tl;dr: MS-associated changes in microbiota alter T lymphocyte differentiation, and microbiota transplants from MS patients into germ-free mice results in more severe experimental autoimmune encephalomyelitis and reduced Tregs. The MS-Associated Gut Microbiome http://journals.sagepub.com/doi/10.1177/1352458517693714 Dr. Sergio E Baranzini, PhD1, Dr. Egle Cekanaviciute, PhD1, Dr. Justine Debelius, PhD2, Ms. Sneha Singh1, Dr. Tessel Runia3, Mr. Bryan Yoo4, Dr. Elizabeth Crabtree-Hartmann, MD1, Dr. Riley Bove, M.D.1, Dr. Jeffrey Gelfand, MD1, Dr. Sherman Jia1, Dr. Jennifer S Graves, MD, PhD, MAS1, Mr. John Morrissey1, Prof. Stephen L Hauser, MD1, Prof. Sarkis Mazmanian5, Prof. Rob Knight6, Dr. Ilana Katz Sand, M.D.7, Prof. Patrizia Casaccia8, Dr. Bruce AC Cree, MD, PhD, MAS1, Mrs. Refujia Gomez1 and Dr. Ari Green1 1University of California, San Francisco, CA, 2University of California San Diego, La Jolla, CA, 3Erasmus MC, Rotterdam, Netherlands, 4TBD, Pasadena, CA, 5Cal Tech, Pasadena, CA, 6University of California, La Jolla, CA, 7Icahn School of Medicine at Mount Sinai, New York, NY, 8Mount Sinai, New York, NY Background: An essential function of the gut microbiota is to regulate immune responses, including T lymphocyte functions in health and disease. Objectives: We hypothesized that gut microbiota contribute to the pathogenesis of MS. Methods: We analyzed the microbiome of stool samples from 64 treatment-naïve MS patients and 68 healthy controls using amplicon sequencing of the 16S V4 region of the rRNA gene. We characterized immune profiles of cultured PBMC in response to specific bacteria harbored by MS patients. Results: We found that MS patients exhibited impaired in-vitro Treg differentiation in response to their own microbiota. No major shifts in microbial community structure were observed. However, we were able to identify individual microbial taxa that were significantly associated with MS and studied their ability to regulate primary human T lymphocyte differentiation in vitro. We next conducted in-vitro assays to characterize the functional properties of the MS gut microbiota. We found that MS-associated Acinetobacter calcoaceticus was sufficient to reduce Treg differentiation and increase both Th1 and Th2 differentiation. The expansion of Th1 lymphocytes was recapitulated by Akkermansia muciniphila, which was also more abundant in MS patients. In contrast, Parabacteroides distasonis, which was significantly reduced in MS microbiomes, stimulated CD4+ T lymphocyte differentiation into a CD25+ IL-10+ regulatory phenotype. Our results suggest that MS-associated changes in microbiota alter T lymphocyte differentiation in a complex fashion and likely through multiple mechanisms. Finally, microbiota transplants from MS patients into germ-free mice results in more severe experimental autoimmune encephalomyelitis and reduced Tregs compared to controls. Conclusion: This study identifies specific human gut bacteria that regulate adaptive autoimmune responses, suggesting therapeutic targeting of the microbiota as a novel treatment for MS.