Comparative Analysis of Root Canal Microbiota in Patients with Diabetes and Systemically Healthy Individuals: A Pilot Next-Generation Sequencing Study

<b>Objectives:</b> The aim of this study is to assess the influence of diabetes mellitus on the microbial flora involved in root canal infections through a comparative analysis with that of systemically healthy individuals. <b>Methods:</b> A total of 39 participants, including 21 patients with diabetes mellitus and 18 systemically healthy individuals (controls), were enrolled in the study. In the diabetic group, 12 teeth were diagnosed with secondary/persistent endodontic infections (SEIs) and 9 with primary endodontic infections (PEIs). In the healthy group, 12 teeth presented with SEIs and 6 with PEIs. Root canal samples were obtained using sterile paper points. The V3-V4 hypervariable regions of 16S rDNA from both sample types were amplified and sequenced using the Illumina MiSeq platform. Microbial richness and diversity were assessed using alpha diversity indices and beta diversity metrics. <b>Results:</b> Faith's Phylogenetic Diversity showed a significant difference between diabetic patients with SEIs and healthy individuals with PEIs (<i>p</i> = 0.02). Both weighted and unweighted UniFrac beta diversity analyses indicated significant differences in microbial composition and phylogenetic structure between diabetic patients with SEIs and healthy individuals with PEIs (<i>p</i> = 0.01 and <i>p</i> = 0.02, respectively). Within the diabetic patient group, significant differences were observed between SEI and PEI groups based on alpha (Fisher's alpha, <i>p</i> = 0.04) and beta diversity analyses (Bray-Curtis and Weighted UniFrac <i>p</i> = 0.02 and <i>p</i> = 0.01, respectively). <b>Conclusions:</b> Diabetic patients showed different microbial profiles compared to healthy individuals.