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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dc.authorid, Bertan/0000-0001-9192-5487
dc.contributor.authorKesim, Bertan
dc.contributor.authorUlger, Seda Tezcan
dc.contributor.authorAslan, Gonul
dc.contributor.authorCudal, Hamza
dc.contributor.authorUstun, Yakup
dc.contributor.authorKucuk, Mustafa Oner
dc.date.accessioned2025-02-24T17:18:44Z
dc.date.available2025-02-24T17:18:44Z
dc.date.issued2023
dc.departmentFakülteler, Diş Hekimliği Fakültesi, Endodonti Ana Bilim Dalı
dc.description.abstractObjectivesTo 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.
dc.description.sponsorshipNuh Naci Yazgan University Scientific Research Projects Department [2020-SA. DH-BP/13]
dc.description.sponsorshipThis study was supported by the Nuh Naci Yazgan University Scientific Research Projects Department (project number: 2020-SA. DH-BP/13).
dc.identifier.doi10.1007/s00784-023-04882-x
dc.identifier.endpage1004
dc.identifier.issn1432-6981
dc.identifier.issn1436-3771
dc.identifier.issue3
dc.identifier.pmid36723715
dc.identifier.scopus2-s2.0-85147184378
dc.identifier.scopusqualityQ1
dc.identifier.startpage995
dc.identifier.urihttps://doi.org/10.1007/s00784-023-04882-x
dc.identifier.urihttps://hdl.handle.net/20.500.14440/833
dc.identifier.volume27
dc.identifier.wosWOS:000925368000002
dc.identifier.wosqualityQ1
dc.indekslendigikaynakWeb of Science
dc.indekslendigikaynakScopus
dc.indekslendigikaynakPubMed
dc.language.isoen
dc.publisherSpringer Heidelberg
dc.relation.ispartofClinical Oral Investigations
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı
dc.rightsinfo:eu-repo/semantics/closedAccess
dc.snmzKA_WOS_20250201
dc.subjectAmplicon sequence variants
dc.subjectMicrobiome
dc.subjectEndodontic infection
dc.subjectNext-generation sequencing
dc.subjectRetreatment
dc.subject16S ribosomal RNA sequencing
dc.titleAmplicon-based next-generation sequencing for comparative analysis of root canal microbiome of teeth with primary and persistent/secondary endodontic infections
dc.typeArticle

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