The evolution and changing ecology of the African hominid oral microbiome.


Type
Article
Change log
Authors
Fellows Yates, James A  ORCID logo  https://orcid.org/0000-0001-5585-6277
Aron, Franziska 
Posth, Cosimo 
Abstract

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.

Description
Keywords
Neanderthal, dental calculus, microbiome, primate, salivary amylase, Africa, Animals, Bacteria, Biofilms, Biological Evolution, Dental Plaque, Ecology, Geography, Gorilla gorilla, Hominidae, Humans, Metagenome, Microbiota, Mouth, Pan troglodytes, Phylogeny
Journal Title
Proc Natl Acad Sci U S A
Conference Name
Journal ISSN
0027-8424
1091-6490
Volume Title
118
Publisher
Proceedings of the National Academy of Sciences
Sponsorship
European Research Council (617627, 677576)