Several studies comparing the gut microbiomes of humans to great apes suggest the importance of host phylogenetic relationships and the co-diversification of microbial lineages with their hosts in shaping the primate microbiome. A better understanding of the primate gut microbiome can provide insight into what aspects of the human microbiome are ancestral and shared among all primates, associated with specific biological or ecological traits throughout the primate phylogeny, or derived and unique to humans.

However, clear gaps exist in our knowledge of the processes shaping the human gut microbiome across evolutionary timescales as well as the potential implications for human adaptation.Ĭomparative analyses of human and non-human primates are powerful tools for exploring the evolutionary history of the human gut microbiome. The gut microbiome likely contributes to these dynamics given that it is strongly influenced by host environmental and lifestyle factors and has diverse influences on host physiology and behavior. A wide body of research explores the influences of these traits on each other in the context of human evolutionary trajectories. Overall, these findings show that diet, ecology, and physiological adaptations are more important than host-microbe co-diversification in shaping the human microbiome, providing a key foundation for comparative analyses of the role of the microbiome in human biology and health.Ĭompared to other primates, humans possess a suite of unique biological and ecological traits, including relatively large brains, increased adiposity, and a diet that incorporates domesticated and cooked foods.

Increased inter-individual variation in the human microbiome may be associated with human dietary diversity or the ability of humans to inhabit novel environments. Given similarities of ancestral human habitats and dietary strategies to those of baboons, these findings suggest that convergent ecologies shaped the gut microbiomes of both humans and cercopithecines, perhaps through environmental exposure to microbes, diet, and/or associated physiological adaptations. Additionally, our data reveal more inter-individual variation in gut microbiome functional potential within the human species than across other primate species, suggesting that the human gut microbiome may exhibit more plasticity in response to environmental variation compared to that of other primates. ResultsĬontrary to expectations from host phylogenetics, we find that human gut microbiome composition and functional potential are more similar to those of cercopithecines, a subfamily of Old World monkey, particularly baboons, than to those of African apes. Here, in an effort to improve our understanding of the human microbiome, we compare gut microbiome composition and functional potential in 14 populations of humans from ten nations and 18 species of wild, non-human primates. Comparative data from non-human primates provide insight into the processes that shaped the evolution of the human gut microbiome and highlight microbiome traits that differentiate humans from other primates.

Old chimpanzee