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00925njm 22002777a 4500 dc Fellows Yates, James A. author Velsko, Irina M. author Aron, Franziska author Posth, Cosimo author Hofman, Courtney A. author Austin, Rita M. author Parker, Cody E. author Mann, Allison E. author Nägele, Kathrin author Arthur, Kathryn Weedman author Arthur, John W. author Bauer, Catherine C. author Crevecoeur, Isabelle author Cupillard, Christophe author Curtis, Matthew C. author Dalén, Love author Díaz-Zorita Bonilla, Marta author Díez Fernández-Lomana, Juan Carlos author Drucker, Dorothée G. author Escribano Escrivá, Elena author Francken, Michael author Gibbon, Victoria E. author González Morales, Manuel author Grande Mateu, Ana author Harvati, Katerina author Henry, Amanda G. author Humphrey, Louise author Menéndez, Mario author Mihailović, Dušan author Peresani, Marco author Rodríguez Moroder, Sofía author Roksandic, Mirjana author Rougier, Hélène author Sázelová, Sandra author Stock, Jay T. author Straus, Lawrence Guy author Svoboda, Jiří author Teßmann, Barbara author Walker, Michael J. author Power, Robert C. author Lewis, Cecil M. author Sankaranarayanan, Krithivasan author Guschanski, Katerina author Wrangham, Richard W. author Dewhirst, Floyd E. author Salazar-García, Domingo C. author Krause, Johannes author Herbig, Alexander author Warinner, Christina author 2021-05 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. 0027-8424 https://hdl.handle.net/10259/11181 10.1073/pnas.2021655118 1091-6490 Dental calculus Microbiome Neanderthal Primate Salivary amylase The evolution and changing ecology of the African hominid oral microbiome