The Role of the Microbiome in Endodontic Treatment Failure

Abstract

Background: Endodontic treatment failure remains a significant clinical challenge, often attributed to persistent or recurrent microbial infections within the root canal system. The complexity of the root canal microbiome, including its diversity and resistance mechanisms, is increasingly recognized as a critical factor influencing treatment outcomes. However, the specific microbial signatures and their correlation with clinical failure remain underexplored. Objective: This study aimed to investigate the microbial composition of endodontically treated teeth with persistent apical infections and to compare microbial diversity, abundance, and resistance profiles between treatment failure and successful outcome groups. The objective was to determine the role of the microbiome in contributing to post-treatment disease and resistance to conventional therapies. Methods: A prospective, cross-sectional study was conducted on 120 adult patients aged 18–65 years who had undergone non-surgical root canal therapy within the past six months. Sixty patients exhibited post-treatment apical periodontitis and persistent symptoms, while 60 age- and tooth-matched patients with successful treatment outcomes served as controls. Clinical evaluations, including symptom severity, radiographic lesions, and oral hygiene status, were recorded. Root canal samples were collected aseptically and analyzed using 16S rRNA gene sequencing and metagenomic shotgun sequencing. Bioinformatics tools (QIIME 2, MetaPhlAn) were used to assess alpha and beta diversity, species identification, and functional pathways. Statistical analyses included t-tests, chi-square, PCA, and multiple regression with significance set at p<0.05. Results: The treatment failure group demonstrated significantly higher alpha diversity (Shannon Index: 3.8 ± 0.5 vs. 2.5 ± 0.4; p=0.001), indicating a richer and more diverse microbial community. Dominant species in the failure group included Enterococcus faecalis (70%), Fusobacterium nucleatum (65%), Porphyromonas gingivalis (60%), and Candida albicans (30%). These microorganisms exhibited strong biofilm-forming abilities and resistance to common antibiotics such as vancomycin, tetracycline, and metronidazole. Positive correlations were found between microbial diversity and both symptom severity (r=0.65, p=0.01) and lesion size (r=0.70, p=0.01), while a negative correlation was observed with oral hygiene status (r=−0.50, p=0.01). Conclusion: The findings highlight the critical role of a diverse and resistant root canal microbiome in endodontic treatment failure. The prevalence of biofilm-forming and antibiotic-resistant species in failed cases underscores the limitations of conventional antimicrobial therapies. Future endodontic strategies should incorporate microbiome-informed diagnostic tools and tailored therapeutic approaches to improve treatment success and long-term outcomes.