The evolution and changing ecology of the African hominid oral microbiome

• Authors: YATES James A. Fellows; VELSKO Irina M.; ARON Franziska; POSTH Cosimo; HOFMAN Courtney A.; AUSTIN Rita M.; PARKER Cody E.; MANN Allison E.; NÄGELE Kathrin; ARTHUR Kathryn Weedman; ARTHUR John W.; BAUER Catherine C.; CREVECOEUR Isabelle; CUPILLARD Christophe; CURTIS Matthew C.; DALÉN Love; BONILLA Marta Díaz-Zorita; FERNÁNDEZ-LOMANA J. Carlos Díez; DRUCKER Dorothée G.; ESCRIVÁ Elena Escribano; FRANCKEN Michael; GIBBON Victoria E.; MORALES Manuel R. González; MATEU Ana Grande; HARVATIT Katerina; HENRY Amanda G.; HUMPHREY Louise; MENÉNDEZ Mario; MIHAILOVIĆ Dušan; PERESANI Marco; MORODER Sofía Rodríguez; ROKSANDIC Mirjana; ROUGIER Hélene; SÁZELOVÁ Sandra; STOCK Jay T.; STRAUS Lawrence Guy; SVOBODA Jiří; TEßMANN Barbara; WALKER Michael J.; POWER Robert C.; LEWIS Cecil M.; SANKARANARAYANAN Krithivasan; GUSCHANSKI Katerina; WRANGHAM Richard W.; DEWHIRST Floyd E.; SALAZAR-GARCÍA Domingo C.; KRAUSE Johannes; HERBIG Alexander; WARINNER Christina
• Year of publication: 2021
• Type: Article in Periodical
• Magazine / Source: Proceedings of the National Academy of Sciences of the United States of America
• MU Faculty or unit: Faculty of Science
• web: https://www.pnas.org/content/pnas/118/20/e2021655118.full.pdf
• Doi: http://dx.doi.org/10.1073/pnas.2021655118
• Keywords: dental calculus; microbiome; Neanderthal; primate; salivary amylase
• Description: The oral microbiome plays key roles in human biology, health, and disease, but little is known about the global diversity, variation, or evolution of this microbial community. To better understand the evolution and changing ecology of the human oral microbiome, we analyzed 124 dental biofilm metagenomes from humans, including Neanderthals and Late Pleistocene to present-day modern humans, chimpanzees, and gorillas, as well as New World howler monkeys for comparison. We find that a core microbiome of primarily biofilm structural taxa has been maintained throughout African hominid evolution, and these microbial groups are also shared with howler monkeys, suggesting that they have been important oral members since before the catarrhine-platyrrhine split ca. 40 Mya. However, community structure and individual microbial phylogenies do not closely reflect host relationships, and the dental biofilms of Homo and chimpanzees are distinguished by major taxonomic and functional differences. Reconstructing oral metagenomes from up to 100 thousand years ago, we show that the microbial profiles of both Neanderthals and modern humans are highly similar, sharing functional adaptations in nutrient metabolism. These include an apparent Homo-specific acquisition of salivary amylase-binding capability by oral streptococci, suggesting microbial coadaptation with host diet. We additionally find evidence of shared genetic diversity in the oral bacteria of Neanderthal and Upper Paleolithic modern humans that is not observed in later modern human populations. Differences in the oral microbiomes of African hominids provide insights into human evolution, the ancestral state of the human microbiome, and a temporal framework for understanding microbial health and disease.