A recent study led by researchers from Toho University and other institutions examined the oral microbiomes of the Japanese population by analyzing DNA preserved in dental calculus from human skeletal remains. This research primarily focused on samples from the Edo period (1603-1868) and compared them with modern dental calculus. The findings revealed significant differences in microbial composition across time periods and regions, highlighting the impact of historical dietary changes and cultural practices on oral health. Notably, the periodontal disease-associated archaeon Methanobrevibacter oralis was frequently detected in Edo-period individuals, suggesting a historical prevalence of oral diseases. The study also identified regional variations, with differences between samples from the Honshu–Kyushu region and Okinawa, indicating that local diets and environments influenced the oral microbiome. Furthermore, the analysis of M. oralis showed a connection to the traditional practice of ohaguro, or tooth blackening, prevalent during the Edo period. This research underscores the potential of dental calculus as a valuable source for understanding past human health, diet, and the relationship between humans and microorganisms. Future studies may further illuminate the lifeways of historical populations in Japan.