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 historical DNA fragments, either human, animal, plant or microbial, and contaminant modern environmental DNA. The aim of this study was to examine the preservation of aDNA in human postmedieval archaeological tooth samples in Latvia dated 15th–17th century CE. 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. No significant differences in alpha or beta diversity indices were found between the short and total DNA fractions. The presence of soil microbiota in the short DNA fractions and the discordance between the microbial patterns suggested the fragmentation of the historical environmental DNA. 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 human 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 CE, 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 historical and modern environmental DNA could provide additional data for deciphering the complete ancient microbiome profiles.