Distinct bacteria profiles in primary and secondary/persistent endodontic infections: a 16S rRNA gene sequencing study

This study investigated the bacterial community composition, phenotypes, and differentially abundant taxa in primary and secondary/persistent endodontic infections. Bacterial profiles of 12 primary and 12 secondary/persistent endodontic infections were analyzed using 16 S V3-V4 next-generation sequencing. Reads were processed into ASVs using DADA2 in Qiime2, and taxonomy was assigned with the SILVA dataset. Alpha and beta diversity were compared between groups using Kruskal-Wallis and PERMANOVA. LEfSe identified differentially abundant taxa (LDA > 2), and Bugbase predicted community phenotypes, which were compared with the Mann-Whitney-Wilcoxon test. The alpha-diversity and beta-diversity are higher in the secondary/persistent group than in the primary one. In the primary group, anaerobic, Gram-negative, and potentially pathogenic microbes are dominant, whereas facultatively anaerobic, Gram-positive microbes are more prevalent in the secondary/persistent group. The bacterial metabolic phenotype is associated with the tooth condition. Linear discriminant analysis effect size analysis reveals that the relative abundance of genera Clostridia_vadinBB60_group and Rothia are higher in the primary group, while Saccharimonadaceae, Veillonella, Actinomyces, Granulicatella, Haemophilus, Bergeyella, Leptotrichia, Capnocytophaga, TM7x, Neisseria, Centipeda, and Saccharimonadales are more dominant in the secondary/persistent group. Significant differences in species and abundance were present between primary and secondary/persistent endodontic infections, with the bacterial community being more diverse in secondary/persistent group than in primary one. The taxonomic and phenotypic information derived from microbiome analysis helps elucidate the microbial basis for primary and secondary/persistent infections, identify potential causes of treatment failure, and guide downstream irrigation protocol, retreatment strategy, and risk assessment.