Although the critical role that our gastrointestinal microbes play in host physiology is now well established, we know little about the factors that influenced the evolution of primate gut microbiomes. To further understand current gut microbiome configurations and diet-microbe co-metabolic fingerprints in primates, from an evolutionary perspective, we characterized fecal bacterial communities and metabolomic profiles in 228 fecal samples of lowland and mountain gorillas (G. g. gorilla and G. b. beringei, respectively), our closest evolutionary relatives after chimpanzees. Our results demonstrate that the gut microbiomes and metabolomes of these two species exhibit significantly different patterns. This is supported by increased abundance of metabolites and bacterial taxa associated with fiber metabolism in mountain gorillas, and enrichment of markers associated with simple sugar, lipid and sterol turnover in the lowland species. However, longitudinal sampling shows that both species' microbiomes and metabolomes converge when hosts face similar dietary constraints, associated with low fruit availability in their habitats. By showing differences and convergence of diet-microbe co-metabolic fingerprints in two geographically isolated primate species, under specific dietary stimuli, we suggest that dietary constraints triggered during their adaptive radiation were potential factors behind the species-specific microbiome patterns observed in primates today.
Bibliographical noteFunding Information:
We thank the government of the Central African Republic, namely the Ministre de l’Education Nationale, de l’Alphabetisation, de l’Enseignement Superieur, et de la Recherche for providing research permits to conduct our work in the Central African Republic; World Wildlife Fund and the administration of DSPA for granting research approval and for assistance with obtaining permits; and the Primate Habituation Programme for providing logistical support in the field. We especially thank Dr Paul Garber (University of Illinois) and two anonymous reviewers for very important comments on this manuscript. Finally, we thank all of our field assistants and trackers for their help in the field. This work was supported by a Grant Agency of the Czech Republic (number 206/09/0927), NSF grant 0935347 and COLCIENCIAS (Colombian Agency for Science and Technology) and its doctoral fellowship program. This publication derives from the HPL-lab, Laboratory for Infectious Diseases Common to Humans and (non-Human) Primates, Czech Republic. This study was supported by the project ‘CEITEC-Central European Institute of Technology’ (CZ.1.05/1.100/02.0068) from European Regional Development Fund and further cofinanced from European Social Fund and state budget of
the Czech Republic (project OPVK CZ.1.07/2.3.00/ 20.0300). The research in Bwindi was supported by Hunter College. We thank Hillary Musinguzi and the park rangers of Bwindi for assisting with sample collection, and Pontious Ezuma, Chemonges Amusa and Simplicious Gessa for logistical support. The Uganda Wildlife Authority and the Uganda National Council for Science and Technology gave JMR permission to conduct this research.