Skip to main content

Advertisement

SpringerLink
Log in

Exploration of bacterial species associated with the salivary microbiome of individuals with a low susceptibility to dental caries

  • Original Article
  • Published:
Clinical Oral Investigations Aims and scope Submit manuscript

Abstract

Objective

Dental caries is caused by acidogenic plaque microbiota formed on saliva-bathed tooth surfaces, in which multiple organisms act collectively to initiate and expand a cavity. We explored bacterial species associated with the salivary microbiome of individuals with low susceptibility to dental caries.

Materials and methods

The bacterial composition of saliva from 19 young adults was analyzed using barcoded pyrosequencing of the 16S rRNA gene; we compared 10 caries-experienced (CE) and nine caries-free (CF) individuals. A quantitative PCR assay of saliva from 139 orally healthy adults aged 40–59 years was carried out to confirm the result obtained by pyrosequencing analysis.

Results

The microbiomes of CF individuals showed more diverse communities with a significantly greater proportion of the genus Porphyromonas. Among operational taxonomic units (OTUs) corresponding to the genus Porphyromonas, the OTU corresponding to P. pasteri was the most predominant and its relative abundance in CF individuals was significantly greater than in CE individuals (P < 0.001, Wilcoxon rank sum test). A quantitative PCR assay of saliva confirmed that the amounts of P. pasteri were significantly higher in individuals with lower caries experience (filled teeth <15, n = 67) than in those with higher caries experience (filled teeth ≥15, n = 72) (P < 0.001, Student’s t test).

Conclusion

These results revealed an association between a greater abundance of P. pasteri and lower susceptibility to dental caries.

Clinical relevance

P. pasteri may be a bacterial species that could potentially be used as a marker for maintaining a healthy oral microbiome against dental caries.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  1. Belstrom D, Fiehn NE, Nielsen CH, Holmstrup P, Kirkby N, Klepac-Ceraj V, Paster BJ et al (2014) Altered bacterial profiles in saliva from adults with caries lesions: a case-cohort study. Caries Res 48:368–375

    Article  PubMed  Google Scholar 

  2. Burne RA, Marquis RE (2000) Alkali production by oral bacteria and protection against dental caries. FEMS Microbiol Lett 193:1–6

    Article  PubMed  Google Scholar 

  3. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N et al (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336

    Article  PubMed  PubMed Central  Google Scholar 

  4. Chen T, Yu WH, Izard J, Baranova OV, Lakshmanan A and Dewhirst FE (2010) The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information. Database (Oxford):baq013

  5. Chhour KL, Nadkarni MA, Byun R, Martin FE, Jacques NA, Hunter N (2005) Molecular analysis of microbial diversity in advanced caries. J Clin Microbiol 43:843–849

    Article  PubMed  PubMed Central  Google Scholar 

  6. Crielaard W, Zaura E, Schuller AA, Huse SM, Montijn RC, Keijser BJ (2011) Exploring the oral microbiota of children at various developmental stages of their dentition in the relation to their oral health. BMC Med Genet 4:22

    Google Scholar 

  7. Edgar RC (2013) UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 10:996–998

    Article  PubMed  Google Scholar 

  8. Eren AM, Borisy GG, Huse SM, Mark Welch JL (2014) Oligotyping analysis of the human oral microbiome. Proc Natl Acad Sci U S A 111:E2875–E2884

    Article  PubMed  PubMed Central  Google Scholar 

  9. Gomar-Vercher S, Cabrera-Rubio R, Mira A, Montiel-Company JM, Almerich-Silla JM (2014) Relationship of children's salivary microbiota with their caries status: a pyrosequencing study. Clin Oral Investig 18:2087–2094

    Article  PubMed  Google Scholar 

  10. Gross EL, Beall CJ, Kutsch SR, Firestone ND, Leys EJ, Griffen AL (2012) Beyond Streptococcus Mutans: dental caries onset linked to multiple species by 16S rRNA community analysis. PLoS One 7:e47722

    Article  PubMed  PubMed Central  Google Scholar 

  11. Gross EL, Leys EJ, Gasparovich SR, Firestone ND, Schwartzbaum JA, Janies DA, Asnani K et al (2010) Bacterial 16S sequence analysis of severe caries in young permanent teeth. J Clin Microbiol 48:4121–4128

    Article  PubMed  PubMed Central  Google Scholar 

  12. Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G, Ciulla D et al (2011) Chimeric 16S rRNA sequence formation and detection in sanger and 454-pyrosequenced PCR amplicons. Genome Res 21:494–504

