Skip to main content


Log in

Evolution of the Oral Microbiome and Dental Caries

  • Microbiology (M Klein, Section Editor)
  • Published:
Current Oral Health Reports Aims and scope Submit manuscript


Purpose of Review

Our paper reviews how dietary changes during human evolution have contributed to the increased incidence and prevalence of dental caries in modern populations by shifting the oral microbiome from a “healthy” to “carious” state. We addressed two questions: (1) what is the microbial difference between the states of health and caries, and (2) how has the development of an agricultural diet impacted the oral microbiome?

Recent Findings

The application of next-generation sequencing has revealed the complexity of the oral microbiome and lack of a simple compositional difference between health and caries. Genetic analysis of the oral microbiome from contemporary and ancient humans has shown that the introduction of agriculture was associated with increased frequency of caries-related bacteria and the evolution of the key carious pathogen, Streptococcus mutans.


The adoption of an agricultural diet has contributed to a modern rise in caries by changing the oral microbiome ecology. Identification of evolutionary factors that have influenced the oral microbiome in health and caries, and how the two states differ functionally, as opposed to compositionally, may help to reduce the current burden of caries.

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

Access this article

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

Instant access to the full article PDF.

Similar content being viewed by others


Papers of particular interest, published recently, have been highlighted as: • Of importance •• Of major importance

  1. Petersen PE, Bourgeois D, Ogawa H, Estupinan-Day S, Ndiaye C. The global burden of oral diseases and risks to oral health. Bull World Health Organ. 2005;83(9):661–9.

    PubMed  PubMed Central  Google Scholar 

  2. Aas JA, Griffen AL, Dardis SR, Lee AM, Olsen I, Dewhirst FE, et al. Bacteria of dental caries in primary and permanent teeth in children and young adults. J Clin Microbiol. 2008;46(4):1407–17. doi:10.1128/JCM.01410-07.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Dewhirst FE, Chen T, Izard J, Paster BJ, Tanner AC, Yu WH, et al. The human oral microbiome. J Bacteriol. 2010;192(19):5002–17. doi:10.1128/JB.00542-10.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Lederberg J, Mc Cray A. ‘Ome Sweet ‘Omics—a genealogical treasury of words. Philadelphia: Scientist Inc; 2001.

  5. D'Aiuto F, Orlandi M, Gunsolley JC. Evidence that periodontal treatment improves biomarkers and CVD outcomes. J Clin Periodontol. 2013;40(Suppl 14):S85–105. doi:10.1111/jcpe.12061.

    Article  PubMed  Google Scholar 

  6. Chavarry NG, Vettore MV, Sansone C, Sheiham A. The relationship between diabetes mellitus and destructive periodontal disease: a meta-analysis. Oral Health Prev Dent. 2009;7(2):107–27.

    PubMed  Google Scholar 

  7. Lopez NJ, Smith PC, Gutierrez J. Higher risk of preterm birth and low birth weight in women with periodontal disease. J Dent Res. 2002;81(1):58–63.

    Article  CAS  PubMed  Google Scholar 

  8. Braidwood RJ, Howe B, Reed CA. The Iranian Prehistoric Project: new problems arise as more is learned of the first attempts at food production and settled village life. Science. 1961;133(3469):2008–10. doi:10.1126/science.133.3469.2008.

    Article  CAS  PubMed  Google Scholar 

  9. Richards MP, Schulting RJ, Hedges RE. Archaeology: sharp shift in diet at onset of Neolithic. Nature. 2003;425(6956):366. doi:10.1038/425366a.

    Article  CAS  PubMed  Google Scholar 

  10. Cordain L, Eaton SB, Sebastian A, Mann N, Lindeberg S, Watkins BA, et al. Origins and evolution of the Western diet: health implications for the 21st century. Am J Clin Nutr. 2005;81(2):341–54.

    CAS  PubMed  Google Scholar 

  11. Larsen CS. Biological changes in human-populations with agriculture. Annu Rev Anthropol. 1995;24:185–213.

    Article  Google Scholar 

  12. Wolfe ND, Dunavan CP, Diamond J. Origins of major human infectious diseases. Nature. 2007;447(7142):279–83. doi:10.1038/nature05775.

    Article  CAS  PubMed  Google Scholar 

  13. Smith BH. Patterns of molar wear in hunter-gatherers and agriculturalists. Am J Phys Anthropol. 1984;63(1):39–56. doi:10.1002/ajpa.1330630107.

