@article {324562,
	title = {The evolution and changing ecology of the African hominid oral microbiome},
	journal = {Proceedings of the National Academy of Sciences},
	volume = {118},
	year = {2021},
	month = {2021/05/18},
	pages = {e2021655118},
	abstract = {<p>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.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{\textendash}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.All newly generated sequencing data have been deposited in the ENA repository (https://www.ebi.ac.uk/ena/browser/home) under project accession ID PRJEB34569. R notebooks, bioinformatic scripts, additional supporting figures, and intermediate analysis files are provided in an external data repository hosted on GitHub (http://github.com/jfy133/Hominid_Calculus_Microbiome_Evolution) and archived with Zenodo under DOI: 10.5281/zenodo.3740493.May 12, 2021: The author line has been updated.</p>
},
	doi = {https://doi.org/10.1073/pnas.2021655118},
	url = {https://www.pnas.org/content/118/20/e2021655118},
	author = {Fellows Yates, James A. and Velsko, Irina M. and Aron, Franziska and Posth, Cosimo and Hofman, Courtney A. and Austin, Rita M. and Parker, Cody E. and Mann, Allison E. and N{\"a}gele, Kathrin and Arthur, Kathryn Weedman and Arthur, John W. and Bauer, Catherine C. and Crevecoeur, Isabelle and Cupillard, Christophe and Curtis, Matthew C. and Dal{\'e}n, Love and D{\'\i}az-Zorita Bonilla, Marta and D{\'\i}ez Fern{\'a}ndez-Lomana, J. Carlos and Drucker, Doroth{\'e}e G. and Escribano Escriv{\'a}, Elena and Francken, Michael and Gibbon, Victoria E. and Gonz{\'a}lez Morales, Manuel R. and Grande Mateu, Ana and Harvati, Katerina and Henry, Amanda G. and Humphrey, Louise and Men{\'e}ndez, Mario and Mihailovi{\'c}, Du{\v s}an and Peresani, Marco and Rodr{\'\i}guez Moroder, Sof{\'\i}a and Roksandic, Mirjana and Rougier, H{\'e}l{\`e}ne and S{\'a}zelov{\'a}, Sandra and Stock, Jay T. and Straus, Lawrence Guy and Svoboda, Ji{\v r}{\'\i} and Te{\ss}mann, Barbara and Walker, Michael J. and Power, Robert C. and Lewis, Cecil M. and Sankaranarayanan, Krithivasan and Guschanski, Katerina and Wrangham, Richard W. and Dewhirst, Floyd E. and Salazar-Garc{\'\i}a, Domingo C. and Krause, Johannes and Herbig, Alexander and Warinner, Christina}
}
