Odontogenesis pp 525-548 | Cite as

The Supragingival Biofilm in Early Childhood Caries: Clinical and Laboratory Protocols and Bioinformatics Pipelines Supporting Metagenomics, Metatranscriptomics, and Metabolomics Studies of the Oral Microbiome

  • Kimon DivarisEmail author
  • Dmitry Shungin
  • Adaris Rodríguez-Cortés
  • Patricia V. Basta
  • Jeff Roach
  • Hunyong Cho
  • Di Wu
  • Andrea G. Ferreira Zandoná
  • Jeannie Ginnis
  • Sivapriya Ramamoorthy
  • Jason M. Kinchen
  • Jakub Kwintkiewicz
  • Natasha Butz
  • Apoena A. Ribeiro
  • M. Andrea Azcarate-Peril
Part of the Methods in Molecular Biology book series (MIMB, volume 1922)


Early childhood caries (ECC) is a biofilm-mediated disease. Social, environmental, and behavioral determinants as well as innate susceptibility are major influences on its incidence; however, from a pathogenetic standpoint, the disease is defined and driven by oral dysbiosis. In other words, the disease occurs when the natural equilibrium between the host and its oral microbiome shifts toward states that promote demineralization at the biofilm-tooth surface interface. Thus, a comprehensive understanding of dental caries as a disease requires the characterization of both the composition and the function or metabolic activity of the supragingival biofilm according to well-defined clinical statuses. However, taxonomic and functional information of the supragingival biofilm is rarely available in clinical cohorts, and its collection presents unique challenges among very young children. This paper presents a protocol and pipelines available for the conduct of supragingival biofilm microbiome studies among children in the primary dentition, that has been designed in the context of a large-scale population-based genetic epidemiologic study of ECC. The protocol is being developed for the collection of two supragingival biofilm samples from the maxillary primary dentition, enabling downstream taxonomic (e.g., metagenomics) and functional (e.g., transcriptomics and metabolomics) analyses. The protocol is being implemented in the assembly of a pediatric precision medicine cohort comprising over 6000 participants to date, contributing social, environmental, behavioral, clinical, and biological data informing ECC and other oral health outcomes.

Key words

Dental caries Microbiome Transcriptome Metabolome Children Protocol 



This work was supported by a grant from the National Institutes of Health, National Institute of Dental and Craniofacial Research, U01-DE025046. DS is supported by the Swedish Research Council (4.1-2016-00416). The Microbiome Core is supported in part by the NIH/National Institute of Diabetes and Digestive and Kidney Diseases grant P30 DK34987.

Supplementary material

431026_1_En_40_MOESM1_ESM.pdf (2.1 mb)
Supragingival plaque collection equipment and supplies (PDF 2192 kb)


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Kimon Divaris
    • 1
    • 2
    Email author
  • Dmitry Shungin
    • 3
    • 4
  • Adaris Rodríguez-Cortés
    • 2
    • 5
  • Patricia V. Basta
    • 2
    • 5
  • Jeff Roach
    • 6
  • Hunyong Cho
    • 11
  • Di Wu
    • 11
    • 12
  • Andrea G. Ferreira Zandoná
    • 7
  • Jeannie Ginnis
    • 1
  • Sivapriya Ramamoorthy
    • 8
  • Jason M. Kinchen
    • 13
  • Jakub Kwintkiewicz
    • 16
  • Natasha Butz
    • 9
    • 10
  • Apoena A. Ribeiro
    • 14
  • M. Andrea Azcarate-Peril
    • 15
  1. 1.Department of Pediatric Dentistry, UNC School of DentistryUniversity of North Carolina-Chapel HillChapel HillUSA
  2. 2.Department of Epidemiology, Gillings School of Global Public HealthUniversity of North Carolina-Chapel HillChapel HillUSA
  3. 3.Department of OdontologyUmeå UniversityUmeåSweden
  4. 4.Broad Institute of the Massachusetts Institute of Technology and Harvard UniversityCambridgeUSA
  5. 5.Biospecimen Core Processing Facility, Gillings School of Global Public HealthUniversity of North Carolina-Chapel HillChapel HillUSA
  6. 6.Research ComputingUniversity of North Carolina-Chapel HillChapel HillUSA
  7. 7.Department of Comprehensive Dentistry, Tufts University School of Dental MedicineTufts UniversityBostonUSA
  8. 8.Metabolon, Inc.DurhamUSA
  9. 9.Microbiome Core Facility, Department of Cell Biology and Physiology, School of MedicineUniversity of North Carolina-Chapel HillChapel HillUSA
  10. 10.Division of Gastroenterology and Hepatology, School of Medicine, Department of MedicineUniversity of North Carolina-Chapel HillChapel HillUSA
  11. 11.Department of Biostatistics, Gillings School of Global Public HealthUniversity of North Carolina-Chapel HillChapel HillUSA
  12. 12.Department of Periodontology, UNC School of DentistryUniversity of North Carolina-Chapel HillChapel HillUSA
  13. 13.Metabolon, Inc.DurhamUSA
  14. 14.Department of Diagnostic Sciences, UNC School of DentistryUniversity of North Carolina-Chapel HillChapel HillUSA
  15. 15.Center for Gastrointestinal Biology and Disease, Division of Gastroenterology and Hepatology, and UNC Microbiome Core, Department of Medicine, School of MedicineUniversity of North CarolinaChapel HillUSA
  16. 16.Division of Gastroenterology and Hepatology, Department of Medicine, Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of MedicineUniversity of North CarolinaChapel HillUSA

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