Profiling of intestinal T cells reveals antigen-specific dependency on early-life programming for the generation of microbiota-reactive Tregs

The generation of appropriate responses to the intestinal microbiota is an essential aspect of immune homeostasis. Studies of microbes that elicit stereotyped, antigen-specific CD4 T cell responses support the view that immune recognition of the microbiota is specific, relatively limited, and largely skewed toward Tregs, but recent profiling efforts have suggested that recognition of the microbiota may be broader and less regulatory. Such studies have mostly tracked responses to single antigens or used mice that acquire their microbiota after weaning, which has made it difficult to generalize the rules that govern microbiota-mediated T cell responses. Here we comprehensively profile, for the first time, the T cell response to the microbiota at homeostasis, and develop a panel of tools to track multiple, endogenous microbiota-reactive CD4 T cell populations in vivo. Our profiling reveals a broad microbiota-reactive T cell response that is Treg-biased but that also contains non-Treg responses to specific microbes. We find that certain microbiota-reactive T cells require priming during early-life to efficiently establish their Treg identity, while others do not. Our findings illustrate an unappreciated antigen-specific complexity in programming of microbiota-reactive T cells and underscore the importance of studying responses to the microbiota under homeostatic conditions.