Archaeomicrobiology of early modern Central European burials

Microbial remains in archaeological contexts have traditionally been studied through ancient DNA, but such approaches are prone to postmortem contamination and DNA degradation. Here we present an alternative perspective, focusing on bacteria that survived long-term burial in encysted or otherwise dormant states. Using Illumina sequencing of samples from two early modern period (1650–1800s) burial sites in Central Bohemia (Czech Republic), we compared bacterial communities preserved in dental remains and abdominal cavity sediments with those from surrounding control soils and additional controls including cow bone and cultivation-derived isolates. Alpha and beta diversity analyses revealed marked differences between anatomical contexts and controls. Shannon indices were consistently higher in control soils, while non-metric multidimensional scaling (NMDS) and PERMANOVA confirmed distinct clustering of dental, abdominal, and soil samples. A SIMPER-like analysis identified Staphylococcus as the dominant genus in abdominal sediments, in contrast to the diverse taxa in control soils, whereas teeth retained oral-associated genera such as Neisseria and Leptotrichia. Cultivation on LB medium yielded a narrower spectrum of taxa, highlighting the selectivity of revival conditions. These findings indicate that microbial communities recovered from archaeological skeletons are not random soil contaminants but reflect encysted bacteria linked to anatomical origin and postmortem processes. By integrating archaeological sampling with microbial ecology, this study contributes to the emerging field of archaeomicrobiology and provides novel insights into long-term bacterial survival in extreme environments.