Subgingival Microbial Signatures Associated With Apical Periodontitis Identified by Next Generation Sequencing and Predictive Modelling

Aims: To assess the relationship between endodontic and subgingival bacterial communities in individuals with apical periodontitis (AP), and to identify disease-associated subgingival microbial signatures. We propose that subgingival microbial communities exhibit a dysbiotic profile, defined by distinct bacterial signatures, which may provide complementary biological insights into AP. Methods: In this cross-sectional study, DNA was extracted from paired endodontic and subgingival samples from mesiobuccal sites of first molars in patients with AP (n = 25 sample pairs), and from subgingival samples from the same sites in healthy individuals (n = 34). Microbiota was explored using 16S rRNA sequencing. Alpha and beta diversity metrics were calculated. Differentially abundant taxa were identified using LEfSe. Random forest models based on the bacterial counts observed in the subgingival samples were trained to classify the individuals with AP from the controls. Results: Within AP individuals, the subgingival communities differed from those present in root canals. Subgingival communities exhibited higher alpha diversity than root canal communities, irrespective of the clinical diagnosis (p < 0.001). Subgingival microbial communities in AP individuals exhibited a dysbiotic profile associated with enrichment of anaerobic and inflammophilic species (p < 0.05). Beta diversity analyses showed compositional differences between AP and control individuals, with Jaccard distance reaching statistical significance (p < 0.05), and Bray–Curtis indicating a borderline effect (p = 0.07). The best predictive model (Streptococcus sanguinis and Prevotella maculosa) achieved an accuracy of 89.8%, sensitivity of 80%, specificity of 97%, precision of 95.2%, and an AUC of 0.98. Conclusions: Subgingival profiles from AP individuals are distinct from those in healthy controls, showing AP-associated dysbiosis. Specific subgingival bacterial signatures achieved high diagnostic accuracy, supporting the potential broader impact of AP on the subgingival microbiota.