The thymus prevents autoimmunity by eliminating or differentiating self-reactive T cells; however, it is unknown whether T cells can be altered to recognize antigens from commensal bacteria, which may prevent diseases such as IBD. Findings from a mouse study indicate that antigen-specific TREG cells are generated in response to an individual's microbiota. This occurs after T cells have been altered in the thymus and could be a mechanism by which a host can tolerate commensal bacteria.