Clinical Oral Investigations

, Volume 23, Issue 3, pp 1489–1493 | Cite as

Deep sequencing reveals specific bacterial signatures in the subgingival microbiota of healthy subjects

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



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.


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.


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.


16S rRNA Bacteria Microbiota Dental plaque Tooth 



We thank Dr. Walter Meinzer for the critical reading of the manuscript.


This study was funded by the Japan Society for the Promotion of Science KAKENHI (grant numbers 26463129 and 17K11981).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

This study has been performed 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.

Informed consent

Written informed consent was obtained from all enrolled individuals.

Supplementary material

784_2019_2805_MOESM1_ESM.docx (2.5 mb)
Supplementary Figure S1 (DOCX 2509 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 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
  1. 1.Department of Periodontology, Graduate School of Medical and Dental SciencesTokyo Medical and Dental UniversityTokyoJapan
  2. 2.RIKEN Center for Integrative Medical SciencesYokohamaJapan
  3. 3.Department of Microbiology and ImmunologyKeio University School of MedicineTokyoJapan
  4. 4.Department of Molecular Immunology, Graduate School of Medical and Dental SciencesTokyo Medical and Dental UniversityTokyoJapan
  5. 5.Faculty of Science and Engineering, Graduate School of Advanced Science and EngineeringWaseda UniversityTokyoJapan

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