Human oral mucosa and oral microbiome interactions following supragingival plaque reconstitution in healthy volunteers: a diet-controlled balanced design proof-of-concept model to investigate oral pathologies

ABSTRACT

Changes in the oral microbiome may contribute to oral pathologies, especially in patients undergoing cancer therapy. Interactions between oral microbiome and oral mucosa may exacerbate inflammation. We determined whether probiotic-controlled plaque formation could impact proximal oral mucosa gene expression profiles in healthy volunteers. A 3-weeks balanced sample collection design from healthy volunteers (HVs) was implemented. At Week-1 plaques samples and labial mucosa brush biopsies were obtained from HVs in the morning (N = 4) and/or in the afternoon (N = 4), and groups were flipped at Week-3. A fruit yogurt and tea diet were given 2-4hrs before sample collection. mRNA gene expression analysis was completed using RNA-Seq and DESeq2. Bacterial taxa relative abundance was determined by 16S HOMINGS. Bacterial diversity changes and metabolic pathway enrichment were determined using PRIMERv7 and LEfSe programs. Alpha- and beta-diversities did not differ morning (AM) vs. afternoon (PM). The most affected KEGG pathway was Toll-like receptor signaling in oral mucosa. Eighteen human genes and nine bacterial genes were differentially expressed in plaque samples. Increased activity for ‘caries-free’ health-associated calcifying Corynebacterium matruchotii and reduced activity for Aggregatibacter aphrophilus, an opportunistic pathogen, were observed. Microbial diversity was not altered after 8 hours plaque formation in healthy individuals as opposed to gene expression.

KEYWORDS:

• Host–microbe interaction
• dental plaque
• oral mucosa
• oral microbiome
• gene expression

Acknowledgments

We would like to thank CDx Diagnostics (Suffern, NY) for providing brush biopsy test kits for research purposes. We also thank Dr Alex Mira (Department of Health and Genomics, Center for Advanced Research in Public Health, FISABIO Foundation, Valencia, Spain) and Dr Alphonso Benittez-Paez (Centro de Investigación Príncipe Felipe, Valencia, Spain) for providing detailed protocols and critical advice to conduct microbiome transcriptomics of the dental plaque samples. We thank Alexis Kokaras for the next-generation sequencing and ProbeSeq program, Molecular Biology Core lab for RNA sequencing and Kathleen Sullivan for her editorial support.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Authors’ contributions

JLM and FBM contributed to the conceptualization of this study. JLM, FBM, MTB, DSM and JN participated in protocol development and implementation of the study. NMS implemented transcriptomics RNA-Seq experiments. JLM wrote the manuscript and directed the statistical analyses implemented and verified by MFB. JLM, FBM, and MFB contributed to the overall analysis and/or biological interpretation. All authors participated in the revisions of the manuscript and/or interpretation of the results. All authors gave their final approval and agreed to be accountable for all aspects of the work.

Consent

This study has been approved by the Institutional Review Board of Carolinas Medical Center-Atrium Health, Charlotte, NC. All patients participating in this study have signed an informed consent (IRB file #01–16-09E).

Data availability statement

All data and accompanying files are available via the Translational Research Lab Github repository (https://github.com/mbeckm01/RNASeq).

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/20002297.2023.2246279.

Additional information

Funding

Funding was obtained from the Atrium Health Foundation.