Characterization of the gut microbiome of wild Peromyscus sonoriensis in New Mexico, USA

The microbiome is highly important to the physiologies of all multicellular organisms, particularly metazoans. However, the microbiomes of many wild animals remain understudied and poorly understood. Peromyscus mice are commonly used as models of adaptation, mental health, and human disease in biomedical research, and are also common in the environment across North America, frequently coming into close contact with humans. Additionally, Peromyscus sonoriensis are implicated as the primary reservoir for Sin Nombre hantavirus, a rare but severe disease of high morbidity and mortality in humans. Here we characterize the fecal microbiomes of 311 Peromyscus sonoriensis, the western deer mouse, collected from across New Mexico, USA, which will further their usefulness as models of disease and behavior as well as increase our understanding of their ecology. The animals used in this study are geographically diverse, collected from multiple ecoregions, and encompass mice of all ages and sexes. We sequenced the entire 16S rRNA gene in a PCR independent approach and characterized the microbiomes with Shannon entropy, Faith phylodiversity, and weighted UNIFRAC. We found that these mice have diverse microbiomes, with individuals varying in the presence and proportions of various identified bacteria. We analyzed the total population of mice according to age, sex, and trapping location, and found that trapping location was the only condition to significantly impact the microbiome. When the mice were subdivided by the location of collection, there were mild effects of age and sex. When comparing mice from archival museum storage, storage of samples in 95% ethanol resulted in significant alterations to the microbiome when compared to cryopreservation. Differential bacterial family presence was determined using ANCOMBC at the 0.05 significance threshold, and there were many differentially abundant families across all groups of mice. This data set can now be used as a reference for further research into the microbiomes of related Peromyscus species, enhance the use of P. sonoriensis as model laboratory animals, and as a source of novel research questions regarding the physiology of these rodents.