Abstract: The present invention provides a method, wherein the method treats a subject having a dysbiosis, the method comprising: determining a first metabolic profile of the gut microbiome of a subject having a dysbiosis; changing the first metabolic profile of the gut microbiome of the subject to a second metabolic profile of the gut microbiome of the subject, by administering to the subject a composition comprising at least one bacterial species selected from the group consisting of: Acidaminococcus intestinalis, Bacteroides ovatus, Bifidobacterium adolescentis, Bifidobacterium longum, Blautia sp., Clostridium sp., Collinsella aerofaciens, Escherichia coli, Eubacterium desmolans, Eubacterium eligens, Eubacterium limosum, Faecalibacterum prausnitzii, Lachnospira pectinoschiza, Lactobacillus casei, Parabacteroides distasonis, Roseburia faecalis, Roseburia intestinalis, Ruminococcus sp.

Abstract: In one embodiment, the present invention provides a method for characterizing a first composition comprising a fecal-derived bacterial population, comprising the steps of: obtaining a live culture of the first composition comprising a fecal-derived bacterial population, supplying factors that selectively expand the at least one bacterial strain at a level below a threshold for detection above the threshold level by seeding a chemostat containing culture medium with a second composition comprising a fecal-derived bacterial population; adding the live culture of the first composition comprising a fecal-derived bacterial population to the seeded chemostat, and culturing the first composition comprising a fecal-derived bacterial population with the second composition comprising a fecal-derived bacterial population in the chemostat for a time sufficient to expand the at least one bacterial strain; removing a sample of the chemostat culture; and identifying the at least one bacterial strain.

Abstract: A media supplement for culturing anaerobic bacteria is provided which comprises a filtrate of eilluent from a chemostat vessel in which a target bacterial ecosystem has been culnn-ed. Methods of using the supplement for culturing or isolating anaerobic microbial strains or cormmmities, particularly anaerobic bacteria from the human gut, are also provided.

Abstract: A method includes reconstituting a lyophilized microbial community. Ribonucleic acid (RNA) is extracted from at least one targeted microbe in the reconstituted microbial community at a plurality of selected time periods. The RNA as extracted at the selected time period is subjected to a multiplex analyzer and determining RNA concentrations at the plurality of selected time periods. An increase in the RNA concentration from a first of the plurality of selected time periods to a second of the plurality of time periods indicates RNA expression from the at least one targeted microbe. RNA expression from the at least one targeted microbe indicates that the at least one targeted microbe is a living microbe.

Abstract: A media supplement for culturing anaerobic bacteria is provided which comprises a filtrate of eilluent from a chemostat vessel in which a target bacterial ecosystem has been culnn-ed. Methods of using the supplement for culturing or isolating anaerobic microbial strains or cormmmities, particularly anaerobic bacteria from the human gut, are also provided.

Abstract: Methods and compositions for culturing and preserving bacteria are described herein, wherein the cultured and preserved bacteria exhibit improved viability/growth when compared to bacteria preserved/stored by means other than the subject methods. More particularly, methods and compositions for improving bacterial viability following cryopreservation are disclosed herein.

Abstract: Anhydrous compositions comprising a co-selected microbiota and methods for using same to treat disorders associated with dysbiosis (an imbalance of the microbial community inhabiting a subject or inhabiting a particular tissue in a subject) are described herein. In particular, anhydrous compositions comprising a co-selected microbiota and methods for treating gastrointestinal disorders associated with dysbiosis are envisioned. The use of such anhydrous compositions comprising a co-selected microbiota for treating disorders associated with dysbiosis (e.g., gastrointestinal disorders associated with dysbiosis) and the use of such anhydrous compositions comprising a co-selected microbiota in the preparation of a medicament for treating disorders associated with dysbiosis (e.g., gastrointestinal disorders associated with dysbiosis) are also embodied herein.

Abstract: The present invention provides a method, wherein the method treats a subject having a dysbiosis, the method comprising: determining a first metabolic profile of the gut microbiome of a subject having a dysbiosis; changing the first metabolic profile of the gut microbiome of the subject to a second metabolic profile of the gut microbiome of the subject, by administering to the subject a composition comprising at least one bacterial species selected from the group consisting of: Acidaminococcus intestinalis, Bacteriodes ovatus, Bifidobacterium adolescentis, Bifidobacterium longum, Blautia sp., Clostridium sp., Collinsella aerofaciens, Escherichia coli, Eubacterium desmolans, Eubacterium eligens, Eubacterium limosum, Faecallbacterum prausnitzii, Lachnospira pectinoshiza, Lactobacillus casei, Parabacteroides distasonis, Roseburia faecalis, Roseburia intestinalis, Ruminococcus sp.