    Article  CAS  PubMed  Google Scholar 

  14. Grine FE, Gwinnett AJ, Oaks JH. Early hominid dental pathology: interproximal caries in 1.5 million-year-old Paranthropus robustus from Swartkrans. Arch Oral Biol. 1990;35(5):381–6.

    Article  CAS  PubMed  Google Scholar 

  15. • Adler CJ, Dobney K, Weyrich LS, Kaidonis J, Walker AW, Haak W, et al. Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions. Nat Genet. 2013;45(4):450–5, 5e1. doi:10.1038/ng.2536. This manuscript represents the first study to genetically analyse the compsoition of the oral microbiome from ancient dental calculus.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. • Cornejo OE, Lefebure T, Bitar PD, Lang P, Richards VP, Eilertson K, et al. Evolutionary and population genomics of the cavity causing bacteria Streptococcus mutans. Mol Biol Evol. 2013;30(4):881–93. doi:10.1093/molbev/mss278. This article presents a comprehsive picture of the population history of Streptococcus mutans.

    Article  CAS  PubMed  Google Scholar 

  17. Nasidze I, Li J, Schroeder R, Creasey JL, Li M, Stoneking M. High diversity of the saliva microbiome in Batwa Pygmies. PLoS One. 2011;6(8):e23352. doi:10.1371/journal.pone.0023352.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Contreras M, Costello EK, Hidalgo G, Magris M, Knight R, Dominguez-Bello MG. The bacterial microbiota in the oral mucosa of rural Amerindians. Microbiology. 2010;156(Pt 11):3282–7. doi:10.1099/mic.0.043174-0.

    Article  CAS  PubMed  Google Scholar 

  19. •• Clemente JC, Pehrsson EC, Blaser MJ, Sandhu K, Gao Z, Wang B, et al. The microbiome of uncontacted Amerindians. Sci Adv. 2015;1(3) doi:10.1126/sciadv.1500183. This paper presented the first large genetic study of the human microbiome in hunter-gatherer populations.

  20. Kilian M, Chapple IL, Hannig M, Marsh PD, Meuric V, Pedersen AM, et al. The oral microbiome—an update for oral healthcare professionals. Br Dent J. 2016;221(10):657–66. doi:10.1038/sj.bdj.2016.865.

    Article  CAS  PubMed  Google Scholar 

  21. Walters W, Hyde ER, Berg-Lyons D, Ackermann G, Humphrey G, Parada A, et al. Improved bacterial 16S rRNA gene (V4 and V4-5) and fungal internal transcribed spacer marker gene primers for microbial community surveys. mSystems. 2016;1(1) doi:10.1128/mSystems.00009-15.

  22. Ghannoum MA, Jurevic RJ, Mukherjee PK, Cui F, Sikaroodi M, Naqvi A, et al. Characterization of the oral fungal microbiome (mycobiome) in healthy individuals. PLoS Pathog. 2010;6(1):e1000713. doi:10.1371/journal.ppat.1000713.

    Article  PubMed  PubMed Central  Google Scholar 

  23. Pride DT, Salzman J, Haynes M, Rohwer F, Davis-Long C, White RA 3rd, et al. Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome. ISME J. 2012;6(5):915–26. doi:10.1038/ismej.2011.169.

    Article  CAS  PubMed  Google Scholar 

  24. Matarazzo F, Ribeiro AC, Feres M, Faveri M, Mayer MP. Diversity and quantitative analysis of Archaea in aggressive periodontitis and periodontally healthy subjects. J Clin Periodontol. 2011;38(7):621–7. doi:10.1111/j.1600-051X.2011.01734.x.

    Article  PubMed  Google Scholar 

  25. Loesche WJ. Role of Streptococcus mutans in human dental decay. Microbiol Rev. 1986;50(4):353–80.

    CAS  PubMed  PubMed Central  Google Scholar 

  26. Loesche WJ, Grenier E. Detection of Streptococcus mutans in plaque samples by the direct fluorescent antibody test. J Dent Res. 1976;55:87–93.

    Article  Google Scholar 

  27. van Houte J. Role of micro-organisms in caries etiology. J Dent Res. 1994;73(3):672–81.

