Local adaptation of host-species specific gut microbiota

Mammalian species harbor compositionally distinct gut microbial communities, but the mechanisms that maintain specificity of symbionts to host species remain unclear. Here we show that natural selection within house mice (Mus musculus domesticus) drives deterministic assembly of the house mouse gut microbiota from mixtures of native and non-native microbiotas. Competing microbiotas from multiple wild-derived lines of house mouse and other mouse species (Mus and Peromyscus spp.) within germ-free wildtype (WT) and Rag1-knockout (Rag1-/-) house mice revealed widespread fitness advantages for native gut bacteria. A minority of native strains favored by selection in WT hosts were not favored or disfavored in Rag1-/-hosts, suggesting that host adaptive immunity mediated selection on these strains. This study demonstrates local adaptation of gut microbiota to a mammalian species.