Multiomics analysis reveals the genetic and metabolic characteristics associated with the low prevalence of dental caries

ABSTRACT

Background

Despite poor oral hygiene, the Baiku Yao (BKY) ethnic group in China presents a low prevalence of dental caries, which may be related to genetic susceptibility. Due to strict intra-ethnic marriage rule, this ethnic has an advantage in studying the interaction between genetic factors and other regulatory factors related to dental caries.

Methods

Peripheral blood from a caries-free adult male was used for whole genome sequencing, and the BKY assembled genome was compared to the Han Chinese genome. Oral saliva samples were collected from 51 subjects for metabolomic and metagenomic analysis. Multiomics data were integrated for combined analysis using bioinformatics approaches.

Results

Comparative genomic analysis revealed the presence of structural variations in several genes associated with dental caries. Metabolomic and metagenomic sequencing demonstrated the caries-free group had significantly higher concentration of antimicrobials and higher abundance of core oral health-related microbiota. The functional analysis indicated that cationic antimicrobial peptide resistance and the lipopolysaccharide biosynthesis pathway were enriched in the caries-free group.

Conclusions

Our study provided new insights into the specific regulatory mechanisms that contribute to the low prevalence of dental caries in the specific population and may provide new evidence for the genetic diagnosis and control of dental caries.

KEYWORDS:

• Baiku Yao
• dental caries
• metabolome
• metagenomic
• multiomics
• antimicrobials

Acknowledgments

We are extremely grateful to all volunteers who donated their samples and all participants who contributed to this study.

Disclosure statement

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

Author contributions

J. L.: Conceptualization, Investigation, Methodology, Validation, Formal analysis, Data curation, Writing – Original draft, Writing -Review & Editing, Visualization; S.-Y. Y.: Methodology, Validation, Formal analysis, Data curation, Writing – Original draft, Writing -Review & Editing, Visualization. X.-D. X.: Validation, Formal analysis, Data curation. Q. L.: Formal analysis, Data curation. F. M.: Formal analysis, Data curation. X. Y.: Formal analysis, Data curation. Y.-H. L.: Formal analysis, Data curation. L.-L. C.: Conceptualization, Writing – Review & Editing, Supervision, Project administration, Funding acquisition. X. Z.: Conceptualization, Investigation, Writing – Review & Editing, Supervision, Project administration, Funding acquisition. All authors read and approved the final manuscript.

Data availability statement

The raw data of genome and metabolome sequencing are available from the National Genomics Data Center [88] under project number PRJCA017955, PRJCA019103 and PRJCA019104.

Ethics approval

This study was approved by Guangxi Medical University College of Stomatology Ethical Review Committee (Approval Number:2023037).

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/20002297.2023.2277271.

Additional information

Funding

This work was supported by the National Natural Science Foundation of China (No.82060202) and the starting research grant for High-level Talents from Guangxi University.