Burial-associated microbial communities in Early Modern human remains: evidence for postmortem ecological restructuring revealed by 16S rRNA sequencing

Microbial communities preserved in archaeological human remains represent dynamic ecological systems shaped by host-associated microbiota, local environmental conditions, and postmortem succession. To investigate the persistence and structure of these communities, bacterial assemblages associated with Early Modern burials (1650–1800 CE) from two Early Modern burial sites in the Czech Republic two sites in Bohemia (the Czech Republic) were analysed using Illumina sequencing of the V3–V4 region of the 16S rRNA gene. Samples included teeth, abdominal sediments, environmental control soils, a non-human bone control, and cultivation-derived isolates. Community composition was evaluated using diversity indices, principal coordinate analysis (PCoA), and multivariate statistics. Burial-associated samples exhibited pronounced heterogeneity and several specimens were characterized by extreme dominance of individual genera. Despite this variability, significant differences in community composition were detected between the two sites, whereas no significant differences were observed between dental samples and abdominal sediments. Filtering analyses based on human-associated taxa revealed clearer separation between burial-associated samples and environmental controls, indicating that dominant soil bacteria partially obscure biologically meaningful patterns. Cultivation-derived communities formed distinct assemblages, demonstrating the strong selective effect of laboratory cultivation. Overall, the results suggest that archaeological microbial communities do not represent simple reflections of surrounding soils or direct preservation of ante-mortem microbiota, but rather dynamic ecological systems shaped by postmortem processes, local environmental conditions, and long-term ecological filtering.