The evolution and changing ecology of the African hominid oral microbiome

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–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.Results - Preservation of Oral Microbiota in Dental Calculus. - The Core African Hominid Oral Microbiome. - African Hominid Oral Microbiome Structure Shows a Weak Relationship with Host Phylogeny. - Evolutionary Histories of Oral Microbial Species Reflect Homo Interactions. - Homo-Specific Shifts in Oral Biofilm Are Linked to Dietary Starch - Availability. Discussion Materials and Methods - Materials. - Laboratory Methods. - Data Processing and Quality Filtering. - Taxonomic Binning and Preservation Assessment. - Microbial Compositional Analysis. - Core Microbiome Analysis. - Genomic Analysis. - Microbial Phylogenetics. - Functional and Metabolic Pathway Analysis