Adaptive immunity increases the pace and predictability of evolutionary change in commensal gut bacteria

Co-evolution between the host immune system and its microbiota is believed to have shaped the astonishing diversity of the mammalian gut microbiota. Here we test the corollary hypothesis that the adaptive immune system, directly or indirectly, influences the evolution of commensal species. We compare the evolution of Escherichia coli upon colonization of the gut of wild-type and Rag2-/- mice, which lack lymphocytes. We show that bacterial adaptation is slower in immune-compromised animals, a phenomenon explained by differences in the action of natural selection within each host. Emerging mutations exhibit strong beneficial effects in healthy hosts but substantial antagonistic pleiotropy in immune-deficient mice. This feature is due to changes in the composition of the gut microbiota, which differs according to the immune status of the host. Our results indicate that the adaptive immune system influences the tempo of E. coli adaptation to the mouse gut, along a more predictable path.