Staging-Dependent Dysbiosis of Plaque Microbiota in Early Childhood Caries

Objectives 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. Methods 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. Results 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. Conclusions 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. Clinical significance 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.