Intestinal CD4+ T cells that are specific for self-, diet-, or commensal-derived antigens are critical for host tolerance but must also be tightly regulated to prevent aberrant activation and conditions like inflammatory bowel disease (IBD). However, it is unclear how the antigen source and location dictate the intestinal TCR repertoire. Here, we hierarchically classified self-, diet-, or microbiota-dependent TCRs using TCliβ TCRβ transgenic mice. This demonstrated that microbiota had a greater influence than diet on CD4+ T cell responses throughout the intestine at homeostasis. Complex bi-directional interactions between microbes and diet were also observed. In the context of murine colitis as a model of IBD, we showed that antigen-free diet substantially altered the microbiota and associated T cell responses, which ameliorated intestinal inflammation. Collectively, these findings suggest how deconvoluting the gut immune interactome may facilitate identifying primary microbial and dietary drivers of T cell responses during health and disease.
We thank Michael Lint (WashU) for his generous assistance with gnotobiotic experiments, Anne Rosen (WashU) for providing the isolate of Akkermansia muciniphila and Bacteroides vulgatus, David L Owen and Michael A. Farrar (U. of Minnesota) for helpful discussion of protocols for 10X sequencing with the fixed TCR\u03B2 mice, and Derek Martin (Inotiv) for helpful discussion regarding custom diets and providing individual diet component samples. GF experiments were performed at the Gnotobiotic Core facility of Washington University in St. Louis. 10X single-cell RNA-seq was conducted at Genome Technology Access Center (GTAC) at Washington University in St. Louis. SFB was kindly provided by Dr. Yoshinori Umesaki (Yakult Cen Inst, Japan). 59 J.Y. was supported by the Ajou University research fund and NRF ( National Research Foundation of Korea ) grants of Basic Science Research Program ( RS-2021-NR060141 ) ( MOE ) and RS-2025-00515400 ( MSIT ); A.L.K. by R01 AI165915 ; and R.N. and C.S.H. by U01 AI163073 , R01 AI173220 , and NIH P30AR073752 .
