Unraveling the Relationship Between Ancient Japanese and Oral Microbes from Dental Calculus DNA

Research Overview A research group led by Associate Professor Fuzuki Mizuno of Toho University School of Medicine and Yuki Kuriyama, a graduate student at the University of Tokyo, analyzed DNA preserved in dental calculus from ancient Japanese human remains, primarily from the Edo period, to uncover characteristics of past oral microbiomes. Dental calculus serves as a valuable information source, as it retains DNA of oral microbes from that time, providing insights into past living conditions and health states.

Methodology and Results In this study, ancient dental calculus samples, mostly from the early modern period excavated from sites in Tokyo, Saitama, Yamanashi, Fukuoka, and Okinawa Prefectures, were compared with modern dental calculus samples from Niigata Prefecture. The analysis revealed the following: - The microbiome composition of ancient dental calculus differs from that of modern times. - Differences in microbial composition were observed between the Honshu/Kyushu regions and the Okinawa region. - In phylogenetic analysis of the periodontal disease-associated archaeon 'Methanobrevibacter oralis (M. oralis),' M. oralis derived from female individuals with reported evidence of teeth blackening (ohaguro) were all found to belong to the same 'Clade B.'

Significance These results indicate that microbial DNA in dental calculus provides a new clue for examining the diet, regional characteristics, cultural habits, and the relationship between humans and microbes in the past. The study will be published in the journal 'Scientific Reports' on June 8, 2026.