The study of the intestinal microbiota has begun to shift from cataloging individual members of the commensal community to understanding their contributions to the physiology of the host organism in health and disease. Here, we review the effects of the microbiome on innate and adaptive immunological players from epithelial cells and antigen-presenting cells to innate lymphoid cells and regulatory T cells. We discuss recent studies that have identified diverse microbiota-derived bioactive molecules and their effects on inflammation within the intestine and distally at sites as anatomically remote as the brain. Finally, we highlight new insights into how the microbiome influences the host response to infection, vaccination and cancer, as well as susceptibility to autoimmune and neurodegenerative disorders.
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The authors thank all their past and present laboratory members for their contributions. We thank our funding agencies for their support to our laboratories: NIH grants DK072201, DK111862, AI073899, AI123284 and AI127658, the Searle Scholars Program, the Burroughs Wellcome Fund, the American Cancer Society and the Leukemia & Lymphoma Society to J.M.B.; NIH grant DK099381, the Crohn's and Colitis Foundation Senior Research Award 346814 and the Charina Foundation to R.S.L.; NIH grants DK098310 and AI123819, and Kenneth Rainin Foundation Innovator and Breakthrough awards to I.D.I.; NIH grants DP5OD012116, AI123368 and DK110262, and the Crohn's and Colitis Foundation, the Searle Scholars Program and the American Asthma Foundation Scholar Award to G.F.S.; NIH grants AI061570, AI087990, AI074878, AI083480, AI095466, AI095608, AI102942 and AI097333, Burroughs Wellcome Fund and the Crohn's & Colitis Foundation of America to D.A.
The authors declare no competing financial interests.
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Blander, J., Longman, R., Iliev, I. et al. Regulation of inflammation by microbiota interactions with the host. Nat Immunol 18, 851–860 (2017). https://doi.org/10.1038/ni.3780
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