Ancient dental calculus, formed from dental plaque, is a rich source of ancient DNA and can provide information regarding the food and oral microbiology at that time. Genomic analysis of dental calculus from Neanderthals has revealed the difference in bacterial composition of oral microbiome between Neanderthals and modern humans. There are few reports investigating whether the pathogenic bacteria of periodontitis, a polymicrobial disease induced in response to the accumulation of dental plaque, were different between ancient and modern humans. This study aimed to compare the bacterial composition of the oral microbiome in ancient and modern human samples and to investigate whether lifestyle differences depending on the era have altered the bacterial composition of the oral microbiome and the causative bacteria of periodontitis. Additionally, we introduce a novel diagnostic approach for periodontitis in ancient skeletons using micro-computed tomography. Ancient 16S rDNA sequences were obtained from 12 samples at the Unko-in site (18th-19th century) of the Edo era (1603–1867), a characteristic period in Japan when immigrants were not accepted. Furthermore, modern 16S rDNA data from 53 samples were obtained from a database to compare the modern and ancient microbiome. The microbial co-occurrence network was analyzed based on 16S rDNA read abundance. Eubacterium species, Mollicutes species, and Treponema socranskii were the core species in the Edo co-occurrence network. The co-occurrence relationship between Actinomyces oricola and Eggerthella lenta appeared to have played a key role in causing periodontitis in the Edo era. However, Porphyromonas gingivalis, Fusobacterium nucleatum subsp. vincentii, and Prevotella pleuritidis were the core and highly abundant species in the co-occurrence network of modern samples. These results suggest the possibility of differences in the pathogens causing periodontitis during different eras in history.

由牙菌斑形成的古代牙结石是古代DNA的丰富来源，可以提供有关当时食物和口腔微生物学的信息。尼安德特人牙结石的基因组分析揭示了尼安德特人和现代人口腔微生物群的细菌组成差异。很少有报道调查牙周炎的致病菌，牙周炎是一种由牙菌斑积聚引起的多种微生物疾病，在古代和现代人类之间是否存在差异。本研究旨在比较古代和现代人类样本中口腔微生物组的细菌组成，并调查不同时代的生活方式差异是否改变了口腔微生物组的细菌组成和牙周炎的致病菌。此外，我们介绍了一种使用微型计算机断层扫描诊断古代骨骼牙周炎的新方法。古代 16S rDNA 序列是从江户时代（1603-1867 年）Unko-in 遗址（18-19 世纪）的 12 个样本中获得的，这是日本不接受移民的典型时期。此外，从数据库中获得了来自 53 个样本的现代 16S rDNA 数据，以比较现代和古代微生物组。基于 16S rDNA 读数丰度分析微生物共现网络。从数据库中获得了来自 53 个样本的现代 16S rDNA 数据，以比较现代和古代微生物组。基于 16S rDNA 读数丰度分析微生物共现网络。从数据库中获得了来自 53 个样本的现代 16S rDNA 数据，以比较现代和古代微生物组。基于 16S rDNA 读数丰度分析微生物共现网络。真杆菌物种，软体动物物种，和索氏密螺旋体是江户共现网络中的核心物种。之间的共现关系放线菌和长豆菌似乎在江户时代导致牙周炎发挥了关键作用。然而，牙龈卟啉单胞菌、具核梭杆菌亚种文森特， 和普雷沃氏菌是现代样本共现网络中的核心和高度丰富的物种。这些结果表明，在历史的不同时期，引起牙周炎的病原体可能存在差异。