Social, Environmental, and Genetic Predictors of Microbiome Composition in Wild Baboons

Microbial communities that reside in the mammalian gut, commonly referred to as the gut microbiome, have profound consequences for host physical functioning, with well-described roles in digestion, vitamin synthesis, and immune regulation. However, our understanding of the factors that shape gut microbial composition, and the relative importance of these forces across scales, is limited. To wit, my dissertation research seeks to answer two main questions: how does a host’s genetic, social, and ecological context shape the gut microbiome? And, furthermore, do the contributions of these factors change across scales, from individual hosts, to their societies and populations?

To address these questions, I used behavioral, environmental, microbial, and genetic analyses to investigate predictors of gut microbial heterogeneities at the level of the host individual, the social group, the population, and the host species. I did so using data from a well-studied population of wild baboons in the Amboseli Ecosystem in Kenya that has become a model for microbiome research. I found that baboon gut microbiomes were strongly predicted by host environments at multiple scales, including both social and abiotic environmental conditions. For instance, for individuals sampled over several years, rainfall and diet were the most important predictors of gut microbiome composition. Over short time scales, social groups harbored distinctive gut microbiota, and immigrant males acquired the local microbiome when they joined a new group. Further, social groups with larger home ranges and more environmental resources harbored more diverse gut microbiota, and social groups that shared environmental resources likewise shared more microbial taxa than pairs of groups with less overlap. Finally, to explore large-scale processes, I tested predictors of gut microbiome composition from baboons living in multiple sites across a hybrid zone in southern Kenya. I found that soil properties were the best predictors of between-population gut microbial heterogeneities, with much stronger effects than either host genetics or geographic distance. Overall, my dissertation lends new insight into the dominant forces shaping the gut microbiome in a wild, group-living animal, and how the gut microbiome is sculpted at the level of the individual, social group, population, and species.