A minimal hybridization capture approach for the parallel enrichment and cost-effective detection of ancient human pathogens.

The preservation of ancient DNA in archaeological remains enables the identification of past disease agents. However, pathogen DNA is typically highly diluted by host and environmental DNA, limiting detection. Here, we present a proof-of-concept study in which RNA probes for in-solution hybridization capture were designed to improve the detectability of a predefined set of 12 pathogens. We validate the method by reporting enrichment rates of ∼2,000-folds for Yersinia pestis in six individuals from 17th and 18th century French plague cemeteries, enabling the detection of the plague agent with minimal sequencing. Pending further empirical validation on a broader set of microbial species, expanding our approach to target biomarkers of virtually any pathogen of interest offers a powerful tool for tracking the prevalence of infectious diseases in ancient populations.