Environmental effects on the gut microbiota of two rodent species

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. Our results suggest that variation in the microbiota of local environments is associated with soil chemistry, and we detect a signal of sampling location on the likelihood of wood mouse (but not bank vole) microbiotas sharing ASVs with the local environment, with these shared ASVs being overwhelmingly aerotolerant. However, this does not explain a significant amount of microbiota variation between individuals. Despite this, 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, or relatedness) are much stronger predictors of microbiota composition than local abiotic factors. 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 factors and other intrinsic factors (which can also act on a local scale) contribute more to microbiota composition.