Abstract: There are provided novel synthetic stool preparations comprising bacteria isolated from a fecal sample from a healthy donor. The synthetic stool preparations are used for treating disorders of the gastrointestinal tract, including dysbiosis, Clostridium difficile infection and recurrent Clostridium difficile infection, prevention of recurrence of Clostridium difficile infection, treatment of Crohn's disease, ulcerative colitis, irritable bowel syndrome, inflammatory bowel disease, and diverticular disease, and treatment of food poisoning such as salmonella. Methods of preparation and methods of use of the synthetic stool preparations are also provided.

Abstract: A media supplement for culturing anaerobic bacteria is provided which comprises a filtrate of eilluent from a chemostat vessel in which a target bacterial ecosystem has been culnn-ed. Methods of using the supplement for culturing or isolating anaerobic microbial strains or cormmmities, particularly anaerobic bacteria from the human gut, are also provided.

Abstract: A media supplement for culturing anaerobic bacteria is provided which comprises a filtrate of eilluent from a chemostat vessel in which a target bacterial ecosystem has been culnn-ed. Methods of using the supplement for culturing or isolating anaerobic microbial strains or communities, particularly anaerobic bacteria from the human gut, are also provided.

Abstract: The present invention is a method of enriching at least one bacterial species from a target bacterial system, including: culturing the target bacterial ecosystem in a culture media in a single-stage chemostat under the following conditions: (i) a system retention time of about 5 to about 290 hours, (ii) a temperature of about 37° C., (iii) a pH of about 6.8 to 7, and (iv) maintenance of Establish anaerobic conditions to the chemostat for a time sufficient to enrich the at least one bacterial species; where the culture media comprises a prepared starch substrate, and where the target bacterial system is a fecal derived sample obtained from a patient that has not been treated with an antibiotic for at least 6 months.

Abstract: A media supplement for culturing anaerobic bacteria is provided which comprises a filtrate of effluent from a chemostat vessel in which a target bacterial ecosystem has been cultured. Methods of using the supplement for culturing or isolating anaerobic microbial strains or communities, particularly anaerobic bacteria from the human gut, are also provided.

Abstract: There are provided novel synthetic stool preparations comprising bacteria isolated from a fecal sample from a healthy donor. The synthetic stool preparations are used for treating disorders of the gastrointestinal tract, including dysbiosis, Clostridium difficile infection and recurrent Clostridium difficile infection, prevention of recurrence of Clostridium difficile infection, treatment of Crohn's disease, ulcerative colitis, irritable bowel syndrome, inflammatory bowel disease, and diverticular disease, and treatment of food poisoning such as salmonella. Methods of preparation and methods of use of the synthetic stool preparations are also provided.

Abstract: There are provided novel synthetic stool preparations comprising bacteria isolated from a fecal sample from a healthy donor. The synthetic stool preparations are used for treating disorders of the gastrointestinal tract, including dysbiosis, Clostridium difficile infection and recurrent Clostridium difficile infection, prevention of recurrence of Clostridium difficile infection, treatment of Crohn's disease, ulcerative colitis, irritable bowel syndrome, inflammatory bowel disease, and diverticular disease, and treatment of food poisoning such as salmonella. Methods of preparation and methods of use of the synthetic stool preparations are also provided.

Abstract: A media supplement for culturing anaerobic bacteria is provided which comprises a filtrate of effluent from a chemostat vessel in which a target bacterial ecosystem has been cultured. Methods of using the supplement for culturing or isolating anaerobic microbial strains or communities, particularly anaerobic bacteria from the human gut, are also provided.

Abstract: Fusobacterium is a genus of gram-negative, filamentous, anaerobic bacteria found as normal flora in the mouth and large bowel, and often in necrotic tissue. A comparison of microbial ribonucleic acids (RNA) between colorectal carcinoma (CRC) tissue and adjacent normal control tissue found the over-representation of F. nucleatum in CRC tissue. RNA abundance was measured by polymerase chain reaction (PCR)-amplifying RNA from the tissue, constructing libraries, sequencing the RNA in the libraries, pairing sequences from CRC and normal tissue, and quantifying RNA abundance. Detection of Fusobacterium in a gastrointestinal sample is indicative of gastrointestinal cancer.