The 84th Annual Meeting of the American Association of Physical Anthropologists (2015)

Hunting for pathogens: ancient DNA and the historical record


Anthropology, McMaster University

March 26, 2015 , Gateway Ballroom 4 Add to calendar

Ancient DNA is an increasingly significant line of evidence in the paleopathological toolkit; yet, when samples are from contexts where no known epidemics or plagues are recorded in the historical record, the identification of potential pathogens raises methodological challenges. To address this, a strategy of directly shotgun sequencing samples to identify the metagenome (e.g., all organisms) was implemented, complemented by evidence from ancient literary and archaeological sources. DNA isolated from the dental samples of 57 individuals (1st to 3rd c. A.D., Italy) enabled a species-level characterization of the human microbiome with its range of commensal, pathogenic and symbiotic microorganisms. The microbial profiles indicate very low levels of genera containing potential human pathogens (0.001-0.08%). Conversely, environmental and microbiomic taxa characterize the majority of the sample constituents (e.g., Actinomycetales, Coriobacteriales, Bacteriodales, Bacillales, Clostridiales). A preliminary evaluation of this dataset relied on a stringent analytical approach to authenticate the species-specificity of the genomic data in order to identify disease-associated pathogens as candidates for targeted enrichment coupled with high-throughput sequencing. This analysis is also situated within an interpretive framework drawn from descriptions of causation and symptomology in written texts and the physical environment as it relates to disease ecology (e.g., palaeoenvironmental evidence). Within this multifaceted approach to retrospective diagnoses, a critical question remains – how much analytical weight can be assigned to preliminary genomic data when the presence (or absence) of a particular pathogen is indicated?

This research was supported by the Social Sciences and Humanities Research Council.