Diet and microbiome analyses of woodrats (Neotoma spp.) based on fecal DNA metabarcoding

Despite evidence that related hosts often harbor similar bacterial communities, it is unclear whether this pattern is due to host genetics or common ecological selection pressures. Here, using herbivorous rodents in the genus Neotoma, we quantify how geography, diet, and phylogeny influence microbiome structure and stability under natural and captive conditions. Using bacterial and plant metabarcoding, we first characterized dietary and microbiome compositions for animals from 25 populations, representing 7 species from 19 sites across the southwestern United States.