Table_14_Comparison of Periodontal Bacteria of Edo and Modern Periods Using Novel Diagnostic Approach for Periodontitis With Micro-CT.xlsx

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（dental plaque）矿化形成的古牙结石（dental calculus）是古DNA（ancient DNA）的优质储存载体，可还原当时的饮食信息与口腔微生物组（oral microbiome）特征。对尼安德特人（Neanderthals）牙结石的基因组分析，已揭示出尼安德特人与现代人类口腔微生物组的细菌组成差异。目前鲜有研究探讨，因牙菌斑堆积诱发的多微生物疾病——牙周炎（periodontitis）的致病菌，在古人类与现代人类之间是否存在差异。本研究旨在对比古人类与现代人类样本的口腔微生物组细菌组成，并探究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构成，以及牙周炎的致病菌群。此外，本研究还介绍了一种利用显微计算机断层扫描（micro-computed tomography）诊断古代骨骼牙周炎的全新检测方法。本研究从日本江户时代（1603–1867，该时期为日本特色历史阶段，不接纳外来移民）的云心院遗址（Unko-in site）的12份样本中，获取了古16S核糖体DNA（16S rDNA）序列。此外，本研究从数据库中获取了53份现代样本的16S rDNA数据，用于对比现代与古代口腔微生物组。研究基于16S rDNA读段丰度，对微生物共现网络（microbial co-occurrence network）开展了分析。江户时代样本的微生物共现网络中，核心物种为真杆菌属（Eubacterium）物种、柔膜菌纲（Mollicutes）物种以及索拉密螺旋体（Treponema socranskii）。口腔放线菌（Actinomyces oricola）与迟缓埃格特菌（Eggerthella lenta）之间的共现关联，似乎在江户时代牙周炎的发病过程中发挥了关键作用。而现代样本的微生物共现网络中，核心且高丰度的物种则为牙龈卟啉单胞菌（Porphyromonas gingivalis）、具核梭杆菌文森亚种（Fusobacterium nucleatum subsp. vincentii）以及胸膜普雷沃菌（Prevotella pleuritidis）。上述结果表明，历史不同时代的牙周炎致病菌群可能存在显著差异。