Investigating short-term dynamics of gut microbiome composition in the Western deer mouse

The gut microbiome plays an important role in mammalian host health and ability to adapt to environmental conditions. While the gut microbiome is often considered fairly stable over short periods of time in the absence of a dramatic stressor, relatively little is known about the actual time scale of microbiome shifts, particularly in wildlife species. Most existing temporal studies utilize captive subjects, while here we employ the Western deer mouse, Peromyscus sonoriensis, in a field-based study to assess short-term microbiome dynamics (less than two days) in the wild. Mice were live-trapped at several urban and rural parks over a two-night trapping period in and around Spokane, Washington, USA in May of 2024. We collected fecal samples from 43 different individuals, capturing two to four time points per individual, and bacterial community composition was determined via 16S profiling with Nanopore sequencing. Genus-level profiles were compared across time points for each individual, showing relative consistency in types of taxa present for most mice, but some marked shifts in Ligilactobacillus in some mice. Calculation of intraclass correlation coefficients, however, showed low stability in alpha diversity (Shannon index) over time, suggesting greater variability than initially anticipated. Analysis with respect to site urbanization, sex, and age showed a significant effect of age when accounting for homogeneity of variance, with additional exploration of urbanization and sex needed in future work. These results provide important insight into the understudied area of host microbiome dynamics and highlight the complex relationships between microbiome, health, and environment.