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Measuring Effects of Dietary Fiber on the Murine Oral Microbiome with Enrichment of 16S rDNA Prior to Amplicon Synthesis

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The Oral Microbiome

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2327))

Abstract

The oral cavity houses a diverse consortium of microorganisms corresponding to specific microbial niches within the oral cavity. The complicated nature of sample collection limits the accuracy, reproducibility, and completeness of sample collection of the dentogingival microbiome. Moreover, large variability among human oral samples introduces inexorable confounds. Here, we introduce a method to study the dentogingival microbiome using a murine model that allows for greater control over experimental variability and permits collection of the dentogingival microbiome in an intact state and in its entirety.

As an example of this approach, this chapter provides a workflow to explore the effect of dietary fiber consumption on the murine dentogingival microbiome . Mice are fed diets corresponding to Fiber, Sugar, Fiber + Sugar, and Control groups for 7 weeks. A whole-mandible extraction technique is described to isolate the mandibular dentogingival surfaces. 16S rRNA gene analysis is coupled with removal of unwanted host DNA amplification products to allow an investigation of the dental microbiome in the presence of increased fiber in terms of microbial taxonomic abundance and diversity.

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Acknowledgments

This protocol was developed and tested at Mercer University (Macon, GA, USA) and was supported by Mercer University grant #213019. Bioinformatics analysis in the project described was piloted at the UIC Research Informatics Core, supported in part by NCATS through Grant UL1TR002003.

Author information

Authors and Affiliations

  1. Department of Orofacial Sciences, School of Dentistry, University of California San Francisco, San Francisco, CA, USA

    Lea M. Sedghi

  2. Research Resources Center, University of Illinois at Chicago, Chicago, IL, USA

    Stefan J. Green

  3. Department of Biology, Mercer University, Macon, GA, USA

    Craig D. Byron

Authors
  1. Lea M. Sedghi
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  2. Stefan J. Green
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  3. Craig D. Byron
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Corresponding author

Correspondence to Lea M. Sedghi .

Editor information

Editors and Affiliations

  1. College of Dentistry, University of Illinois at Chicago, Chicago, IL, USA

    Guy R. Adami

1 Electronic Supplementary Material

Supplemental Table S1

Taxonomic abundance of dietary groups (DOCX 89 kb)

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Sedghi, L.M., Green, S.J., Byron, C.D. (2021). Measuring Effects of Dietary Fiber on the Murine Oral Microbiome with Enrichment of 16S rDNA Prior to Amplicon Synthesis. In: Adami, G.R. (eds) The Oral Microbiome. Methods in Molecular Biology, vol 2327. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1518-8_16

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  • DOI: https://doi.org/10.1007/978-1-0716-1518-8_16

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1517-1

  • Online ISBN: 978-1-0716-1518-8

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