Biology Faculty Proceedings, Presentations, Speeches, Lectures

Adventures in Museuomics: The Use of Next Generation Sequencing to Uncover Great Ape Host and Microbial Genomes

Event Name/Location

88th Annual Meeting of the American Association of Physical Anthropologists / Cleveland, Ohio, USA

Presntation Date


Document Type

Conference Presentation





Proceeding Title

Program of the 88th Annual Meeting of the American Association of Physical Anthropologists


An understanding of the great ape microbiome is imperative to assessing the distribution of commensal and pathogenic bacteria across primates. As access to saliva or plaque samples from living wild chimpanzees and gorillas is typically not feasible, an alternative resource is calcified dental plaque removed from skeletons in museum collections. Here, we use dental caclulus recovered from great ape collections from four U.S. museums to address questions of host and microbial genetic variation; specifically, how do oral microbiomes differ by host species and how much does the human microbiome differ from that of other primates? Decontamination and extraction protocols were used to process 40 calculus samples in a dedicated ancient DNA facility, followed by shotgun amplification and Illumina next generation sequencing. In a normalized MEGAN analysis, a Bray-Curtis PCoA of great ape oral microbial signatures showed no evidence of clustering based on host species or the museum from which they were initially collected. We also report significant differences in abundance across members of the red complex including Porphyromonas gingivalis(higher in chimpanzees and gorillas) and Treponema denticola (higher in orangutans and historic human samples). Despite obtaining primarily microbial sequences from our analyses, we were able to reconstruct full mitogenomes in 5 of the samples and discern subspecies (for those unreported in museum records). We will discuss the implications of these findings on our understanding of the evolution of the human and non-human primate oral ecosystem and assess future directions of research utilizing museum collections.

First Page


Last Page



Funding for this research was provided by the Center for Evolution and Medicine at Arizona State University and the Extreme Science and Engineering Discovery Environment (XSEDE) (NSF ACI-1548562).