferum, Fusobacterium nucleatum, Holdemania filiformis, Hydrogenoanaerobacterium saccharovorans, Klebsiella oxytoca, Lachnospiraceae bacterium 3_1_57FAA_CT1 , Lachnospiraceae bacterium 7_1_58FAA, Lachnospiraceae bacterium 5_1_57FAA, Lactobacillus casei, Lactobacillus rhamnosus, Lactobacillus ruminis, Lactococcus casei, Odoribacter splanchnicus, Oscillibacter valericigenes, Parabacteroides gordonii, Parabacteroides johnsonii, Parabacteroides merdae, Pediococcus acidilactici, Peptostreptococcus asaccharolyticus, Propionibacterium granulosum, Roseburia intestinalis, Roseburia inulinivorans, Ruminococcus faecis, Ruminococcus gnavus, Ruminococcus sp. ID8, Ruminococcus torques, Slackia piriformis, Staphylococcus epidermidis, Staphylococcus saprophyticus, Streptococcus cristatus, Streptococcus dysgalactiae subsp. equisimilis, Streptococcus infantis, Streptococcus oralis, Streptococcus sanguinis, Streptococcus viridans, Streptococcus thermophiles, Veillonella dispar , and combinations thereof.