Abstract The microbiome contributes to the development and maturation of the immune system 1–3 In response to commensal bacteria, CD4 + T cells can differentiate into distinct functional subtypes with regulatory or effector functions along the intestine. Peripherally-induced Foxp3 + -regulatory T cells (pTregs) maintain immune homeostasis at the intestinal mucosa by regulating effector T cell responses against dietary antigens and microbes 4 . Similarly to pTregs, a subset of small intestine intraepithelial lymphocytes CD4 + CD8αα + (CD4 IELS ) exhibit regulatory properties and promote tolerance against dietary antigens 5 . Development of CD4 IELS from conventional CD4 + T cells or from Treg precursors depends on the microbiota 5,6 . However, the identity of the microbial antigens recognized by CD4 IELs remains unknown. We identified species belonging to the Bacteroidetes phylum as commensal bacteria capable of generating CD4 IEL from naïve CD4 + T cells expressing the pTreg transnuclear (TN) monoclonal TCR 6 as well as from polyclonal WT T cells. We found that β-hexosaminidase, a widely conserved carbohydrate-metabolizing enzyme in the Bacteroidetes phylum, is recognized by TN T cells, which share their TCR specificity with CD4 + T cells found in the intraepithelial compartment of polyclonal specific-pathogen-free (SPF) mice. In a mouse model of colitis, β-hexosaminidase-specific CD4 IELs provided protection from ulceration of the colon and weight loss. Thus, a single T cell clone can recognize a variety of abundant commensal bacteria and elicit a regulatory immune response at the intestinal epithelial surface.

Antigen-specific induction of CD4+CD8αα+ intraepithelial T lymphocytes by Bacteroidetes species