![]() ![]() The relative importance of these different ecological processes in shaping wild animal microbiomes remains a key open question. Each individual’s gut microbiota constitutes a diverse community of microbes shaped by environmental influences such as diet, habitat and xenobiotics, microbial interactions, metacommunity-level processes such as transmission among hosts, and mechanisms of host selection, arising, for example, through physiological differences among host genotypes or age. Vertebrate gut microbiotas are typified by immense compositional variation, both among individuals and within individuals over time. ![]() Yet the emerging picture from microbiome research firmly contradicts this. With such important roles, one might expect these symbiotic communities to be under strong host influence, such that individuals of a given species harbour a characteristic and relatively invariant community. These include regulating the immune system ( Round and Mazmanian, 2009), extracting nutrients from otherwise indigestible parts of the diet ( Flint et al., 2012), and defence against pathogens ( Buffie and Pamer, 2013). The gastrointestinal tracts of vertebrates harbour complex microbial communities known as the gut microbiota, that can perform a wide range of important functions for the host. This provides a platform for future work to understand the drivers and functional implications of such predictable seasonal microbiome restructuring, including whether it might provide the host with adaptive seasonal phenotypic plasticity. These findings reveal highly repeatable seasonal gut microbiota dynamics in multiple populations of this species, despite different taxa being involved. While the microbiota was highly individualised, some seasonal convergence occurred in late winter/early spring. We identified a strong and consistent pattern of seasonal microbiota restructuring that occurred at both sites, in all years, and within individual mice. Despite not sharing any ASVs, the two wild populations shared a phylogenetically more similar microbiota than either did with the colony, and the factors predicting compositional variation in each wild population were remarkably similar. Meanwhile, the laboratory-housed colony shared many ASVs with one of the wild populations from which it is thought to have been founded decades ago. Although the microbiota was broadly similar at high taxonomic levels, the two wild populations did not share a single bacterial amplicon sequence variant (ASV), despite being only 50km apart. Between 20 we used capture-mark-recapture and 16S rRNA profiling to intensively monitor two wild wood mouse populations and their gut microbiota, as well as characterising the microbiota from a laboratory-housed colony of the same species. Here, we use a multi-population dataset from a common rodent species (the wood mouse, Apodemus sylvaticus), to test whether a consistent “core” gut microbiota is identifiable in this species, and to what extent the predictors of microbiota variation are consistent across populations. ![]() However, the factors that drive individual microbiota variation in wild animals and to what extent these are predictable or idiosyncratic across populations remains poorly understood. The gut microbiome performs many important functions in mammalian hosts, with community composition shaping its functional role. 5Institute of Evolutionary Biology, School of Biology, University of Edinburgh, Edinburgh, United Kingdom.4Department of Life Sciences, Imperial College London, Silwood Park, Ascot, United Kingdom.3Department of Zoology, University of Oxford, Oxford, United Kingdom.2College of Life and Environmental Sciences, University of Exeter, Cornwall, United Kingdom.1Department of Pathobiology and Population Sciences, The Royal Veterinary College, University of London, Hatfield, United Kingdom. ![]() English 1,3, Bryony Allen 4, Rohan Raval 4, Saudamini Venkatesan 5, Amy B. Raulo 3, Marc Brouard 3, Tanya Troitsky 3, Holly M. ![]()
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