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

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Odontogenesis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1922))

Abstract

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.

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Acknowledgments

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.

Author information

Authors and Affiliations

  1. Department of Pediatric Dentistry, UNC School of Dentistry, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA

    Kimon Divaris & Jeannie Ginnis

  2. Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA

    Kimon Divaris, Adaris Rodríguez-Cortés & Patricia V. Basta

  3. Department of Odontology, Umeå University, Umeå, Sweden

    Dmitry Shungin

  4. Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA

    Dmitry Shungin

  5. Biospecimen Core Processing Facility, Gillings School of Global Public Health, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA

    Adaris Rodríguez-Cortés & Patricia V. Basta

  6. Research Computing, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA

    Jeff Roach

  7. Department of Comprehensive Dentistry, Tufts University School of Dental Medicine, Tufts University, Boston, MA, USA

    Andrea G. Ferreira Zandoná

  8. Metabolon, Inc., Durham, NC, USA

    Sivapriya Ramamoorthy

  9. Microbiome Core Facility, Department of Cell Biology and Physiology, School of Medicine, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA

    Natasha Butz

  10. Division of Gastroenterology and Hepatology, School of Medicine, Department of Medicine, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA

    Natasha Butz

  11. Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA

    Hunyong Cho & Di Wu

  12. Department of Periodontology, UNC School of Dentistry, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA

    Di Wu

  13. Metabolon, Inc., Durham, NC, USA

    Jason M. Kinchen

  14. Department of Diagnostic Sciences, UNC School of Dentistry, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA

    Apoena A. Ribeiro

  15. Center for Gastrointestinal Biology and Disease, Division of Gastroenterology and Hepatology, and UNC Microbiome Core, Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC, USA

    M. Andrea Azcarate-Peril

  16. Division of Gastroenterology and Hepatology, Department of Medicine, Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Chapel Hill, NC, USA

    Jakub Kwintkiewicz

Authors
  1. Kimon Divaris
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  2. Dmitry Shungin
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  3. Adaris Rodríguez-Cortés
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  4. Patricia V. Basta
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  5. Jeff Roach
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  6. Hunyong Cho
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  7. Di Wu
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  8. Andrea G. Ferreira Zandoná
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  9. Jeannie Ginnis
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  10. Sivapriya Ramamoorthy
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  11. Jason M. Kinchen
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  12. Jakub Kwintkiewicz
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  13. Natasha Butz
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  14. Apoena A. Ribeiro
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  15. M. Andrea Azcarate-Peril
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Corresponding author

Correspondence to Kimon Divaris .

Editor information

Editors and Affiliations

  1. School of Dentistry, University of Michigan, Ann Arbor, MI, USA

    Petros Papagerakis

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Divaris, K. et al. (2019). The Supragingival Biofilm in Early Childhood Caries: Clinical and Laboratory Protocols and Bioinformatics Pipelines Supporting Metagenomics, Metatranscriptomics, and Metabolomics Studies of the Oral Microbiome. In: Papagerakis, P. (eds) Odontogenesis. Methods in Molecular Biology, vol 1922. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9012-2_40

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  • DOI: https://doi.org/10.1007/978-1-4939-9012-2_40

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-9011-5

  • Online ISBN: 978-1-4939-9012-2

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