The gastrointestinal tract is a unique organ which is constitutively exposed to countless numbers of antigens including commensal bacteria. In order to exclude pathogenic microorganisms and create symbiotic relationships with non-pathogenic bacteria, the host prepares a sophisticated gut immune system. Segmented filamentous bacteria (SFB), a kind of commensal bacteria, have been reported to induce T helper 17 cells (Th17), which are immune cells providing protection against infection by pathogenic bacteria including Citrobacter rodentium. In this study, we examined the detailed mechanisms of the induction of Th17 by SFB. Our results reveal that antigen presentation by dendritic cells (DCs) mediates the induction of Th17 cells, and that the differentiation of Th17 cells is negatively regulated by major histocompatibility complex (MHC) II on group 3 innate lymphoid cells (ILC3). Our results also revealed that SFB are the bacteria responsible for the induction of α1,2-fucose on intestinal epithelial cells. Furthermore, ILC3 are critical inducers of intestinal epithelial α1,2-fucose that is mediated by the production of interleukin 22. α1,2-Fucose on epithelial cells plays a role in protection against infection by pathogenic bacteria such as Salmonella typhimurium. These results unveil a novel function of segmented filamentous bacteria, which not only induce Th17 cells but also induce α1,2-fucose, leading to the establishment of a protective platform against pathogenic microorganisms in rodents.

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Although recent progress in DNA sequencing technology has revealed the comprehensive profile of the intestinal microbiota, many species are still not-yet-culturable in vitro. However, efforts to isolate and characterize the not-yet-culturable or difficult-to-cultivate bacteria have succeeded to some extent. Here we introduce the classification and characteristics of several bacterial species or groups, including segmented filamentous bacteria (SFB), which were isolated in vitro or in vivo using germ-free animals.

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Eleven phyla of the domain Bacteria and 1 phylum of the domain Archaea have been detected in the human gut. The majority of human intestinal bacteria belong to the following four phyla: Firmicutes, Bacteroidetes, Actinobacteria and Proteobacteria. A total of 957 species belonging to the domain Bacteria and 8 belonging to the domain Archaea have been identified. The taxonomy of Gram-positive anaerobic bacteria isolated from the human gut that belong to the phyla Firmicutes and Actinobacteria are described here.

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