Root Canal Microbiome in Patients Undergoing Antineoplastic Therapy: A Next-generation Sequencing Study

This study compared the intracanal microbiome of teeth with apical periodontitis in oncologic and healthy patients using 16S rRNA gene-based next generation sequencing.

Root canal samples were taken from 46 teeth with pulp necrosis and primary apical periodontitis (23 from oncologic patients and 23 from healthy controls). DNA was extracted and sequenced using the Illumina MiSeq platform targeting the V3-V4 region of the 16S rRNA gene. Bioinformatics processing was conducted using QIIME2 and DADA2. Alpha and beta diversity analyses, genus-level abundance comparisons, and indicator species analyses were performed.

After quality filtering, 3,307,822 sequence reads were retained, averaging 68,912.96 reads/sample, and resulting in 3,241 unique amplicon sequence variants. Oncologic patients exhibited significantly higher bacterial richness (P = .01), while Shannon diversity showed no significant difference between groups. Beta diversity analysis (Bray-Curtis, MDS stress = 0.14) did not reveal significant differences between groups. Indicator species analysis identified some specific taxa more associated with oncologic patients, including the candidate endodontic pathogens Prevotella, Selenomonas, Alloprevotella, Rothia, and Fretibacterium.

The root canal microbiome of oncologic patients with apical periodontitis was broadly similar to that of healthy controls. The oncologic group showed higher species richness, but no significant differences in the overall bacterial diversity or community structure.