Metagenomics as an Effective Diagnostic Approach for Exploring Oral Microbial Diversity and Dental Diseases: A Narrative Review.

Abstract

Aim and background: The oral cavity harbors a diverse microbiota that significantly influences oral health and disease. Conventional microbiological techniques have limitations in detecting the full range of microbial species, particularly those that are uncultivable. Metagenomics, through culture-independent, high-throughput sequencing methods, offers a comprehensive approach to studying oral microbial diversity. This narrative review aims to evaluate the role of metagenomics in exploring the oral microbiome and its association with dental diseases.

Methods: This review systematically synthesized current literature and research on metagenomic technologies, including 16S ribosomal RNA (rRNA) sequencing, shotgun metagenomics, metatranscriptomics, metaproteomics, and metabolomics. It highlighted their principles, diagnostic capabilities, and limitations in analyzing microbial communities in caries, endodontic infections, and periodontitis. It also reviewed auxiliary tools such as quantitative polymerase chain reaction (qPCR), microarrays, fluorescence in situ hybridization (FISH), and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), and discussed the integration of artificial intelligence (AI) in metagenomic data interpretation.

Results: Metagenomic studies have expanded the scope of known microbial species involved in dental caries beyond Streptococcus mutans, highlighting the contributions of Lactobacillus, Veillonella, Actinomyces, and Candida albicans. In endodontics, resistant species such as Enterococcus faecalis, Porphyromonas endodontalis, and Fusobacterium nucleatum are implicated in persistent infections. In periodontitis, a dysbiotic microbial shift has been associated with the presence of complex microbial consortia, including red and orange complex bacteria.

Conclusion: Metagenomics is a powerful diagnostic tool that provides an in-depth characterization of the complex microbial ecosystem of the oral cavity. It offers diagnostic potential through early and accurate detection of pathogenic shifts, promotes personalized treatment planning, and opens avenues for the development of potential biomarkers of disease progression.

Clinical significance: The integration of metagenomics into dental practice can revolutionize caries risk assessment, treatment precision, and disease prevention strategies. Although challenges such as high cost, data complexity, and lack of standardization remain, ongoing advancements in sequencing technologies and bioinformatics are expected to enhance its accessibility and clinical relevance.

How to cite this article: Walia T, Srivastava N, Shetty RM, et al. Metagenomics as an Effective Diagnostic Approach for Exploring Oral Microbial Diversity and Dental Diseases: A Narrative Review. Int J Clin Pediatr Dent 2026;19(2):278-284.