Animals host trillions of bacteria and other microorganisms that play a crucial role in digestion, immune system development, and toxin metabolism. Although changes in this microbiome are linked to negative fitness outcomes, healthy individuals also exhibit extensive natural variation. Factors such as diet, geography, and evolutionary history can influence microbiome structure, but their relative importance remains contested. Here, using the herbivorous rodent genus Neotoma, we experimentally measured how diet, geography, and evolutionary history contribute to gut microbiome structure. We sampled 25 Neotoma populations, representing 7 species from 19 sites in Southwestern North America. We collected feces from free-ranging individuals and then brought animals into captivity for one month, on a common diet, before resampling. We characterized the gut microbiome and natural diets using 16s rRNA and chloroplast trnL gene sequencing, respectively, and then quantified how diet, geography, and evolutionary history contributed to structuring the gut microbiome under both natural and controlled conditions.
Results/Conclusions
Diet analyses revealed substantial variation in both diet composition and specialization. Across all sampled populations, the native microbiome was predominantly composed of bacteria from the orders Bacteroidales, Clostridiales, and Lactobacillales. Native microbiomes differed among populations in both alpha and beta diversity. In wild animals, geography, diet, and evolutionary history together explained approximately 50% of observed variation in the microbiome. Although all three significantly contributed to microbiome structure, diet, followed closely by phylogeny, explained the majority of variation. Captivity significantly altered the microbiome in species-specific ways. When the selective forces of diet and geography were removed by housing animals in a controlled captive environment, phylogeny became the most important predictor of observed variation, although differences due to past diet and geography were still detectable. These results suggest that geography, diet and evolutionary history all contribute to structuring the gut microbiome, particularly in natural environments. Furthermore, by controlling the substantial influence of dietary differences, the results provide strong evidence of “phylosymbiosis” and host genetic control of the gut microbiome.