Researchers at Toho University and collaborating institutions analyzed dental calculus from human skeletal remains to characterize the oral microbiomes of the Japanese population across time. The study found differences in microbial composition associated with time period, region, and the phylogeny of several oral bacterial species. The findings suggest that microbial DNA preserved in dental calculus can provide new evidence for examining past diet, regional variation, cultural practices, and the history of relationships between humans and microorganisms.
Researchers at Toho University , the University of Tokyo, Kyushu University, and collaborating institutions characterized the oral microbiomes of the Japanese population during the Edo period by analyzing the DNA preserved in dental calculus from human skeletal remains.
The researchers compared microbial composition in dental calculus from ancient to modern individuals, and identified the differences associated with time period, region, and the phylogeny of several oral bacterial species. They also conducted a phylogenetic analysis of the periodontal disease-associated archaeon Methanobrevibacter oralis (M. oralis) and found that the archaea present in the blackened teeth of Edo-period women belonged to the same clade.
These findings suggest that microbial DNA preserved in dental calculus can provide new evidence for examining past diet, regional variation, cultural practices, and the history of relationships between humans and microorganisms. The study was published in Scientific Reports. The human body hosts diverse microorganisms everywhere including the mouth, gut, and skin. These microbial communities and their genetic information are collectively referred to as the microbiome.
The microbiome changes in response to factors such as diet, hygiene, lifestyle, and medication, and is widely known to be associated with an individual's health. Oral microorganisms, in particular, are related not only to oral diseases such as cavities and periodontal disease but may also reflect the living environments and food culture the person is exposed to.
However, how the oral microbiome varied across time, regions, and cultural practices among the people of Japan has not been fully understood. In recent years, researchers have increasingly used dental calculus attached to ancient teeth to investigate past oral microorganisms. Dental calculus is mineralized dental plaque and can preserve DNA of oral microorganisms and other biological sources in the mouth at the time.
DNA preserved in dental calculus can therefore serve as a valuable source of information on past lifestyles and health conditions. In this study, the research group collected and analyzed dental calculus samples from human skeletal remains excavated from archaeological and burial sites across Japan in Tokyo, Saitama, Yamanashi, Fukuoka, and Okinawa, primarily from the Edo period together with modern dental calculus samples.
Along with previously published data of dental calculus from Jomon-period and other Edo-period individuals, the team compared the microbial composition, functional profiles, and phylogenetic relationships of microorganisms across these different time periods. Because dental calculus from human skeletal remains can be affected by contamination from soil-derived microorganisms, the analysis focused on microorganisms considered to be of oral origin using existing oral microbiome databases.
The results showed that the oral microbiome preserved in dental calculus primarily from Edo-period individuals differed in composition from that of modern samples. In particular, the periodontal disease-associated archaeon Methanobrevibacter oralis (M. oralis) was frequently detected in dental calculus from Edo-period individuals. Differences in microbial composition were also observed between samples from the Honshu-Kyushu region and those from the Okinawa region, suggesting that regional living environments and dietary habits may have been associated with oral microbial composition.
The researchers also compared Jomon-period samples with samples from the Edo period and found phylogenetic differences among several oral bacterial species across time. These findings suggest that human mobility, the introduction of agriculture, dietary change, and other historical processes in Japan may have been associated not only with human populations, but also with the diversity of microorganisms that lived alongside them.
The study also focused specifically on the phylogenetic distribution of the periodontal disease-associated archaeon M. oralis and examined its relationship with ohaguro, the traditional practice of tooth blackening that was widely observed during the Edo period. The analysis showed that M. oralis was divided into two major lineages, Clade A and Clade B, with the Clade A lineage being associated with ohaguro
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