ABSTRACT
Diet and host identity play fundamental roles in digestive physiology and the assembly of gut microbial communities. Research shows that microbial communities are plastic, with abundances of taxa and community interactions exhibiting changes in response to diet. Few studies considering the influence of diet on host and microbial plasticity disentangle the unique roles of specific nutrients, such as protein and fiber. Additionally, in the context of host–microbiome interactions, few studies have explored how host dietary strategies shape the plastic responses of microbial communities within the host digestive tract. To address these current gaps, we fed rodents with distinct dietary strategies (Peromyscus leucopus, Microtus montanus and Onychomys torridus) diets varying in fiber and protein content. Species varied in the degree of cecum size plasticity, with the carnivore showing no significant changes and the omnivore responding to both fiber and protein manipulation. There were also differences in the diversity indices of bacterial and fungal communities across hosts, and the microbes driving those differences were largely unique across rodent species. Additionally, community network interactions varied across treatments, and hub taxa that play a role in regulating network properties were identified. For example, bacteria in the Eubacterium groups, which are known to aid in fiber fermentation, were identified as hub taxa in all three species, but no group shared the same Eubacterium as a hub taxa. Overall, our data suggest that hosts with unique dietary strategies and their microbiomes respond uniquely to changes in the nutrient composition of their diets.
Footnotes
Author contributions
Conceptualization: N.B., B.T., K.D.K.; Data curation: N.B., B.T., K.D.K.; Formal analysis: N.B.; Funding acquisition: K.D.K.; Investigation: N.B., B.T., M.D.D., R.M.-M., B.P., K.D.K.; Methodology: N.B., B.T., R.M.-M., B.P., K.D.K.; Project administration: M.D.D., K.D.K.; Resources: M.D.D., B.P., K.D.K.; Validation: M.D.D.; Visualization: N.B., K.D.K.; Writing – original draft: N.B.; Writing – review & editing: N.B., B.T., M.D.D., R.M.-M., B.P., K.D.K.
Funding
This project was funded by the National Science Foundation (IOS 1942587 to K.D.K.).
Data and resource availability
Data and code are available at https://github.com/nickrbarts/Rodent_Microbiome
Special Issue
This article is part of the special issue ‘The Integrative Biology of the Gut’, guest edited by Carol Bucking, Matt Regan and John Terblanche. See related articles at https://journals.biologists.com/jeb/issue/228/14.
