Mucosal Associated Invariant T (MAIT) cells are abundant innate-like T cells restricted by the non-classical MHC molecule MR1. Both MR1 and the T cell receptor alpha (TCRa) chain of MAIT cells first appeared in mammals and remained strikingly conserved in evolution. The MAIT cell transcriptional program is also conserved across species, indicating that MAIT cells probably fulfill conserved function(s) linked to antigen recognition. The MAIT TCR recognizes riboflavin pathway-derived (5-OP/E-RU) and bile acid-derived (CA7S) metabolites that are constantly produced by the intestinal microbiota and lacking in germ-free mice, suggesting a role for MAIT cells in host-microbiota interactions. We hypothesized that MAIT cell function under selection pressure may relate to the recognition of microbiota-derived ligands. We will present our published and non-published work on the origin, regulation and dynamics of microbiota-derived MAIT ligands in vivo and speculate on how MAIT cell activation in barrier tissues may provide a fitness advantage to the host.