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 km² in south-west France and collected 203 wild Mus musculus domesticus. We profiled the ear skin microbiota on standing and active communities (DNA-based 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 unique in their composition within the Staphylococcus genus, with a majority of sequences most closely matching known novobiocin-resistant 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 up the majority of the core skin microbiota 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.

家鼠是皮肤研究（包括宿主-微生物群相互作用）中的关键模型生物，但对自由生存小鼠的皮肤微生物群知之甚少。同样不清楚的是，通常生活在异常卫生条件下的实验室小鼠与野生动物中微生物变异的祖先状态有多接近。在本研究中，我们在法国西南部采样了一个面积为270 km ²的区域，并收集了203只野生小家鼠。我们分析了站立和活动社区（分别基于DNA和基于RNA的16 rRNA基因测序）上的耳部皮肤微生物群，并比较了保存在不同设施中的野生和实验室饲养小鼠之间的多个社区方面。与实验室小鼠相比，我们一方面揭示了野生小鼠的皮肤微生物群在葡萄球菌中的组成是独特的属，其大多数序列与已知的新霉素抗性物种最接近，并显示出罕见的生物圈证据。另一方面，尽管自然环境与实验室环境之间存在巨大差异，但我们发现共享类群仍然构成了野生和实验室皮肤群落核心皮肤微生物的大部分，这表明哺乳动物皮肤是一种高度专业化的栖息地，能够从可用物种库中进行选择。最后，环境因素的影响表明基于RNA的谱图分析是减少环境噪音的首选方法。