Data from: Spatiotemporal variation in the gut microbiomes of co-occurring wild rodent species

Mammalian gut microbiomes differ within and among individual hosts. Hosts
that occupy a range of environmental conditions may exhibit greater
spatiotemporal variation in their microbiome than those constrained as
specialists to narrower subsets of resources or habitats. This can occur
because widespread host species encounter a variety of ecological
conditions that act to diversify their gut microbiomes and/or because
generalized host species tend to form large populations that promote
sharing and maintenance of diverse microbes. We studied spatiotemporal
variation in the gut microbiomes of three co-occurring rodent species
across an environmental gradient in a Kenyan savanna. We hypothesized: (i)
the taxonomic, phylogenetic, and predicted functional composition of gut
microbiomes differ significantly among host species, (ii) microbiome
richness increases with population size for all host species, and (iii)
host species exhibit different rates of seasonal change in their gut
microbiomes, reflecting different sensitivities to environmental change.
We evaluated changes in gut microbiome according to species identity,
site, and host population density using three years of
capture-mark-recapture data and 351 microbiome samples. Host species
differed significantly in microbiome composition, though those with the
more specialized diets and higher demographic sensitivities showed only
slightly greater microbiome variability than those of a widespread dietary
generalist. Total microbiome richness in populations of all species
increased significantly with population size, but only one of the more
specialized species also exhibited greater within-individual microbiome
richness with population size. Across co-occurring rodent species with
diverse diets and life histories, host population growth in response to
rainfall was associated both with strong increases in population-level
microbiome richness (sampling effects) and turnover in the relative
abundance of bacterial taxa (environmental effects), but there was not
consistent change in intra-individual richness (individual variation).
Together, our results show that maintenance of large host populations
contributes to the maintenance of gut microbiome diversity in wild
mammals.