Dietary and gut microbial variation among urban and rural populations of house mice (Mus musculus domesticus)

Urbanization can result in shifts in abiotic and biotic factors, including temperature, pollution, habitat type, pathogens, and diet, among others. These shifts can, in turn, shape the ecological and evolutionary trajectory of urban wildlife. The gut microbiota has the potential to mediate host-environment interactions, especially in the context of diet and disease, and thus may be a useful lens for understanding the impacts of urbanization. House mice (Mus musculus domesticus) are a cosmopolitan human commensal with a wealth of genomic and metagenomic resources. Here, we investigate patterns of variation in diet and gut microbial diversity, community composition, and function using a paired urban-rural sampling design in house mice from three metro regions in the eastern United States. First, using stable isotope analysis, we found that habitat, urban versus rural, was a major driver of variation in delta15N, suggesting a diet richer in animal proteins in cities. Next, using short-read sequencing of the 16S rRNA gene, we found that urban mice have lower gut microbial taxonomic diversity than their rural counterparts. We also found that community composition varied among urban and rural habitats, with differences largely reflecting shifts among closely related taxa. In particular, Prevotellaceae, a family known to be responsive to dietary quality, was differentially abundant, with lower abundance in urban habitats. Finally, we found differentiation in a few predicted microbial functions across habitat, primarily related to metabolism. Together, data across three independent sampling regions provide strong evidence that urbanization has the potential to shape the diet and the microbiome of house mice.