Exploring DNA preservation and taxonomic diversity in postmedieval human tooth samples in Latvia.

Ancient DNA (aDNA) provides unique opportunities to explore various evolutionary and ecological processes. In particular, aDNA studies offer new possibilities for the in-depth investigation of historical social structures at local and regional scales, reconstruction of ancient human microbiomes, and identification of ancient pathogens. The success of these studies depends on the preservation of aDNA, as well as on our ability to distinguish between authentic aDNA, either human, animal or microbial, and contaminant DNA from other sources. The aim of this study was to examine the preservation of aDNA in human postmedieval archaeological tooth samples in Latvia dated 15th–17th century AD. The taxonomic composition of the short DNA fragment fractions was compared to that of the total DNA samples to explore the presence and diversity of environmental bacteria in aDNA datasets.Samples were analyzed by a shotgun metagenomics-based approach. The taxonomic profiles of metagenomics data revealed that the majority of microbial phyla/genera/species belonged to the typical soil microbiota, indicating the contamination of archaeological samples by environmental microorganisms. The proportions of both human and oral microbial DNA were significantly higher in the short DNA fragment libraries than in the total DNA samples, and DNA reads showed characteristic damage patterns, suggesting severe degradation of endogenous aDNA. The aDNA yield obtained in this study was sufficient to perform molecular sex typing, and the genetic results confirmed morphological data in all cases.Overall, sufficient preservation of endogenous aDNA was detected in human archaeological tooth samples in Latvia dated 15th–17th century AD, which enables future studies on early-modern populations and pre-industrial oral microbial communities. The analysis of total DNA samples along with short DNA fragments may provide additional information, such as the microbial composition of the burial environment. Concomitant analysis of environmental DNA could provide additional data for deciphering the complete ancient microbiome profiles.