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

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Mar 19, 2024 version files 59.66 MB

Abstract

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.