The evolution and changing ecology of the African hominid oral microbiome
James A. Fellows Yates, Irina M. Velsko, Franziska Aron, Cosimo Posth, Courtney A. Hofman, Rita M. Austin, Cody Parker, Allison E. Mann, Kathrin Nägele, Kathryn Weedman Arthur, John Arthur, Catherine Bauer, Isabelle Crèvecoeur, Christophe Cupillard, Matthew C. Curtis, Love Dalén, Marta Díaz‐Zorita Bonilla, Juan Carlos Díez Fernández-Lomana, Dorothée G. Drucker, Elena Escribano Escrivá, Michael Francken, Victoria E. Gibbon, Manuel R. González Morales, Ana Grande Mateu, Katerina Harvati, Amanda G. Henry, Louise Humphrey, Mario Menéndez, Dušan Mihailović, Marco Peresani, Sofía Rodríguez Moroder, Mirjana Roksandić, Hélène Rougier, Sandra Sázelová, Jay T. Stock, Lawrence Guy Straus, Jiřı́ Svoboda, Barbara Teßmann, Michael Walker, Robert C. Power, Cecil M. Lewis, Krithivasan Sankaranarayanan, Katerina Guschanski, Richard W. Wrangham, Floyd E. Dewhirst, Domingo C. Salazar‐García, Johannes Krause, Alexander Herbig, Christina Warinner
Abstract
Significance The microbiome plays key roles in human health, but little is known about its evolution. We investigate the evolutionary history of the African hominid oral microbiome by analyzing dental biofilms of humans and Neanderthals spanning the past 100,000 years and comparing them with those of chimpanzees, gorillas, and howler monkeys. We identify 10 core bacterial genera that have been maintained within the human lineage and play key biofilm structural roles. However, many remain understudied and unnamed. We find major taxonomic and functional differences between the oral microbiomes of Homo and chimpanzees but a high degree of similarity between Neanderthals and modern humans, including an apparent Homo -specific acquisition of starch digestion capability in oral streptococci, suggesting microbial coadaptation with host diet.