The root canal microbiome diversity and function. A whole‐metagenome shotgun analysis

• Published in: International endodontic journal Vol. 57; no. 7; pp. 872 - 884
• Main Authors: Ordinola‐Zapata, Ronald, Costalonga, Massimo, Dietz, Matthew, Lima, Bruno P., Staley, Christopher
• Format: Journal Article
• Language: English
• Published: England Wiley Subscription Services, Inc 01-07-2024
• Subjects: Adult; apical periodontitis; Bacteria - classification; Bacteria - genetics; Community composition; Dental Pulp Cavity - microbiology; Endodontics; Eubacterium; Female; Glucosaminidase; Gum disease; Humans; Male; Metagenome; microbiome; Microbiomes; Microbiota; Middle Aged; Periapical Periodontitis - microbiology; Periodontitis; Phospholipase C; Relative abundance; Root canals; Secondary infection; Taxonomy; toxins; virulence factors; whole‐genome sequencing; whole‐genome sequencing; apical periodontitis; microbiome; virulence factors; toxins
• ISSN: 0143-2885; 1365-2591
• DOI: 10.1111/iej.13911

Aim
To evaluate the root canal microbiome composition and bacterial functional capability in cases of primary and secondary apical periodontitis utilizing whole‐metagenome shotgun sequencing.
Methodology
Twenty‐two samples from patients with primary root canal infections, and 18 samples obtained from previously treated teeth currently diagnosed with apical periodontitis were analysed with whole‐metagenome shotgun sequencing at a depth of 20 M reads. Taxonomic and functional gene annotations were made using MetaPhlAn3 and HUMAnN3 software. The Shannon and Chao1 indices were utilized to measure alpha diversity. Differences in community composition were evaluated utilizing analysis of similarity (ANOSIM) using Bray‐Curtis dissimilarities. The Wilcoxon rank sum test was used to compare differences in taxa and functional genes.
Results
Microbial community variations within a community were significantly lower in secondary relative to primary infections (alpha diversity p = .001). Community composition was significantly different in primary versus secondary infection (R = .11, p = .005). The predominant taxa observed among samples (>2.5%) were Pseudopropionibacterium propionicum, Prevotella oris, Eubacterium infirmum, Tannerella forsythia, Atopobium rimae, Peptostreptococcus stomatis, Bacteroidetes bacterium oral taxon 272, Parvimonas micra, Olsenella profusa, Streptococcus anginosus, Lactobacillus rhamnosus, Porphyromonas endodontalis, Pseudoramibacter alactolyticus, Fusobacterium nucleatum, Eubacterium brachy and Solobacterium moorei. The Wilcoxon rank test revealed no significant differences in relative abundances of functional genes in both groups. Genes with greater relative abundances (top 25) were associated with genetic, signalling and cellular processes including the iron and peptide/nickel transport system. Numerous genes encoding toxins were identified: exfoliative toxin, haemolysins, thiol‐activated cytolysin, phospholipase C, cAMP factor, sialidase, and hyaluronic glucosaminidase.
Conclusions
Despite taxonomic differences between primary and secondary apical periodontitis, the functional capability of the microbiomes was similar.