Food or family? How gut microbes respond to diet and phylogeny in two deer species

Vertebrate herbivores require symbiotic gastrointestinal (GI) microbes to extract energy and nutrients from fibrous and sometimes toxic plant diets. Because GI microbes vary in their relative abundance, function, and degree of specialization, the microbial community depends on both the characteristics of plants consumed and the anatomical, physiological, and behavioral characteristics of the herbivore host. To tease apart the relative contribution of diet and herbivore phylogeny to the microbiome, we leveraged a unique study system in which mule deer (Odocoileus hemionus) and white-tailed deer (O. virginianus) had been hand-raised from neonates to adulthood in identical conditions on a pelleted ration, then transitioned over 2 weeks in the spring onto natural plant diets as they foraged together in the same habitats across summer, then transitioned back onto the pelleted ration in late summer. We determined the plant composition and nutritional quality of the deers' diets using bite count techniques and analyzed 16S rRNA genes of their feces to determine microbial diversity and composition. Our experiments demonstrated that the GI microbial community of congeneric deer responded to characteristics of both diet and deer species. Alpha and beta microbial diversity and microbial composition differed when deer consumed the pelleted ration versus natural browse and varied with other dietary characteristics including plant diversity, composition of plant functional groups, and nutritional constituents. Microbial communities of the two deer species responded differently to dietary changes, but most strongly when deer selected different natural plant diets. Despite controlling early experience, innate behavior and physiological differences between species likely influenced the GI microbiome. Our findings underscore the potential disruption in GI microbial communities with rapid diet changes and the importance of diverse, high-quality forages for wild ruminants. A better understanding of how sympatric herbivores use the same available resources is crucial for predicting the consequences of increasing overlap in wildlife distributions with climate change and human disturbances.