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Japanese subgingival microbiota in health vs disease and their roles in predicted functions associated with periodontitis

  • Eri Ikeda
  • Takahiko Shiba
  • Yuichi Ikeda
  • Wataru Suda
  • Akinori Nakasato
  • Yasuo TakeuchiEmail author
  • Miyuki Azuma
  • Masahira Hattori
  • Yuichi Izumi
Original Article


The present study aimed to identify and compare the microbial signatures between periodontally healthy and periodontitis subjects using 454 sequences of 16S rRNA genes. Subgingival plaque samples were collected from ten periodontally healthy subjects and ten matched chronic periodontitis patients. Bacterial DNA was extracted and next-generation sequencing of 16S rRNA genes was performed. The microbial composition differed between healthy subjects and periodontitis patients at all phylogenetic levels. Particularly, 16 species, including Lautropia mirabilis and Neisseria subflava predominated in healthy subjects, whereas nine species, including Porphyromonas gingivalis and Filifactor alocis predominated in periodontitis. UniFrac, a principal coordinate and network analysis, confirmed distinct community profiles in healthy subjects and periodontitis patients. Using predicted function profiling, pathways involved in phenylpropanoid, GPI-anchor biosynthesis, and metabolism of alanine, arginine, aspartate, butanoate, cyanoamino acid, fatty acid, glutamate, methane, proline, and vitamin B6 were significantly over-represented in periodontitis patients. These results highlight the oral microbiota alterations in microbial composition in periodontitis and suggest the genes and metabolic pathways associated with health and periodontitis. Our findings help to further elucidate microbial composition and interactions in health and periodontitis.


16S rRNA Bacteria Oral microbiome Periodontitis Pyrosequencing 



This work was supported by the Japan Society for the Promotion of Science KAKENHI; under Grant 26463129 and under Grant 17K11981. We also thank Dr. Walter Meinzer and Dr. Daiki Tanaka for critical reading of the manuscript.

Compliance with ethical standards

Conflicts of interest

The authors declare that they have no conflict of interests.

Research involving human participants

All procedures performed in studies involving human participants were in accordance with the ethical standards of Tokyo Medical and Dental University Institutional Review Board (No. 1138) and with the 1964 Helsinki Declaration and its later amendments or comparable ethical standards.

Informed consent

Written informed consent was obtained from all enrolled individuals.

Supplementary material

10266_2019_452_MOESM1_ESM.docx (1.6 mb)
Supplementary material 1 (DOCX 1663 kb)


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Copyright information

© The Society of The Nippon Dental University 2019

Authors and Affiliations

  • Eri Ikeda
    • 1
  • Takahiko Shiba
    • 1
  • Yuichi Ikeda
    • 1
  • Wataru Suda
    • 2
    • 3
  • Akinori Nakasato
    • 1
  • Yasuo Takeuchi
    • 1
    Email author
  • Miyuki Azuma
    • 4
  • Masahira Hattori
    • 2
    • 5
  • Yuichi Izumi
    • 1
    • 6
  1. 1.Department of Periodontology, Graduate School of Medical and Dental SciencesTokyo Medical and Dental UniversityBunkyoJapan
  2. 2.RIKEN Center for Integrative Medical SciencesYokohamaJapan
  3. 3.Department of Microbiology and ImmunologyKeio University School of MedicineShinjukuJapan
  4. 4.Department of Molecular Immunology, Graduate School of Medical and Dental SciencesTokyo Medical and Dental UniversityBunkyoJapan
  5. 5.Faculty of Science and Engineering, Graduate School of Advanced Science and EngineeringWaseda UniversityShinjukuJapan
  6. 6.Oral Care Perio Center, Southern TOHOKU General HospitalSouthern TOHOKU Research Institute for NeuroscienceKoriyamaJapan

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