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    Amplicon-based next-generation sequencing for comparative analysis of root canal microbiome of teeth with primary and persistent/secondary endodontic infections
    (Springer Heidelberg, 2023) Kesim, Bertan; Ulger, Seda Tezcan; Aslan, Gonul; Cudal, Hamza; Ustun, Yakup; Kucuk, Mustafa Oner
    ObjectivesTo compare the root canal microbiome profiles of primary and persistent/secondary infections using high-throughput sequencing with the help of a reliable bioinformatics algorithm.Materials and methodsRoot canal samples of 10 teeth in the primary endodontic infection (PEI) group and 10 teeth in the persistent/secondary endodontic infection (SEI) group were included resulting in a total of 20 samples. After DNA extraction from the samples, sequencing was performed on the Illumina MiSeq platform. Pair-end Illumina reads were imported to QIIME 2; amplicon sequence variants (ASVs) generated by DADA2 were mapped to GreenGenes database. Weighted UniFrac distances were calculated and principal coordinates analysis (PCoA) was used to compare beta diversity patterns. The multiple response permutation procedure (MRPP), the analysis of similarities (ANOSIM), and permutational multivariate analysis of variance (adonis) were conducted for testing group differences. Linear discriminant analysis effect size (LEfSe) analysis was utilized to identify differentially abundant taxa between the groups. The linear discriminant analysis (LDA) score threshold was set to 4.0.ResultsWithin the Gram-negative facultative anaerobic Gammaproteobacteria class outgroup, two orders (Pasteurellales, Vibrionales) and two families (Pasteurellaceae, Vibrionaceae) were significantly more abundant in the PEI group, whereas Gram-positive bacteria, Actinomycetales order, and Gram-positive anaerobic taxa, one genus (Olsenella) and one species (Olsenella uli), were identified as significantly more abundant in the SEI group.ConclusionsA few taxa were differentially abundant within either the PEI or SEI group.
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    Effects of Sequential Antimicrobial Phases on Root Canal Microbiome Dynamics in Two-Visit Treatment of Primary Apical Periodontitis: A Longitudinal Experimental Study
    (Mdpi, 2024) Kesim, Bertan; Ulger, Seda Tezcan; Aslan, Gonul; Ustun, Yakup; Avci, Ayse Tugba; Kucuk, Mustafa Oner
    Background: Effective management of primary apical periodontitis depends on understanding the dynamic interactions within the root canal microbiome. This study aimed to investigate the effect of sequential antimicrobial phases on the root canal microbiome during a two-visit treatment approach, with a focus on calcium hydroxide medication. Methods: Samples were collected from three teeth across four treatment phases: initial infection (S1), after chemomechanical preparation (S2), after intracanal medication (S3), and after a final flush (S4). DNA was extracted, and the V3-V4 regions of the 16S rRNA gene were sequenced using Illumina MiSeq. Sequencing data were analyzed with QIIME 2, and differentially abundant taxa were identified using linear discriminant analysis effect size (LEfSe). Results: While microbial community composition did not differ significantly between phases, the Firmicutes/Bacteroidetes ratio decreased after the antimicrobial stages. LEfSe analysis revealed higher abundances of Lactobacillales, Arthrobacter, and Veillonella in the untreated (CMP) group. Bifidobacterium longum was relatively more abundant in the intracanal medication (ICM) phase, and Dorea formicigenerans was more abundant in the final-flush (FF) phase. Conclusions: Although calcium hydroxide treatment did not induce statistically significant changes in overall root canal microbial composition, trends such as a reduction in the Firmicutes/Bacteroidetes ratio and a relative increase in Bifidobacterium longum numbers suggest potential ecological shifts. The observed relative increase in Bifidobacterium longum numbers may represent a hypothesis-driven observation reflecting indirect ecological effects rather than direct pH modulation. While visual patterns (e.g., PCA clustering) were observed, they lacked statistical support. Further studies with larger sample sizes are needed to validate these observations and assess the potential role of beneficial bacteria in root canal treatments.
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    Evaluation of the Efficacy of 2% Chlorhexidine in Combination with Passive Ultrasonic Irrigation on Enterococcus faecalis Biofilm
    (Galenos Yayincilik, 2020) Kesim, Bertan; Ulger, Seda Tezcan; Topcuoglu, Huseyin Sinan; Aslan, Gonul; Kurnaz, Nurbanu; Sagsen, Burak
    Objective: This study aimed to evaluate the combined effectiveness of 2% chlorhexidine (CHX) and passive ultrasonic irrigation (PUI) against Enterococcus faecalis (E. faecalis) biofilm. Materials and Methods: The root canals of 66 single-rooted extracted human mandibular premolar teeth (n=66) were enlarged up to a size of 40/0.06 taper and autoclaved. Fifty-nine roots were inoculated with E. faecalis and incubated for 4 weeks, whereas 7 roots served as the negative control group and were filled with sterile brain heart infusion broth. The remaining specimens (n=59) were assigned into 4 experimental groups (n=13) and a positive control group (n=7): CHX via standard needle irrigation (SNI), sodium hypochloride (NaOCl) via SNI, CHX via PUI, NaOCl via PUI and non-treated positive controls. Bacteriological samples were collected before and after the intervention, and microbiological analysis was performed by counting the colony forming units. Reduction in colony count (RCC) between before and after the intervention in each group were compared using One-Way ANOVA. Results: The highest RCC was determined in NaOCl/PUI and the lowest in CHX/SNI (p<0.05). Regarding RCC, CHX/PUI showed statistically similar results with NaOCl/PUI and NaOCl/SNI (p>0.05). Conclusion: A PUI of 2% CHX induced a statistically similar amount of RCC with both a PUI of 2.5% NaOCl and SNI of 2.5 % NaOCl. PUI combined with 2 % CHX can be used in secondary endodontic infections and during routine endodontic treatment due to increased antibacterial efficiency against E. faecalis.