    Article  PubMed  PubMed Central  Google Scholar 

  13. Huang X, Exterkate RA, ten Cate JM (2012) Factors associated with alkali production from arginine in dental biofilms. J Dent Res 91:1130–1134

    Article  PubMed  Google Scholar 

  14. Kassebaum NJ, Bernabe E, Dahiya M, Bhandari B, Murray CJ, Marcenes W (2015) Global burden of untreated caries: a systematic review and metaregression. J Dent Res 94:650–658

    Article  PubMed  Google Scholar 

  15. Kolenbrander PE, Palmer RJ Jr, Periasamy S, Jakubovics NS (2010) Oral multispecies biofilm development and the key role of cell-cell distance. Nat Rev Microbiol 8:471–480

    Article  PubMed  Google Scholar 

  16. Ling Z, Kong J, Jia P, Wei C, Wang Y, Pan Z, Huang W et al (2010) Analysis of oral microbiota in children with dental caries by PCR-DGGE and barcoded pyrosequencing. Microb Ecol 60:677–690

    Article  PubMed  Google Scholar 

  17. Loesche WJ (1986) Role of Streptococcus mutans in human dental decay. Microbiol Rev 50:353–380

    PubMed  PubMed Central  Google Scholar 

  18. Lozupone C, Knight R (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71:8228–8235

    Article  PubMed  PubMed Central  Google Scholar 

  19. Luo AH, Yang DQ, Xin BC, Paster BJ, Qin J (2012) Microbial profiles in saliva from children with and without caries in mixed dentition. Oral Dis 18:595–601

    Article  PubMed  Google Scholar 

  20. Marcenes W, Kassebaum NJ, Bernabe E, Flaxman A, Naghavi M, Lopez A, Murray CJ (2013) Global burden of oral conditions in 1990-2010: a systematic analysis. J Dent Res 92:592–597

    Article  PubMed  PubMed Central  Google Scholar 

  21. Moritani K, Takeshita T, Shibata Y, Ninomiya T, Kiyohara Y, Yamashita Y (2015) Acetaldehyde production by major oral microbes. Oral Dis 21:748–754

    Article  PubMed  Google Scholar 

  22. Obata J, Takeshita T, Shibata Y, Yamanaka W, Unemori M, Akamine A, Yamashita Y (2014) Identification of the microbiota in carious dentin lesions using 16S rRNA gene sequencing. PLoS One 9:e103712

    Article  PubMed  PubMed Central  Google Scholar 

  23. Price MN, Dehal PS, Arkin AP (2009) FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 26:1641–1650

    Article  PubMed  PubMed Central  Google Scholar 

  24. Rasiah IA, Wong L, Anderson SA, Sissons CH (2005) Variation in bacterial DGGE patterns from human saliva: over time, between individuals and in corresponding dental plaque microcosms. Arch Oral Biol 50:779–787

    Article  PubMed  Google Scholar 

  25. Sakamoto M, Li D, Shibata Y, Takeshita T, Yamashita Y and Ohkuma M (2015) Porphyromonas pasteri sp. nov., isolated from human saliva. Int J Syst Evol Microbiol

  26. Simon-Soro A, Mira A (2015) Solving the etiology of dental caries. Trends Microbiol 23:76–82

    Article  PubMed  Google Scholar 

  27. Stahringer SS, Clemente JC, Corley RP, Hewitt J, Knights D, Walters WA, Knight R et al (2012) Nurture trumps nature in a longitudinal survey of salivary bacterial communities in twins from early adolescence to early adulthood. Genome Res 22:2146–2152

    Article  PubMed  PubMed Central  Google Scholar 

  28. Takeshita T, Matsuo K, Furuta M, Shibata Y, Fukami K, Shimazaki Y, Akifusa S et al (2014) Distinct composition of the oral indigenous microbiota in South Korean and Japanese adults. Sci Rep 4:6990

    Article  PubMed  PubMed Central  Google Scholar 

  29. Takeshita T, Nakano Y, Kumagai T, Yasui M, Kamio N, Shibata Y, Shiota S et al (2009) The ecological proportion of indigenous bacterial populations in saliva is correlated with oral health status. ISME J 3:65–78

    Article  PubMed  Google Scholar 

  30. Takeshita T, Yasui M, Shibata Y, Furuta M, Saeki Y, Eshima N, Yamashita Y (2015) Dental plaque development on a hydroxyapatite disk in young adults observed by using a barcoded pyrosequencing approach. Sci Rep 5:8136

