Evolution and Ecology of the Human Oral Microbiome

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The human microbiome, the sum total of bacteria that live in and on the human body, harbors 90% of our cells and 99% of our genes, and plays a critical role in performing many basic human life functions. And yet, we know very little about its diversity, variation, and evolution. The human oral cavity alone harbors a complex ecosystem containing more than 1,000 microbial species, and this oral microbiome has been associated with tooth decay, cardiovascular disease and a range of respiratory illnesses. Recently it has been discovered that dental calculus (calcified dental plaque) entraps a rich record of the oral microbiome that preserves for thousands of years. The objective of this study is to use metagenomic and metaproteomic approaches to systematically characterize the oral microbiome of chimpanzees and humans from the Paleolithic to the present. This study will contribute to reconstructing the human oral microbiome through time and understanding the origins of common oral pathogens and diseases. Findings from this study will also contribute to student training, and public science outreach and education. Few studies have conducted basic research on the natural variation of the human oral microbiome or on changes in the oral microbiome through time. As a result little is known about the origins and evolutionary ecology of the human oral microbiome. Recently it has been discovered that dental calculus (calcified dental plaque) entraps a rich biomolecular record of the oral microbiome that preserves for thousands of years. This project will use state-of-the-art metagenomic and metaproteomic technologies to characterize the microbes of the oral cavity collected from chimpanzees and extinct and extant members of Homo: archaic Homo heidelbergensis (ca. 430,000 BP), Paleolithic H. sapiens (ca. 23,000 BP and 20,000 BP), Chalcolithic H. sapiens (ca. 4,000 BP), and present-day humans and chimpanzees. These samples will provide a path to reconstructing the the human oral microbiome over the course of hominin evolution.