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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

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Abstract

Objectives

To 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 methods

Root 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.

Results

Within 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.

Conclusions

A few taxa were differentially abundant within either the PEI or SEI group.

Clinical relevance

Reliable bioinformatic tools are needed to define microbial profiles of endodontic infections. Based on a limited number of samples, no distinct variation was determined between the bacterial diversity of initial and recurrent endodontic infections.

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Data Availability

The datasets generated during and/or analysed during the current study are not publicly available as consent for publication of raw data was not obtained from study participants, but are available from the corresponding author on reasonable request.

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Funding

This study was supported by the Nuh Naci Yazgan University Scientific Research Projects Department (project number: 2020-SA.DH-BP/13).

Author information

Authors and Affiliations

  1. Department of Endodontics, Faculty of Dentistry, Nuh Naci Yazgan University, Kayseri, Turkey

    Bertan Kesim & Hamza Cudal

  2. Kuzey Çevreyolu Erkilet Dere Mah, Nuh Naci Yazgan Üniversitesi Yerleşkesi, Kocasinan, Kayseri, Turkey

    Bertan Kesim

  3. Department of Medical Microbiology, Faculty of Medicine, Mersin University, Mersin, Turkey

    Seda Tezcan Ülger & Gönül Aslan

  4. Department of Endodontics, Faculty of Dentistry, Erciyes University, Kayseri, Turkey

    Yakup Üstün

  5. Department of Microbiology, Faculty of Dentistry, Nuh Naci Yazgan University, Kayseri, Turkey

    Mustafa Öner Küçük

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  1. Bertan Kesim
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  3. Gönül Aslan
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Correspondence to Bertan Kesim.

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Ethics approval

All procedures performed in this study involving human participants were approved by Mersin University Clinical Research Ethics Committee (Mersin, Turkey) (number 2020/359) and were carried out in accordance with the 1964 Helsinki Declaration and its later amendments or comparable ethical standards.

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Informed consent was obtained from all individual participants included in the study.

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The authors declare no competing interests.

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Figure 1

Shannon-Weaver index plot shows species richness in the microbiome of the two types of infection (PNG 1242 kb)

High resolution image (TIF 147103 kb)

Figure 2

The percentages of bacteria in endodontic infections based on the oxygen requirement (PNG 926 kb)

High resolution image (TIF 105495 kb)

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Kesim, B., Ülger, S.T., Aslan, G. et al. Amplicon-based next-generation sequencing for comparative analysis of root canal microbiome of teeth with primary and persistent/secondary endodontic infections. Clin Oral Invest 27, 995–1004 (2023). https://doi.org/10.1007/s00784-023-04882-x

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