    Article  PubMed  PubMed Central  Google Scholar 

  31. Tong H, Chen W, Merritt J, Qi F, Shi W, Dong X (2007) Streptococcus oligofermentans inhibits Streptococcus mutans through conversion of lactic acid into inhibitory H2O2: a possible counteroffensive strategy for interspecies competition. Mol Microbiol 63:872–880

    Article  PubMed  Google Scholar 

  32. Yamanaka W, Takeshita T, Shibata Y, Matsuo K, Eshima N, Yokoyama T, Yamashita Y (2012) Compositional stability of a salivary bacterial population against supragingival microbiota shift following periodontal therapy. PLoS One 7:e42806

    Article  PubMed  PubMed Central  Google Scholar 

  33. Yang F, Zeng X, Ning K, Liu KL, Lo CC, Wang W, Chen J et al (2012) Saliva microbiomes distinguish caries—active from healthy human populations. ISME J 6:1–10

    Article  PubMed  Google Scholar 

  34. Ye J, Coulouris G, Zaretskaya I, Cutcutache I, Rozen S, Madden TL (2012) Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics 13:134

    Article  PubMed  PubMed Central  Google Scholar 

  35. Yoshida A, Suzuki N, Nakano Y, Kawada M, Oho T, Koga T (2003) Development of a 5' nuclease-based real-time PCR assay for quantitative detection of cariogenic dental pathogens Streptococcus mutans and Streptococcus sobrinus. J Clin Microbiol 41:4438–4441

    Article  PubMed  PubMed Central  Google Scholar 

  36. Zaura E, Brandt BW, Teixeira de Mattos MJ, Buijs MJ, Caspers MP, Rashid MU, Weintraub A et al (2015) Same exposure but two radically different responses to antibiotics: resilience of the salivary microbiome versus long-term microbial shifts in feces. MBio 6

  37. Zhou Y, Gao H, Mihindukulasuriya KA, La Rosa PS, Wylie KM, Vishnivetskaya T, Podar M et al (2013) Biogeography of the ecosystems of the healthy human body. Genome Biol 14:R1

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Section of Preventive and Public Health Dentistry, Division of Oral Health, Growth and Development, Kyushu University Faculty of Dental Science, Fukuoka, Japan

    Haruna Yasunaga, Toru Takeshita, Yukie Shibata, Michiko Furuta & Yoshihisa Yamashita

  2. Section of Orthodontics and Dentofacial Orthopedics, Division of Oral Health, Growth and Development, Kyushu University Faculty of Dental Science, Fukuoka, Japan

    Haruna Yasunaga & Ichiro Takahashi

  3. Department of Preventive Dentistry and Dental Public Health, School of Dentistry, Aichi-Gakuin University, Nagoya, Japan

    Yoshihiro Shimazaki

  4. Department of Oral Health Management, School of Oral Health Science, Kyushu Dental University, Kitakyushu, Japan

    Sumio Akifusa

  5. Department of Epidemiology and Public Health, Graduate School of Medial Sciences, Kyushu University, Fukuoka, Japan

    Toshiharu Ninomiya

  6. Department of Environmental Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan

    Yutaka Kiyohara

Authors
  1. Haruna Yasunaga
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Toru Takeshita
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yukie Shibata
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Michiko Furuta
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Yoshihiro Shimazaki
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Sumio Akifusa
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Toshiharu Ninomiya
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Yutaka Kiyohara
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Ichiro Takahashi
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Yoshihisa Yamashita
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Yoshihisa Yamashita.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Funding

This study was supported in part by Grants-in Aid for Scientific Research 25463249 (T. T.), 25293428 (Y. Y.), and 15K15774 (Y. Y.) from the Ministry of Education, Culture, Sports, Science and Technology of Japan.

Ethical approval

All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards. The Ethics Committee of Kyushu University approved this study design (reference numbers: 26–130 for the barcoded pyrosequencing analysis and 19B-1 for the quantitative PCR analysis) and the procedure for obtaining informed consent.

Informed consent

Informed consent was obtained from all individual participants included in this study.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Yasunaga, H., Takeshita, T., Shibata, Y. et al. Exploration of bacterial species associated with the salivary microbiome of individuals with a low susceptibility to dental caries. Clin Oral Invest 21, 2399–2406 (2017). https://doi.org/10.1007/s00784-016-2035-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00784-016-2035-5

Keywords

Search

Navigation