Wild house mice have a more dynamic and aerotolerant gut microbiota than laboratory mice

Abstract
The mammalian gut microbiota is a complex microbial community with diverse impacts on host biology. House
mice (Mus musculus) are the major model organism for research on mammals, but laboratory domestication
has altered their gut microbiota from that of their wild counterparts. Knowledge about how and why the gut
microbiota of this species varies between lab and wild settings and among natural populations could improve its
utility as a model organism. Here, we use a large dataset comprising over 800 house mouse samples from multiple
laboratory facilities and strains and wild mice from mainland and island populations to investigate gut microbiota
variation in this species across contrasting genetic and environmental settings. Across geographically disparate
populations, we find that wild mice possess a gut microbiota that is compositionally distinct, displays a higher
relative abundance and richness of aerotolerant taxa, and is taxonomically and functionally more diverse than
that of lab mice. Longitudinally sampled wild mice also display markedly higher temporal turnover in microbiota
composition than lab mice. Wild mice from oceanic islands harboured microbiotas that differed subtly from those
of mainland wild mice and were more divergent from lab mouse microbiotas. These findings highlight much
greater spatial and temporal turnover of gut microbes in wild compared to laboratory mice