This funding supported the investigation of the evolution and ecology of the human oral microbiome. Recently, our research team demonstrated that calcified dental plaque, also known as  tooth tartar or dental calculus, is a robust and long-term reservoir of DNA from the oral microbiome. Being mineralized, dental calculus is resistant to decay, but until now it was not known how long DNA survived in dental calculus or what insights might be gained about the history and origins of oral microbiome-associated diseases, such as periodontal disease and caries, by studying this substrate in archaeological and historical skeletal collections. Focusing on an extraordinary set of more than 300 dental calculus samples obtained from New World monkeys (howler monkeys), great apes (gorillas, chimpanzees), Neanderthals, and humans (Paleolithic through present-day), we document the evolution of the oral microbiome in the hominoid lineage. We find that by applying advanced ancient DNA technologies, authentic DNA from the oral microbiome can be successfully recovered from dental calculus samples more than 70,000 years old. Through this research we describe the core hominoid oral microbiome, define the bacterial taxa and ecological patterns that characterize specific primate species, and establish the antiquity of periodontal pathogens. We show that oral bacteria generally exhibit patterns of co-speciation with their hosts, and that the genetic diversity of oral bacteria in Neanderthals is distinct from that of the great apes and typically falls within the range of variation of anatomically modern humans. We additionally find that contrary to previous studies, health-associated bacterial taxa, such as Streptococcus and Neisseria, are more abundant in calculus today than in the past, which may be the result of modern oral hygiene regimens. We also find that Tannerella forsythia, a species associated today with periodontal disease, was both prevalent and abundant in past human populations - irrespective of disease - and that it is today found at relatively high levels in living chimpanzee populations. Finally, our findings additionally call into question whether bacterial species conventionally regarded in clinical contexts as pathogenic, such as Porphyromonas gingivalis, Treponema denticola, Tannerella forsythia, Methanobrevibacter oralis, and Desulfobulbus spp., are in fact causal of pathology or simply markers of biofilm maturity. Such findings have broad-scale implications for the diagnosis of periodontal diseases and their treatment. In addition to these main findings, we have also published the first major study of small molecule metabolite preservation in dental calculus, and we have substantially contributed to the understanding of protein preservation in dental calculus. To date, this project has resulted in 14 conference presentations and 12 peer-reviewed publications, of which 9 are open access publications, and all genetic and proteomic data associated with project publications have been made available through public repositories. This project has contributed to the STEM training of three postdocs, six PhD students, and two Master's students. Finally, this project has resulted in 15 public lectures, contributed to K-12 educational material made available on the PI's research website, and contributed to interactive exhibits on genetics and microscopy at K-12 public science education events. 

Last Modified: 10/05/2018
Modified by: Christina G Warinner