Dental caries remains the most prevalent oral disease worldwide. The development of dental caries is highly associated with the microbiota in the oral cavity. Microbiological research of dental caries has been conducted for over a century, with conventional culture-based methods and targeted molecular methods being used in order to identify the microorganisms related to dental caries. These methods’ major limitation is that they can identify only part of the culturable microorganisms in the oral cavity. Introducing sequencing-based technology and bioinformatics analysis has boosted oral microbiome research and greatly expanded the understanding of complex oral microbiology. With the continuing revolution of molecular technologies and the accumulated sequence data of the oral microbiome, researchers have realized that microbial composition alone may be insufficient to uncover the relationship between caries and the microbiome. Most updated evidence has coupled metagenomics with transcriptomics and metabolomics techniques in order to comprehensively understand the microbial contribution to dental caries. Therefore, the objective of this article is to give an overview of the research of the oral microbiome and the development of dental caries. This article reviews the classical concepts of the microbiological aspect of dental caries and updates the knowledge of caries microbiology with the results of current studies on the oral microbiome. This paper also provides an update on the caries etiological theory, the microorganisms related to caries development, and the shifts in the microbiome in dental caries development.

To review the application of omics technologies in the field of Cariology research and provide critical insights into the emerging opportunities and challenges. Publications on the application of omics technologies in Cariology research up to December 2022 were sourced from online databases, including PubMed, Web of Science and Scopus. Two independent reviewers assessed the relevance of the publications to the objective of this review. Studies that employed omics technologies to investigate dental caries were selected from the initial pool of identified publications. A total of 922 publications with one or more omics technologies adopted were included for comprehensive bibliographic analysis. (Meta)genomics (676/922, 73%) is the predominant omics technology applied for Cariology research in the included studies. Other applied omics technologies are metabolomics (108/922, 12%), proteomics (105/922, 11%), and transcriptomics (76/922, 8%). This study identified an emerging trend in the application of multiple omics technologies in Cariology research. Omics technologies possess significant potential in developing strategies for the detection, staging evaluation, risk assessment, prevention, and management of dental caries. Despite the numerous challenges that lie ahead, the integration of multi-omics data obtained from individual biological samples, in conjunction with artificial intelligence technology, may offer potential avenues for further exploration in caries research. This review presented a comprehensive overview of the application of omics technologies in Cariology research and discussed the advantages and challenges of using these methods to detect, assess, predict, prevent, and treat dental caries. It contributes to steering research for improved understanding of dental caries and advancing clinical translation of Cariology research outcomes.

To explore the effects of silver diamine fluoride (SDF) on the microbial community of carious lesions. Original studies evaluating the effect of SDF treatment on the microbial community of human carious lesions were included. A systematic search of English-language publications was performed in PubMed, EMBASE, Scopus, and Web of Science. Gray literature was searched in ClinicalTrials.gov and Google Scholar. This review included seven publications reporting the effects of SDF on microbial community of dental plaque or carious dentin, including the microbial biodiversity, relative abundance of microbial taxa, and predicted functional pathways of the microbial community. The studies on microbial community of dental plaque reported that SDF did not have a significant effect on both the within-community species diversity (alpha-diversity) and inter-community microbial compositional dissimilarity (beta-diversity) of the plaque microbial communities. However, SDF changed the relative abundance of 29 bacterial species of plaque community, inhibited carbohydrate transportation and interfered with the metabolic functions of the plaque microbial community. A study on the microbial community in dentin carious lesions reported that SDF affected its beta-diversity and changed the relative abundance of 14 bacterial species. SDF showed no significant effects on the biodiversity of the plaque microbial community but changed the beta-diversity of the carious dentin microbial community. SDF could change the relative abundance of certain bacterial species in the dental plaque and the carious dentin. SDF could also affect the predicted functional pathways of the microbial community. This review provided comprehensive evidence on the potential effect of SDF treatment on the microbial community of carious lesions.

This review compares the oral microbiota profiles of preschool children with early childhood caries (ECC) to those of caries-free controls. PubMed, Web of Science, Embase, and Scopus were systematically searched for English-language reports published before January 1, 2026. Studies using next-generation sequencing (NGS) to compare the oral microbiota of systemically healthy preschool children (≤6 years) with and without ECC were included. Data on study characteristics, participant and sample information, study methods, and key study outcomes were extracted. Data were qualitatively synthesized, stratified by oral sample type and microbial kingdom. Twenty-one studies published between 2013 and 2025 were included. Some studies include overlapping sample types and microbial kingdoms, with three examining both plaque and salivary samples, and three analyzing both bacterial and fungal microbiota. Nine studies examined plaque bacterial microbiota. Eight reported no differences in alpha diversity between ECC-affected children and caries-free controls, whereas all studies reported significant differences in beta diversity between groups. Based on replication criteria, ten bacterial species were enriched and nine were depleted in ECC. Four studies examining plaque fungal microbiota yielded no consistent findings regarding fungal diversity, reflecting heterogeneity and limited replication across studies. However, two fungal species were found to be enriched in ECC in two studies. Twelve studies assessed salivary bacterial microbiota. Ten reported similar alpha diversity between ECC and control groups, while findings on beta diversity were inconsistent across studies. Based on replication criteria, four bacterial species were enriched in ECC and one was depleted. Three studies examined salivary fungal microbiota, with no consistent findings on fungal diversity and limited concordance between studies. This review indicates that bacterial communities exhibit similar species diversity between ECC-affected children and caries-free controls in both sample types. While plaque bacterial communities consistently differed in beta diversity and species abundance between the two groups, salivary bacterial communities show less consistent differences in beta diversity between ECC and controls. Fungal microbiota in both plaque and saliva remain understudied. This review provided comprehensive evidence on the microbial features associated with ECC, highlighting stronger associations between plaque-specific dysbiosis and clinical caries status in preschool children.

The stage-specific ecological and functional microbial features of ECC remains poorly defined. This study aimed to characterize the lesion-associated microbiome and evaluate stage-specific microbial signatures of ECC. Paired supragingival plaque samples were collected from an active cavitated lesion (caries) and a spatially-matched intact surface (control) of 84 ECC-affected children aged 3 - 4 years. Lesions were classified by depth as enamel caries and dentine caries. Microbial profiles were generated by 16S rRNA sequencing and analysed for community diversity, structure, and differentially abundant taxa. PICRUSt2 was used for functional prediction. Alpha diversity did not differ between caries and controls, but beta diversity revealed significant compositional separation. PERMANOVA identified disease status as the main driver of community variation, with disease staging as an additional significant factor. Caries lesions were enriched with classical and emerging cariogenic taxa, including Streptococcus mutans, Prevotella histicola, Prevotella salivae, Selenomonas sputigena, Scardovia wiggsiae, and Veillonella dispar. A 13-species panel distinguished caries from controls with an AUC of 0.85. Stratification by caries staging revealed pronounced dysbiosis confined to the dentine caries subgroup. Functional prediction suggested that dentine caries had a distinct inferred profile, with predicted enrichment of carbohydrate metabolism pathways, the phosphotransferase system, and the pentose phosphate pathway. In ECC-affected children, plaque microbiome in carious lesions showed distinct compositional, ecological and functional alterations versus unaffected surfaces, with further dysbiosis driven by caries progression. Dentine caries featured a stage-specific consortium of cariogenic taxa and a predicted functional shift toward intensified carbohydrate uptake and fermentation, informing potential microbiome-targeted strategies for ECC management. The identified ecological progression of ECC offers key microbial biomarkers to inform microbiome-targeted preventive and therapeutic strategies, ultimately improving clinical outcomes in pediatric dentistry.