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ISME J. 2015 Nov;9(11):2423-34. doi: 10.1038/ismej.2015.53. Epub 2015 May 29.

Marked seasonal variation in the wild mouse gut microbiota.

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FAS Center for Systems Biology, Harvard University, Cambridge, MA, USA.
Centre for Immunity, Infection and Evolution (CIIE), School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire, UK.
Gladstone Institutes, San Francisco, CA, USA.
Institute for Human Genetics and Division of Biostatistics, University of California San Francisco, San Francisco, CA, USA.
Institute of Integrative Biology, University of Liverpool, Biosciences Building, Liverpool, UK.
Department of Microbiology and Immunology, G.W. Hooper Research Foundation, University of California San Francisco, San Francisco, CA, USA.


Recent studies have provided an unprecedented view of the microbial communities colonizing captive mice; yet the host and environmental factors that shape the rodent gut microbiota in their natural habitat remain largely unexplored. Here, we present results from a 2-year 16 S ribosomal RNA gene sequencing-based survey of wild wood mice (Apodemus sylvaticus) in two nearby woodlands. Similar to other mammals, wild mice were colonized by 10 bacterial phyla and dominated by the Firmicutes, Bacteroidetes and Proteobacteria. Within the Firmicutes, the Lactobacillus genus was most abundant. Putative bacterial pathogens were widespread and often abundant members of the wild mouse gut microbiota. Among a suite of extrinsic (environmental) and intrinsic (host-related) factors examined, seasonal changes dominated in driving qualitative and quantitative differences in the gut microbiota. In both years examined, we observed a strong seasonal shift in gut microbial community structure, potentially due to the transition from an insect- to a seed-based diet. This involved decreased levels of Lactobacillus, and increased levels of Alistipes (Bacteroidetes phylum) and Helicobacter. We also detected more subtle but statistically significant associations between the gut microbiota and biogeography, sex, reproductive status and co-colonization with enteric nematodes. These results suggest that environmental factors have a major role in shaping temporal variations in microbial community structure within natural populations.

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