In alternative embodiments, the invention provides compositions, e.g., formulations, used for gastric, gastrointestinal and/or colonic treatments or lavage, e.g., orthostatic lavage, e.g., for inducing the purgation (e.g., cleansing) of a gastrointestinal (GI) tract, including a colon; and methods for making and using them. In alternative embodiments, compositions and methods of the invention are used for the stabilization, amelioration, treatment and/or prevention of constipation, for the treatment of abdominal pain, particularly non-specific abdominal pain, and diarrhea, including diarrhea caused by a drug side effect, a psychological condition, a disease or a condition such as Crohn's Disease, a poison, a toxin or an infection, e.g., a toxin-mediated travelers diarrhea, or C. difficile or the pseudo-membranous colitis associated with this infection. In alternative embodiments, the invention provides pharmaceuticals and products (articles) of manufacture for delivering these compositions and formulations to an individual, e.g., a human or an animal. The invention also provides devices for delivering a fecal material to a patient.

Microbiota restoration therapy compositions and methods for manufacturing, processing, and/or delivering microbiota restoration therapy compositions are disclosed. An example method for manufacturing a microbiota restoration therapy composition may include collecting a human fecal sample and adding a diluent to the human fecal sample to form a diluted sample. The diluent may include a cryoprotectant. The method may also include mixing the diluted sample with a mixing apparatus and filtering the diluted sample. Filtering may form a filtrate. The method may also include transferring the filtrate to a sample bag and sealing the sample bag.

Microbiota restoration therapy compositions and methods for manufacturing, processing, and/or delivering microbiota restoration therapy compositions are disclosed. An example method for manufacturing a microbiota restoration therapy composition may include collecting a human fecal sample and adding a diluent to the human fecal sample to form a diluted sample. The diluent may include a cryoprotectant. The method may also include mixing the diluted sample with a mixing apparatus and filtering the diluted sample. Filtering may form a filtrate. The method may also include transferring the filtrate to a sample bag and sealing the sample bag.

Methods are described herein for generating beneficial compounds and/or materials such as bacteriocins that include contacting ‘challenger’ microbes with the ‘protagonist’ microorganisms. The challenger microbes do not directly manufacture the beneficial compounds and/or materials and instead stimulate the protagonist microorganisms to produce beneficial compounds and materials. The protagonist and/or challenger microorganisms can be administered to a subject so the beneficial compounds and/or materials can be made in vivo. Compositions and methods of using beneficial compounds and/or materials are also described herein.

Methods are described herein for generating beneficial compounds and/or materials such as bacteriocins that include contacting ‘challenger’ microbes with the ‘protagonist’ microorganisms. The challenger microbes do not directly manufacture the beneficial compounds and/or materials and instead stimulate the protagonist microorganisms to produce beneficial compounds and materials. The protagonist and/or challenger microorganisms can be administered to a subject so the beneficial compounds and/or materials can be made in vivo. Compositions and methods of using beneficial compounds and/or materials are also described herein.

Methods are described herein for generating beneficial compounds and/or materials such as bacteriocins that include contacting ‘challenger’ microbes with the ‘protagonist’ microorganisms. The challenger microbes do not directly manufacture the beneficial compounds and/or materials and instead stimulate the protagonist microorganisms to produce beneficial compounds and materials. The protagonist and/or challenger microorganisms can be administered to a subject so the beneficial compounds and/or materials can be made in vivo. Compositions and methods of using beneficial compounds and/or materials are also described herein.

The present disclosure relates to probiotics and probiotic compositions having modified energy metabolisms (e.g., modifying, metabolizing, or storing energy molecules, e.g., lipids, before the energy molecules are absorbed by a host subject), and thus modulating the absorption of the energy molecules by the host subject. The present disclosure also relates to methods of making such probiotics and probiotic compositions. The present disclosure further relates to methods of regulating (e.g., maintaining or reducing) body weight in a subject (e.g., a subject having a healthy BMI, a subject having an overweight BMI, a subject having an obese BMI), using the probiotics and probiotic compositions disclosed herein.

Described herein are methods and compositions for using microbial agents (probiotics) and agents that promote growth of certain microbes (prebiotics) for management (including prevention and treatment) of musculoskeletal disorders, including osteoporosis, osteopenia, Paget's disease, stunting, osteoarthritis, osteomyelitis, and delayed or non-union fractures.

Described herein are methods and compositions for using microbial agents (probiotics) and agents that promote growth of certain microbes (prebiotics) for management (including prevention and treatment) of musculoskeletal disorders, including osteoporosis, osteopenia, Paget's disease, stunting, osteoarthritis, osteomyelitis, and delayed or non-union fractures.

Provided herein are methods of treating graft-versus-host disease in a subject by administering pharmaceutical compositions containing bacterial strains of the Clostridia class. Also described herein are exemplary human-derived bacteria belonging to the Clostridia class, combinations of which have been shown to induce accumulation of regulatory T cells (Treg cells) in the colon and suppress immune functions, and are therefore useful for mitigating pathological immune responses. Pharmaceutical compositions containing these and/or related bacteria can be used to prevent and treat immune-mediated diseases such as graft-versus-host disease.