Analysis of dental calculus from historical Japanese populations revealed differences in oral microbial composition across time periods and regions, according to a study published in Scientific Reports.
Researchers used shotgun metagenomic sequencing to analyze dental calculus from 118 historical Japanese individuals, primarily from the Edo period (17th–19th centuries), and compared the findings with samples from modern Japanese individuals. The study identified 285 oral microbial species and found clear differences between ancient and modern oral microbiomes.
One of the most notable findings was the increased prevalence of Methanobrevibacter oralis, an archaeal species associated with periodontitis, in historical samples. The researchers also observed regional variation between mainland Japan and Okinawa, with differences in the prevalence of M. oralis, Actinomyces sp. oral taxon 414, and Actinomyces dentalis.
Phylogenetic analyses identified distinct microbial lineages associated with different historical periods. Several species, including Anaerolineaceae sp. oral taxon 439 and Streptococcus sinensis, showed divergence between Jomon and Edo period populations, suggesting that demographic and lifestyle changes may have influenced oral microbial evolution.
The study also identified two major historical clades of M. oralis. Clade membership was associated with host sex, and all previously reported individuals with evidence of ohaguro – the Edo-period practice of tooth blackening – belonged to the same clade. Comparative genomic analysis revealed differences in genes involved in metabolic pathways, including iron-associated functions.
The findings highlight the value of dental calculus as a source of preserved microbial DNA for metagenomic and phylogenetic analysis. The authors noted that ancient microbiome studies may help reconstruct long-term changes in microorganisms associated with oral disease and provide insight into the historical evolution of oral microbial communities.
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