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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

Abstract

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.

Keywords

16S rRNA Bacteria Microbiota Dental plaque Tooth 

Notes

Acknowledgements

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

Funding

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)

References

  1. 1.
    Aas JA, Paster BJ, Stokes LN, Olsen I, Dewhirst FE (2005) Defining the normal bacterial flora of the oral cavity. J Clin Microbiol 43:5721–5732CrossRefGoogle Scholar
  2. 2.
    Segata N, Haake SK, Mannon P, Lemon KP, Waldron L, Gevers D, Huttenhower C, Izard J (2012) Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biol 13:R42CrossRefGoogle Scholar
  3. 3.
    Dewhirst FE, Chen T, Izard J, Paster BJ, Tanner ACR, Yu WH, Lakshmanan A, Wade WG (2010) The human oral microbiome. J Bacteriol 192:5002–5017CrossRefGoogle Scholar
  4. 4.
    Simón-Soro A, Tomás I, Cabrera-Rubio R, Catalan MD, Nyvad B, Mira A (2013) Microbial geography of the oral cavity. J Dent Res 92:616–621CrossRefGoogle Scholar
  5. 5.
    Wade WG (2013) The oral microbiome in health and disease. Pharmacol Res 69:137–143CrossRefGoogle Scholar
  6. 6.
    Said HS, Suda W, Nakagome S, Chinen H, Oshima K, Kim S, Kimura R, Iraha A, Ishida H, Fujita J, Mano S, Morita H, Dohi T, Oota H, Hattori M (2014) Dysbiosis of salivary microbiota in inflammatory bowel disease and its association with oral immunological biomarkers. DNA Res 21:15–25CrossRefGoogle Scholar
  7. 7.
    Camanocha A, Dewhirst FE (2014) Host-associated bacterial taxa from Chlorobi, Chloroflexi, GN02, Synergistetes, SR1, TM7, and WPS-2 Phyla/candidate divisions. J Oral Microbiol 6Google Scholar
  8. 8.
    Ehrmann E, Handal T, Tamanai-Shacoori Z, Bonnaure-Mallet M, Fosse T (2014) High prevalence of β-lactam and macrolide resistance genes in human oral Capnocytophaga species. J Antimicrob Chemother 69:381–384CrossRefGoogle Scholar
  9. 9.
    Nørskov-Lauritsen N (2014) Classification, identification, and clinical significance of Haemophilus and Aggregatibacter species with host specificity for humans. Clin Microbiol Rev 27:214–240CrossRefGoogle Scholar
  10. 10.
    Persson GR, Weibel M, Hirschi R, Katsoulis J (2008) Similarities in the subgingival microbiota assessed by a curet sampling method at sites with chronic periodontitis. J Periodontol 79:2290–2296CrossRefGoogle Scholar
  11. 11.
    Haffajee AD, Teles RP, Patel MR, Song X, Yaskell T, Socransky SS (2009) Factors affecting human supragingival biofilm composition. II. Tooth position. J Periodontal Res 44:520–528CrossRefGoogle Scholar

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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