Biology Faculty Proceedings, Presentations, Speeches, Lectures


Profiles of Microbial Diversity and Function with Museum Dental Calculus Samples Extracted from Wild Great Apes

Event Name/Location

8th International Symposium on Biomolecular Archaeology (ISBA) 2018 / Friedrich-Schiller-University of Jena

Document Type

Conference Presentation

Publication Date



An understanding of the great ape microbiome is imperative to assessing the distribution of commensal and pathogenic oral bacteria across all primates. As access to saliva or plaque samples from living wild chimpanzees and gorillas is not feasible, an abundant alternative resource is calcified dental plaque removed from skeletons housed within museums. We obtained permission to remove dental calculus from 191 great apes (Gorilla n=76, Pan n=90, Pongo n=25) from four museums across the United States: Academy of Natural Sciences (Philadelphia, PA), Cleveland Museum of Natural History (Cleveland, OH), Field Museum of Natural History (Chicago, IL), and National Museum of Natural History (Washington D.C.). Twenty-four of those samples that yielded the highest abundance of DNA (yields range from 0.1 ng/µl to 70.3 ng/µl) have been selected to represent the oral microbial environment of wild apes. Each calculus sample was thoroughly decontaminated and extracted in a dedicated ancient lab at Arizona State University and shotgun prepped and sequenced using Illumina next generation sequencing. These samples will be quality filtered and examined using MEGAN and Humann2, with additional comparisons to Pan troglodytes schweinfurthii calculus from Gombe National Park in Tanzania and previously published metagenomic data from ancient and historic human calculus. Wild P. t. schweinfurthii oral microbiomes show an abundance of bacteria belonging to the "Red Complex", particularly Porphyromonas gingivalis, but the extent of this abundance across species and geography is not well known. We will discuss the implications of these commensal and pathogenic microbes along with their functional profiles on our understanding of the evolution of the human and non-human primate oral ecosystem and assess future directions of research utilizing museum collections.