Dental calculus metagenomics suggest that ecology, rather than host phylogeny, shapes the oral microbiome in closely related gorilla species

Abstract: The oral microbiome can reveal a diverse range of information about its host: dietary habits, oral and respiratory health state and evolutionary past, all influence its composition. Nonetheless, little is known about the relative importance of these factors in shaping the oral microbiome. In this study, we focused on three closely related gorilla subspecies that diverged 10,000-250,000 years ago to evaluate the importance of host ecology and evolutionary relationships in shaping the oral microbiome in closely related species. By using a shotgun metagenomic approach on dental calculus from 43 museum specimens, we found that the oral microbiomes of mountain gorillas are functionally and taxonomically distinct from the other gorilla subspecies, despite close evolutionary relationships between mountain and Grauer’s gorillas. Grauer’s gorillas occupy an intermediate position in terms of taxonomic composition and function of the oral microbiome. This is in line with subspecies-specific differences in dietary components we identified in dental calculus, as well as with the ecological placement of the gorilla subspecies. Our results suggest that ecology or diet, rather than evolutionary relationships, primarily shape the gorilla oral microbiome. Further research will be needed to establish if this is a common feature of oral microbiome differentiation at the early stages of speciation.