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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., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Shiba, Komatsu, Sudo, Sawafuji, Saso, Ueda, Watanabe, Nemoto, Kano, Nagai, Ohsugi, Katagiri, Takeuchi, Kobayashi and Iwata.)

Objectives: This study aimed to define the comprehensive bacterial flora of the healthy oral cavity by identifying and comparing bacterial species in different subgingival sites using 454 sequencing of 16S rRNA genes., Materials and Methods: Subgingival plaque samples were taken from six target teeth (central incisor, first premolar, and first molar in both the maxilla and mandible) of 10 periodontally healthy patients. Bacterial DNA was extracted and next-generation sequencing of 16S rRNA genes was performed., Results: Bacterial composition in phylum level was similar for all sites within the same individual irrespective of tooth location. Unweighted UniFrac distance values of microbiome also showed that average distance was significantly larger between subjects than between tooth locations of the same subjects., Conclusions: The present results clarify the lack of effect of tooth location in the healthy subgingival microbiota. Results may suggest that any subgingival site can demonstrate similar subject-specific microbiota., Clinical Relevance: This investigation offers a better understanding of the uniqueness of the oral microbiome. The present study will facilitate sampling in future subgingival microbiological studies.

Polymicrobial diseases, which can be life threatening, are caused by the presence and interactions of multiple microbes. Peri-implantitis and periodontitis are representative polymicrobial diseases that show similar clinical symptoms. To establish a means of differentiating between them, we compared microbial species and functional genes in situ by performing metatranscriptomic analyses of peri-implantitis and periodontitis samples obtained from the same subjects (n = 12 each). Although the two diseases differed in terms of 16S rRNA-based taxonomic profiles, they showed similarities with respect to functional genes and taxonomic and virulence factor mRNA profiles. The latter-defined as microbial virulence types-differed from those of healthy periodontal sites. We also showed that networks based on co-occurrence relationships of taxonomic mRNA abundance (co-occurrence networks) were dissimilar between the two diseases. Remarkably, these networks consisted mainly of taxa with a high relative mRNA-to-rRNA ratio, with some showing significant co-occurrence defined as interacting core taxa, highlighting differences between the two groups. Thus, peri-implantitis and periodontitis have shared as well as distinct microbiological characteristics. Our findings provide insight into microbial interactions in polymicrobial diseases with unknown etiologies.

Aim: The microbial differences between peri-implantitis and periodontitis in the same subjects were examined using 16S rRNA gene clone library analysis and real-time polymerase chain reaction., Materials and Methods: Subgingival plaque samples were taken from the deepest pockets of peri-implantitis and periodontitis sites in six subjects. The prevalence of bacteria was analysed using a 16S rRNA gene clone library and real-time polymerase chain reaction., Results: A total of 333 different taxa were identified from 799 sequenced clones; 231 (69%) were uncultivated phylotypes, of which 75 were novel. The numbers of bacterial taxa identified at the sites of peri-implantitis and periodontitis were 192 and 148 respectively. The microbial composition of peri-implantitis was more diverse when compared with that of periodontitis. Fusobacterium spp. and Streptococcus spp. were predominant in both peri-implantitis and periodontitis, while bacteria such as Parvimonas micra were only detected in peri-implantitis. The prevalence of periodontopathic bacteria was not high, while quantitative evaluation revealed that, in most cases, prevalence was higher at peri-implantitis sites than at periodontitis sites., Conclusions: The biofilm in peri-implantitis showed a more complex microbial composition when compared with periodontitis. Common periodontopathic bacteria showed low prevalence, and several bacteria were identified as candidate pathogens in peri-implantitis., (© 2012 John Wiley & Sons A/S.)

Terminal restriction fragment-length polymorphism (T-RFLP) analysis was applied to characterize oral bacterial flora in saliva from 18 healthy subjects and 18 patients with periodontitis. The 16S rRNA genes (rDNAs) of oral bacteria and spirochaetes in saliva were amplified by PCR with a 6'carboxy-fluorescein (6-FAM)-labelled universal forward primer (27F) and a universal reverse primer (1492R) or the Spirochaeta-selective reverse primer. The 16S rDNAs were digested with restriction enzymes with 4 bp recognition sites (HhaI or MspI) and analysed by using an automated DNA sequencer. T-RFLP patterns were numerically analysed using a computer program. From analysis of the oral bacterial community, patterns derived from periodontally healthy subjects and patients with periodontitis were grouped into different clusters, though with some uncertainty. Samples from patients with periodontitis tended to cluster into their respective types (aggressive and chronic periodontitis), although this was not very clear. Analysis of spirochaetal community using T-RFLP showed that the patterns derived from patients with periodontitis were grouped more as compared with the analysis of the oral bacterial community. These results suggest that samples from patients with periodontitis contain an unexpected diversity. T-RFLP patterns of 16S rDNAs from saliva samples of two periodontally healthy subjects over a 5-week period showed host-specific relatively stable oral bacterial flora. Our study indicates that T-RFLP analysis is useful for the assessment of diversity of oral bacterial flora and rapid comparison of the community structure between subjects with and without periodontitis.

