Amplicon-based next-generation sequencing for comparative analysis of root canal microbiome of teeth with primary and persistent/secondary endodontic infections

• Published in: Clinical oral investigations Vol. 27; no. 3; pp. 995 - 1004
• Main Authors: Kesim, Bertan, Ülger, Seda Tezcan, Aslan, Gönül, Cudal, Hamza, Üstün, Yakup, Küçük, Mustafa Öner
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01-03-2023; Springer Nature B.V
• Subjects: Bioinformatics; Coinfection; Comparative analysis; Dental Pulp Cavity - microbiology; Dentistry; Discriminant analysis; Endodontics; Gram-positive bacteria; High-Throughput Nucleotide Sequencing - methods; Humans; Infections; Medicine; Microbiomes; Microbiota - genetics; Multivariate analysis; Next-generation sequencing; Original Article; Persistent infection; RNA, Ribosomal, 16S - genetics; Root Canal Therapy; Root canals; Teeth; Amplicon sequence variants; Retreatment; Next-generation sequencing; 16S ribosomal RNA sequencing; Endodontic infection; Microbiome
• ISSN: 1436-3771; 1432-6981; 1436-3771
• DOI: 10.1007/s00784-023-04882-x

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.