Doing DNA differently: A bioarchaeological secondary exploration of Brucella in ancient metagenomes in the NCBI SRA

Abstract

The use of biomolecular methods in bioarchaeological studies of health and disease offer novel insights into the dynamics of disease presence and prevalence in the past, such as pathogen evolution, human–pathogen–environmental interactions, and contexts of disease transmission. However, a growing awareness among public stakeholders and anthropologists of the ethical imperative to preserve human remains wherever possible has given rise to non- and minimally-destructive methods for biomolecular research. Metagenomic approaches represent one such avenue for research when applied to secondary analyses of previously sequenced aDNA. To this end, this study screened for the presence of Brucella aDNA in archaeological human metagenomes published in the NCBI Sequence Read Archive (SRA) using three methods—one alignment-based and two alignment-free. The results suggest the possible but still unconfirmed presence of Brucella or related sequences in a set of sequencing runs from two Late/Final Jomon individuals from the Sanganji Shell Mound site, Japan (ca. 2994 ± 19 BP and ca. 3061 ± 19 BP). Given the inconclusive results, alternate explanations are also explored and future analyses in this regard are proposed. In situating the utility of bioinformatics approaches and tools within a research framework inspired by biocultural theory, this study presents a heuristic approach to integrating non-destructive secondary analyses of mined metagenomic data with anthropological insights.