Taxonomic Diversity and Clinical Correlations in Periapical Lesions by Next-Generation Sequencing Analysis

Objectives: The aim of this study was to assess the taxonomic diversity of the microbiota associated with periapical lesions of endodontic origin and to determine whether microbial profiles vary across different populations and clinical characteristics using a unified in silico analysis of next-generation sequencing (NGS) data. Methods: Raw 16S rRNA sequencing data from three published studies were retrieved from the NCBI Sequence Read Archive and reprocessed using a standardized bioinformatics pipeline. Amplicon sequence variants were inferred using DADA2, and taxonomic assignments were performed using BLASTN against a curated 16S rRNA reference database. Alpha and beta diversity analyses were conducted using QIIME 2 and R, and differential abundance was assessed with ANCOM-BC2. Statistical comparisons were made based on population, sex, symptomatology, and other clinical metadata. Results: A total of 38 periapical lesion samples yielded 566,223 high-confidence reads assigned to 347 bacterial species. Significant differences in microbial composition were observed between geographic regions (China vs. Spain), sexes, and symptoms. Core species such as Fretibacterium sp. HMT 360 and Porphyromonas endodontalis were prevalent across datasets. Porphyromonas gingivalis and Fusobacterium nucleatum were found in abundance across all three studies. Beta diversity metrics revealed distinct clustering by study and country. Symptomatic lesions were associated with higher abundance of Alloprevotella tannerae and Prevotella oris. Conclusions: The periapical lesion microbiota is taxonomically diverse and varies significantly by geographic and clinical features.