The trillions of microorganisms populating the mammalian mucosal surfaces (i.e. the microbiome) participate in the development and function of the host immune system that acts to balance clearance of pathogens with tolerance of beneficial commensals. Recent advances in mucosal immunology and culture-independent sequencing of microbial communities provide support for the hypothesis that the alterations in commensal microbiota alter the host immune response and can enhance risk for autoimmune disease in distant organs. Further explorations of the host-microbiota relationship will improve our understanding of autoimmune disorders and facilitate the discovery of a bacterial-based immunomodulators.
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