Abstract
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.
Highlights
There is tremendous interest in studying the evolutionary ecology of the microbiome through the comparative analysis of both ancient and modern forms (Warinner et al, 2015)
The presence or absence of periodontal disease in ancient skeletons has been evaluated based on antemortem tooth loss (AMTL) (Clarke et al, 1986; Lavigne and Molto, 1995)
The distance from the cemento-enamel junction (CEJ) to the alveolar crest (AC) and morphological assessment of inflammation of the interdental septum have often been used for the diagnosis of periodontal disease (Clarke et al, 1986; Kerr, 1988; Kerr, 1991; Lavigne and Molto, 1995)
Summary
There is tremendous interest in studying the evolutionary ecology of the microbiome through the comparative analysis of both ancient and modern forms (Warinner et al, 2015). Genomic analysis of calculus derived from Neanderthals and other ancient humans revealed the diet of that era and how the bacterial composition in ancient humans differed from that of modern humans (Adler et al, 2013; Warinner et al, 2014; Lloyd-Price et al, 2017; Weyrich et al, 2017; Velsko et al, 2019). Periodontitis is a disease triggered by dental plaque accumulation, causing an inflammatory reaction and bone destruction (Kinane et al, 2017). Many environmental factors, such as smoking habit, diabetes, and host genetics, are known risk factors for periodontitis. There is no general consensus for diagnostic criteria of periodontal disease in ancient skeletons
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