This large-scale study cross-sectionally examined the periodontal status and prevalence of "red complex" bacteria (Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia) in Japanese adults. A total of 977 participants were enrolled in the study. Probing depth (PD), bleeding on probing (BOP), and bone crest level (BCL) were recorded, and the presence of red complex bacteria in the saliva was examined using polymerase chain reaction. The mean BCL value and the percentage of sites with a PD ≥4 mm or the presence of BOP were significantly higher in older participants. The detection rates of P. gingivalis, T. denticola, and T. forsythia were 46.3%, 76.4%, and 61.1%, respectively. The P. gingivalis detection rate significantly increased with age, while those of T. denticola and T. forsythia were comparably high for all age groups. A close correlation between P. gingivalis and the percentage of sites with PD ≥4 mm was indicated by nonlinear canonical correlation analysis. Current smokers exhibited a more advanced disease condition and a significantly higher P. gingivalis detection rate than non-smokers. In conclusion, periodontal condition worsens with age, and P. gingivalis appears to be the red complex bacterium most closely associated with periodontitis. [ABSTRACT FROM AUTHOR]

Umeda M, Miwa Z, Takeuchi Y, Ishizuka M, Huang Y, Noguchi K, Tanaka M, Takagi Y, Ishikawa I. The distribution of periodontopathic bacteria among Japanese children and their parents. J Periodont Res 2004; doi: 10.1111/j.1600-0765.2004.00754.x© Blackwell Munksgaard 2004It is not well known how periodontopathic bacteria colonize in the oral cavity during childhood. The purpose of this study was to investigate the distribution of periodontopathic bacteria in oral cavities of children and their parents and the relationship between the bacterial findings and clinical parameters.Fifty-six children (mean age: 8.3 ± 3.5, range: 1–15 years), including 15 with deciduous dentition, 26 with mixed dentition and 15 with permanent dentition, and their parents participated in this study. Whole saliva and dental plaque of the children and whole saliva of their parents were collected for detection of seven species of periodontopathic bacteria (Actinobacillus actinomycetemcomitans,Tannerella forsythensis(Bacteroides forsythus),Campylobacter rectus,Porphyromonas gingivalis,Prevotella intermedia,Prevotella nigrescensandTreponema denticola) using the polymerase chain reaction method. Clinical parameters including simplified Oral Hygiene Index and Papillary-Marginal-Attachment Index were recorded for the children and their accompanied parents.The detection frequencies ofT. forsythensis,C. rectus,P. nigrescens,T. denticola,A. actinomycetemcomitans and P. gingivalisin the oral cavities of children were 42.9%, 94.6%, 42.9%, 48.2%, 1.8% and 8.9%, respectively.T. forsythensis,P. gingivalisandT. denticolawere detected more frequently in the saliva of parents (54.8%, 54.8%, 88.1%, respectively) than in the saliva of children (25.5%, 7.3%, 41.8%, respectively). Different detection frequencies ofP. nigrescenswere found among the oral cavities of children with deciduous, mixed and permanent dentitions. In mixed dentition, females harboredT. forsythensismore frequently than males did. Children who harboredT. forsythensis,P. intermedia,P. nigrescensandT. denticolashowed high scores for oral debris measurement by simplified Oral Hygiene Index.T. forsythensis,P. intermediaandP. nigrescenswere detected more frequently in children whose parents were positive for these pathogens than in children whose parents were negative.High plaque retention seems to promote the colonization of periodontal pathogens in the oral cavities of children.T. forsythensis,P. intermediaandP. nigrescenswere detected more frequently in the oral cavities of children whose parents already harbored these bacteria. Familial transmission of these bacteria is suggested. [ABSTRACT FROM AUTHOR]