Abstract
AIM: Bacterial biofilms around the apex are crucial in disease progression and persistence of apical periodontitis. While intracanal biofilms initiate infection, extraradicular biofilms contribute to treatment resistance and persistence. Thus, a comprehensive understanding of these biofilms may help elucidate mechanisms underlying persistent apical periodontitis. Therefore, in this study, we aimed to compare the microbiome and predicted functional profiles in matched apical root canals with those of extraradicular biofilms associated with persistent apical periodontitis. METHODOLOGY: Seventeen root apices from patients with persistent apical periodontitis were collected via surgery. After extraradicular biofilm was collected, intracanal biofilm was obtained by cryopulverisation. Bacterial communities were detected by amplicon sequencing of the V1-V2 region of the 16S rRNA gene. Diversity, microbial composition and predicted bacterial functions were compared between matched intracanal and extraradicular biofilms. RESULTS: Alpha diversity analysis of the microbiome revealed no significant differences between the two sampling sites. In contrast, the beta diversity of the microbiota of the same root (matched samples) was significantly lower than that of the microbiota of unpaired samples. There were no statistically significant differences in permutational multivariate analysis of variance for the microbiome between paired extraradicular and intracanal biofilms, regardless of the presence of the sinus tract. The abundances of the predominant genera, namely Fusobacterium, Treponema, Prevotella, Porphyromonas and Bacteroides as well as gram-positive bacteria, including Actinomyces, were similar between extraradicular and intraradicular biofilms. Linear discriminant analysis effect size analysis identified bacterial taxa significantly enriched in extraradicular biofilms, whereas no taxa were significantly enriched in intraradicular biofilms. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States analysis revealed several differences in Kyoto Encyclopaedia of Genes and Genomes pathways between these biofilms. CONCLUSION: While comparison of the microbiome between extraradicular and intracanal biofilms of the same root apices revealed differences in bacterial composition, certain similarities were noted, particularly in dominant bacterial species abundance, indicating a close microbial relationship between intracanal and extraradicular biofilms, with some exceptions. Additionally, some differences in predicted functional profiles were observed between the two biofilm types. Thus, the characterisation of bacterial communities around the apical foramen may guide the development of appropriate antimicrobial strategies.