Table_3_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.

由牙菌斑矿化形成的古老牙结石是古DNA的优质储库，可提供古代人类的饮食与口腔微生物学相关信息。针对尼安德特人牙结石开展的基因组分析，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。牙周炎是一种因牙菌斑堆积诱发的多微生物疾病，目前鲜有研究探讨古代与现代人类的牙周炎致病菌是否存在差异。本研究旨在对比古代与现代人类样本的口腔微生物组细菌组成，并探究时代差异带来的生活方式改变，是否会影响口腔微生物组的细菌构成以及牙周炎的致病菌种类。此外，本研究还提出了一种利用显微计算机断层扫描（micro-computed tomography）诊断古代骨骼标本牙周炎的全新方法。本研究从日本1603–1867年江户时代（该时期为日本不接纳外来移民的典型锁国阶段）的运庆院遗址（Unko-in site，18–19世纪）的12份样本中，获取了古老的16S rDNA序列。同时，本研究从公共数据库中调取了53份现代人类样本的16S rDNA数据，用于与古代微生物组开展对比分析。本研究基于16S rDNA序列读段丰度，对微生物共现网络展开了分析。江户时代样本的共现网络核心物种为真杆菌属（Eubacterium）物种、柔膜菌纲（Mollicutes）物种以及索氏密螺旋体（Treponema socranskii）。奥氏放线菌（Actinomyces oricola）与迟缓埃格特菌（Eggerthella lenta）之间的共现关系，似乎在江户时代的牙周炎发病过程中发挥了关键作用。而在现代样本的共现网络中，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）为核心且高丰度物种。上述研究结果表明，历史上不同时代的牙周炎致病菌可能存在差异。