Assessing similarities and disparities in the skin microbiota between wild- and laboratory populations of house mice

The house mouse is a key model organism in skin research including host-microbiota interactions, yet little is known about the skin microbiota of free-living mice. It is similarly unclear how closely laboratory mice, which typically live under exceptionally hygienic conditions, resemble the ancestral state of microbial variation in the wild. In this study, we sampled an area spanning 270 square-kilometers in south-west France and collected 203 wild Mus musculus domesticus. We profiled skin microbiota on standing and active communities (DNA- and RNA-based 16 rRNA gene sequencing, respectively), and compared multiple community aspects between wild-caught and laboratory-reared mice kept in distinct facilities. Compared to lab mice, we reveal the skin microbiota of wild mice on the one hand to be uniquely dominated by Novobiocin-resistant Staphylococcus species and display evidence of a rare biosphere. On the other hand, despite drastic disparities between natural and laboratory environments, we find that shared taxa nonetheless make of the vast majority (approx. 99%) of the total abundances of both wild- and laboratory skin communities, suggesting that mammalian skin is a highly specialized habitat capable of strong selection from available species pools. Finally, the influence of environmental factors suggests RNA-based profiling as a preferred method to reduce environmental noise.