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

Meriem Belheouane,Aleksa Čepić,Saleh Ibrahim,Marie Vallier,John F Baines,Cecilia J Chung

doi:10.1038/s41396-020-0690-7

Meriem Belheouane, Aleksa Čepić + Show 4 more

Open Access

https://doi.org/10.1038/s41396-020-0690-7

Copy DOI

Abstract

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.

Highlights

The skin serves critical functions as a physical and immunological barrier, but is a dynamic ecosystem inhabited by diverse microbial symbionts
To compare these data to skin microbial composition typically observed in a laboratory environment, we included three different groups of laboratory mice reared in distinct facilities: HL-Lab [49], MPI-Lab, and C57BL/6J (Table 1, Supplementary Table 1)
We assessed the relative abundances of the five most abundant phyla, and five most abundant genera. This reveals Firmicutes to be the most abundant phylum in wild, MPI-Lab, and C57BL/ 6J mice on the DNA level, which is significantly lower in HL-Lab mice, whereas Proteobacteria is more abundant in C57BL/6J

Summary

Introduction

The skin serves critical functions as a physical and immunological barrier, but is a dynamic ecosystem inhabited by diverse microbial symbionts. This ecosystem is influenced by fundamental processes of community assembly including dispersal, local diversification, environmental selection, and ecological drift [1,2,3]. Several recent studies [6,7,8], revealed that wild mice reflect the immune responses of adult humans far better than laboratory mice, suggesting that wild mice may be valuable to inspect aspects of the hygiene hypothesis, immune functioning and potential treatment of autoimmune and inflammatory disorders

Methods

Results

Conclusion