Ecological trajectories and microbial network reorganization across caries-associated oral niches

Abstract

Dental caries is a biofilm-mediated disease associated with ecological changes in the oral microbiome. How microbial community organization differs among healthy plaque, caries-associated plaque, and carious dentin remains incompletely defined. We used 16S rRNA gene sequencing to profile paired supragingival plaque and carious dentin samples from patients with caries, together with supragingival plaque from healthy controls. Caries-associated plaque showed higher diversity than healthy plaque, whereas diversity was lower in carious dentin. Ecological ordering placed the three sample types along a health-plaque-dentin continuum. Association-network analysis showed distinct network structures in caries-associated plaque and carious dentin, with the dentin network displaying greater density and lower modularity. By integrating differential-abundance and network centrality results, we identified taxa associated with the dentin niche. A sparse logistic regression model using three genera distinguished plaque from dentin in patient-grouped cross-validation (AUROC, 0.780; AUPRC, 0.718). These cross-sectional findings describe niche-associated microbiome organization in dental caries and provide candidate features for future validation in independent, clinically relevant cohorts.