Seasonal restructuring facilitates compositional convergence of gut microbiota in free-ranging rodents

Gut microbes provide essential services to their host and shifts in their composition can impact host fitness. However, despite advances in our understanding of how microbes are assembled in the gut, we understand little about the stability of these communities within individuals, nor what factors influence its composition over the life of an animal. For this reason, we conducted a longitudinal survey of the gut microbial communities of individual free-ranging woodrats (Neotoma spp.) across a hybrid zone in the Mojave Desert, USA, using amplicon sequencing approaches to characterize gut microbial profiles and diet. We found that gut microbial communities were individualized and experienced compositional restructuring as a result of seasonal transitions and changes in diet. Turnover of gut microbiota was highest amongst bacterial subspecies and was much lower at the rank of Family, suggesting there may be selection for conservation of core microbial functions in the woodrat gut. Lastly, we identified an abundant core gut bacterial community that may aid woodrats in metabolizing a diet of plants and their specialized metabolites. These results demonstrate that the gut microbial communities of woodrats are highly dynamic and experience seasonal restructuring which may facilitate adaptive plasticity in response to changes in diet. The gut bacterial communities of herbivorous woodrats were repeatedly sampled for 2 years to identify what factors influence the stability of microbes in the gut of individuals over their natural lifespan.

Automated summary

This study investigated the gut microbial communities of free-ranging woodrats and found that they exhibited high individuality and underwent compositional restructuring in response to seasonal and dietary changes. The turnover of bacterial subspecies was high, while it was lower at the family level, suggesting conservation of core microbial functions. Additionally, a core gut bacterial community was identified that may aid woodrats in metabolizing plants and specialized metabolites.