The gut microbiome plays a crucial role in the nutritional ecology of mammalian herbivores, yet studies in nature often rely on fecal samples from a single time period to inventory gut microbial communities. Although we know that environmental variables such as diet and season can impact the stability of the microbiome, we have little understanding of whether these communities vary within an individual overtime, particularly in natural setting. To test the temporal stability of the gut microbiome at the individual level, we marked and recaptured Bryant’s woodrats (Neotoma bryanti) in the Mojave Desert. We inventoried the gut microbial community of each individual with 16s rRNA gene sequencing and used plant metabarcoding for diet quantification across 2 years of sampling.
Results/Conclusions:
We found that gut microbiota as estimated in fecal samples remained largely stable at the individual level over time, even spanning several months. However, some individuals displayed large shifts in microbial community structure that were correlated with changes in diet, season, and reproductive phases. We identified microbial families that remain mostly stable in relative abundance over time (e.g. Muribaculaceae and Ruminococcaceae), and families that were more variable (e.g. Lactobacillaceae and Lachnospiraceae). These results suggest that while there is strong host influence over the gut microbial community, seasonal changes in diet and reproductive status can alter its structure.