The gut microbiota of two rodents varies over fine spatial scales yet is minimally influenced by the environmental microbiota

The gut microbiota of animals varies considerably between individuals within the same population. Given the importance of gut microbiota composition for animal biology and ultimately fitness (e.g., via effects on physiology, immunity and even behaviour), there is considerable interest in understanding which factors shape its variation. Here, we tested whether local environments are an important source of microbial diversity for mammalian guts, by sampling the faecal microbiota of wood mice (Apodemus sylvaticus) and bank voles (Myodes glareolus), as well as environmental microbiotas, across Wytham Woods. We first find that both species share a low proportion of their microbiotas with local environments and that most shared microbes are aerotolerant. We then detect that microgeographic patterns (namely soil chemistry) are associated with variation in the microbiota of local environments but this does not translate to microbiota variation between animals. Nevertheless, between-individual gut microbiota variation is strongly associated with where animals are sampled, suggesting that other local factors (e.g., biotic environment, interactions between individuals) are much stronger predictors of microbiota composition than local abiotic factors. Finally, we find that wood mice (but not bank voles) are more likely to share microbes with local than non-local environments, but that local environments still contribute little to animal microbiotas. Our findings challenge the prevailing view that mammalian microbiotas are strongly affected by local soil chemistry or the abiotic environment, while further supporting the prediction that biotic and/or other intrinsic factors (which can also act on a local scale) contribute more to microbiota composition.