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

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.

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Publication Details

Journal
Scientific Reports
Published
2026-06-08
DOI
https://doi.org/10.1038/s41598-026-55286-2
Primary Topic
Oral microbiology and periodontitis research
Type
article
Field-Weighted Citation Impact
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article

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

Noriko Seguchi, Fuzuki Mizuno, Eisaku Kanazawa, Chiaki Katagiri et al.
Scientific Reports
Oral microbiology and periodontitis research
article

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

Noriko Seguchi, Fuzuki Mizuno, Eisaku Kanazawa, Chiaki Katagiri, Takashi Yamada, Masami Matsushita, Shuuji Namiki, Soichiro Mizushima, Izumi Naka, Takashi Nara, Aiko Saso, Kazuhiro Sakaue, Kyoko Funahashi, Masahiko Kumagai, Hisako Saitoh, Ryohei Sawaura, 平田 和明, Kunihiko Kurosaki, Shintaroh Ueda, Tomoki Maekawa, Shiori Yonemoto, Masaki Tanaka, Jun Ohashi, Takayuki Matsushita, Yuki Kuriyama
article en

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.

Scientific ReportsVol. 16(1)
Nihon University (JP), Tokyo Medical and Dental University (JP), Toho University (JP), National Agriculture and Food Research Organization (JP), Kyushu University (JP), St. Marianna University School of Medicine (JP), Kamakura Women's University (JP), Juntendo University (JP), Okinawa Prefectural Board of Education (JP), Toho University Omori Medical Center (JP), Kyushu University Hospital (JP), Okinawa Prefectural Education Center (JP), International Medical And Welfare College (JP), National Museum of Nature and Science (JP), Niigata University of Health and Welfare (JP), University of Montana (US), Niigata University (JP), The University of Tokyo (JP), International University of Health and Welfare (JP)
Gender equality
Openalex Percentile: Top 6%
Oral microbiology and periodontitis research
DOIOpen Access PDFOpenAlex
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