Insights into demographic and cultural influences on the oral microbiome from historical Japanese dental calculus

Abstract

Recent advances in genomic technologies have enabled detailed analyses of ancient microbiomes using dental calculus. While most studies have focused on European and North American populations, ancient Japanese oral microbiomes remain largely unexplored. Here, we analyzed dental calculus primarily from Edo period individuals (17th–19th centuries) to investigate the compositional, functional, and phylogenetic diversity of ancient oral microbiomes. Our results revealed clear differences between ancient and modern Japanese microbiomes, as well as phylogenetic divergence between the Final Jomon (ca. 1000 BCE) and Edo periods. We also identified regional variation in ancient oral microbiomes and clade-level diversity within the periodontitis-associated archaeon Methanobrevibacter oralis. Interestingly, individuals with traces of tooth blackening (ohaguro), a custom practiced by Edo period women, were all assigned to the same clade, suggesting cultural influences on the oral microbiome. These findings highlight the important role of human culture and demography in shaping the evolutionary dynamics of microbiomes. Supplementary Information The online version contains supplementary material available at 10.1038/s41598-026-55286-2.