    Article  PubMed  Google Scholar 

  28. Munson MA, Banerjee A, Watson TF, Wade WG. Molecular analysis of the microflora associated with dental caries. J Clin Microbiol. 2004;42(7):3023–9. doi:10.1128/JCM.42.7.3023-3029.2004.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Becker MR, Paster BJ, Leys EJ, Moeschberger ML, Kenyon SG, Galvin JL, et al. Molecular analysis of bacterial species associated with childhood caries. J Clin Microbiol. 2002;40(3):1001–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. •• Yang F, Zeng X, Ning K, Liu KL, Lo CC, Wang W, et al. Saliva microbiomes distinguish caries-active from healthy human populations. ISME J. 2012;6(1):1–10. doi:10.1038/ismej.2011.71. This manuscript presented the first large-scale, next-generation sequencing analysis of the oral microbiome composition in health and caries.

    Article  PubMed  Google Scholar 

  31. Kianoush N, Adler CJ, Nguyen KA, Browne GV, Simonian M, Hunter N. Bacterial profile of dentine caries and the impact of pH on bacterial population diversity. PLoS One. 2014;9(3):e92940. doi:10.1371/journal.pone.0092940.

    Article  PubMed  PubMed Central  Google Scholar 

  32. Rocas IN, Alves FR, Rachid CT, Lima KC, Assuncao IV, Gomes PN, et al. Microbiome of deep dentinal caries lesions in teeth with symptomatic irreversible pulpitis. PLoS One. 2016;11(5):e0154653. doi:10.1371/journal.pone.0154653.

    Article  PubMed  PubMed Central  Google Scholar 

  33. Jiang W, Ling Z, Lin X, Chen Y, Zhang J, Yu J, et al. Pyrosequencing analysis of oral microbiota shifting in various caries states in childhood. Microb Ecol. 2014;67(4):962–9. doi:10.1007/s00248-014-0372-y.

    Article  PubMed  Google Scholar 

  34. •• Belda-Ferre P, Alcaraz LD, Cabrera-Rubio R, Romero H, Simon-Soro A, Pignatelli M, et al. The oral metagenome in health and disease. ISME J. 2012;6(1):46–56. doi:10.1038/ismej.2011.85. This manuscript presented the first next-generation sequencing analysis of the oral metagenome in health and caries.

    Article  CAS  PubMed  Google Scholar 

  35. Yang F, Ning K, Zeng X, Zhou Q, Su X, Yuan X. Characterization of saliva microbiota's functional feature based on metagenomic sequencing. Spring. 2016;5(1):2098. doi:10.1186/s40064-016-3728-6.

    Article  Google Scholar 

  36. Boraas JC, Messer LB, Till MJ. A genetic contribution to dental caries, occlusion, and morphology as demonstrated by twins reared apart. J Dent Res. 1988;67(9):1150–5. doi:10.1177/00220345880670090201.

    Article  CAS  PubMed  Google Scholar 

  37. Wang X, Shaffer JR, Weyant RJ, Cuenco KT, DeSensi RS, Crout R, et al. Genes and their effects on dental caries may differ between primary and permanent dentitions. Caries Res. 2010;44(3):277–84. doi:10.1159/000314676.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Holbrook WP, Arnadottir IB, Takazoe I, Birkhed D, Frostell G. Longitudinal study of caries, cariogenic bacteria and diet in children just before and after starting school. Eur J Oral Sci. 1995;103(1):42–5.

    Article  CAS  PubMed  Google Scholar 

  39. Seow WK, Clifford H, Battistutta D, Morawska A, Holcombe T. Case-control study of early childhood caries in Australia. Caries Res. 2009;43(1):25–35. doi:10.1159/000189704.

    Article  CAS  PubMed  Google Scholar 

  40. •• Weyrich LS, Duchene S, Soubrier J, Arriola L, Llamas B, Breen J, et al. Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus. Nature. 2017; doi:10.1038/nature21674. This manuscript represents the first study to genetically analyse the oral metagenome of Neanderthals from ancient dental calculus.

Download references

Author information

Authors and Affiliations


Corresponding author

Correspondence to Christina J Adler.

Ethics declarations

Conflict of Interest

All authors declare that they have no conflict of interest.

Human and Animal Rights and Informed Consent

This article does not contain any studies with human or animal subjects performed by any of the authors.

Additional information

This article is part of the Topical Collection on Microbiology

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Adler, C.J., Browne, G.V., Sukumar, S. et al. Evolution of the Oral Microbiome and Dental Caries. Curr Oral Health Rep 4, 264–269 (2017).

Download citation

  • Published:

  • Issue Date:

  • DOI: