Hominid Dental Metagenomes for Pathogen Evolution Research

Dental cavities and periodontal disease, both major oral health problems in today’s world, are caused by opportunistic bacterial pathogens found in the mouth. This project focuses on the evolutionary history of these pathogens, examining how the genomes of oral pathogens differ across a comparative sample of primate species, and, within humans, how they are impacted by changes in dietary practices, geographic space, and time.

Through this comparative research and the study of oral pathogen genomes recovered from ancient human populations, this project advances knowledge about pathogen evolution in humans over thousands of years and provides further insight into the relationships between host behavior and pathogen evolution. The project benefits from a team-science approach that involves close collaboration, as well as academic attribution, for descendent communities of the ancient human populations being studied.

Project findings are communicated to these communities through public talks focusing on the impact of oral disease, contextualized by microbiome research. The project also contributes to the professional development of researchers through online workshops focusing on ancient microbiome data analysis, supports open science by publication in open-access journals and sharing data through public repositories, and promotes the broader participation of women in STEM through student training and mentoring activities.

The transition from a hunter-gatherer to an agricultural lifestyle, as well as the advent of industrialization, are thought to have increased the prevalence of oral disease in humans. However, the way that these transitions affected oral pathogens at a genomic level, especially in terms of their diversity and virulence, have not been fully characterized.

Additionally, the broader primate comparative context of oral pathogen diversity is not well understood. In this project, the investigators reconstruct oral pathogen genomes from dental calculus, a calcified form of dental plaque. Dental calculus is known to preserve biomolecules for thousands of years and provides a wealth of information regarding the host, oral bacteria, and diet.

Calculus samples are collected from museum specimens of nonhuman primates (chimpanzees, gorillas, and orangutans), and from ancient human populations from the continents of Africa and the Americas. From both continents, samples are retrieved from the same geographic location but from time periods associated with different dietary strategies (hunter-gatherer versus agriculture).

The investigators use state-of-the-art ancient DNA protocols, metagenomic sequencing, and target enrichment strategies to generate high-quality genome data for oral pathogens found in these samples. These genome data provide a nuanced understanding of the evolutionary relationships between oral pathogen strains affecting different host species, and how oral pathogen strain diversity and genomic architecture have changed over time and space.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.