[Colleen CUTCLIFFE, John S. EID, Tomer ALTMAN, Orville G. KOLTERMAN, James H. BULLARD] US CA San Francisco Disclosed herein are methods and compositions for treatment of a microbiome associated disorder. Further, disclosed herein are methods and compositions for modulating short chain fatty acid production in a subject.

[JUSTICE, Nicholas B., STOEVA, Magdalena K., EID, John S., MYERS, Julia, CHENG, Andrew, BRANDI, Moe, MCMURDIE, Paul, BULLARD, James] 933 20th StreetSan Francisco, California 94107;80048 Jasper Park AveIndio, California 92201 The disclosure provides microbial compositions (e.g., compositions comprising one or more microbes or protein components thereof), that can be administered to subjects to confer beneficial effects. Disclosed compositions can, for example, be useful in reducing visceral hypersensitivity, or pain in response to colorectal distension.

[Colleen CUTCLIFFE, John S. EID, James H. BULLARD] US CA San Francisco The present disclosure provides methods for profiling a microbiome and therapeutic compositions for treatment. Additionally, the methods, systems, compositions and kits provided herein are directed to assessing or predicting health status in a subject. Some of the embodiments include generating a report.

[EID JOHN S, CHENG ANDREW T, JUSTICE NICHOLAS B, MYERS JULIA N] US

[CUTCLIFFE, Colleen, EID, John S., BULLARD, James H., SCHICKLBERGER, Marcus F.] 933 20th Street, San Francisco, CA 94107, US The present disclosure provides methods, systems, compositions, and kits to address the need for microbiome-related treatment of health conditions and disease. The present disclosure provides for treatment of metabolic conditions using microbial compositions.

[CHENG, Andrew, SCHICKLBERGER, Marcus, MORENO, David, STONEBURNER, Brendon, HERNANDEZ, Jaime] 933 20th StreetSan Francisco, California 94107 Provided herein are methods and compositions comprising microbial populations with increased tolerability and improved shelf life. Disclosed, herein, in some aspects, is a composition comprising at least one powdered microbial population, lactate, and trehalose. In some embodiments, the lactate is a lactate salt. In some embodiments, the lactate is sodium lactate. In some embodiments, the lactate and trehalose are present in sufficient amount to act as a cryoproteclant. Provided herein are methods and compositions comprising microbial populations with increased tolerability and improved shelf life. Disclosed, herein, in some aspects, is a composition comprising at least one powdered microbial population, lactate, and trehalose. In some embodiments, the lactate is a lactate salt. In some embodiments, the lactate is sodium lactate. In some embodiments, the lactate and trehalose are present in sufficient amount to act as a cryoproteclant.

[Nicholas B. Justice, Magdalena K. Stoeva, John S. Eid] US CA San Francisco Methods to increase viability and revivability of bacteria compared to their wild type counterparts, are disclosed herein. New strains of an anerobic bacteria is also disclosed obtained by the methods described herein. Further, disclosed are compositions comprising these bacteria as well as methods of treatment including the use of the bacteria described.

[KOLTERMAN, Orville, PERRAUDEAU, Fanny, BULLARD, James, EID, John, CUTCLIFFE, Colleen] 933 20th StreetSan Francisco, California 94107 Compositions and methods are provided for treating, mitigating, managing, reducing or preventing the onset of symptoms, signs or indicators of liver disorders as well as the disorders themselves. The compositions and methods include microbial compositions that are selected to improve gut function in the subjects to which they are administered, so as to bring about treatment of liver disorders and/or the signs, symptoms and indicators of those disorders. Compositions and methods are provided for treating, mitigating, managing, reducing or preventing the onset of symptoms, signs or indicators of liver disorders as well as the disorders themselves. The compositions and methods include microbial compositions that are selected to improve gut function in the subjects to which they are administered, so as to bring about treatment of liver disorders and/or the signs, symptoms and indicators of those disorders.

[EID, John S., MCMURDIE, Paul, KOLTERMAN, Orville G.] 933 20th StreetSan Francisco, California 94107 Provided are methods of increasing ursodeoxycholic acid (UDCA) levels in a mammalian subject. The methods comprise orally administering to the mammalian subject a composition comprising one or more bacterial strains in an amount effective to increase UDCA levels in the mammalian subject. Also provided are methods of antagonizing farnesoid X receptor (FXR) in intestinal cells of a mammalian subject. Such methods comprise orally administering to the mammalian subject a composition comprising one or more bacterial strains in an amount effective to antagonize FXR in intestinal cells of the mammalian subject. In certain embodiments, the mammalian subject has diabetes, e.g., type 2 diabetes. According to some embodiments, the mammalian subject suffers from a liver disorder, obesity, or both. In certain embodiments, the mammalian subject has colorectal cancer. According to some embodiments, the mammalian subject has gallstones. Provided are methods of increasing ursodeoxycholic acid (UDCA) levels in a mammalian subject. The methods comprise orally administering to the mammalian subject a composition comprising one or more bacterial strains in an amount effective to increase UDCA levels in the mammalian subject. Also provided are methods of antagonizing farnesoid X receptor (FXR) in intestinal cells of a mammalian subject. Such methods comprise orally administering to the mammalian subject a composition comprising one or more bacterial strains in an amount effective to antagonize FXR in intestinal cells of the mammalian subject. In certain embodiments, the mammalian subject has diabetes, e.g., type 2 diabetes. According to some embodiments, the mammalian subject suffers from a liver disorder, obesity, or both. In certain embodiments, the mammalian subject has colorectal cancer. According to some embodiments, the mammalian subject has gallstones.

[LECLERC, Marion, EID, John S.] 933 20th StreetSan Francisco, California 94107 Provided are methods of treating skin inflammation in a subject in need thereof. The methods comprise administering to the subject a composition comprising Akkermansia muciniphila and/or an Akkermansia muciniphila supernatant or fraction thereof comprising one or more agents that reduce skin inflammation (e.g., gluconic acid, gluconolactone, 5-aminolevulinic acid, azelaic acid, glycero-phosphatidylcholine, glycero-phosphatidylinositol, or any combination thereof), in an amount effective to treat the skin inflammation. According to some embodiments, the composition is administered orally or topically. In certain embodiments, prior to the administering, the subject has been identified as having an inflammatory skin disorder, e.g., actinic keratoses, psoriasis, acne, rosacea, seborrheic dermatitis, eczema, or the like. Also provided are topical formulations comprising an Akkermansia muciniphila supernatant or fraction thereof comprising one or more agents that reduce skin inflammation. According to some embodiments, the topical formulation is a lotion, cream, ointment, gel, paste, aerosol spray, aerosol foam, or transdermal patch.