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Updated: Mar 14, 2026
Oral Biofilm Sampling for Microbiome Analysis in Healthy Children
Published on: December 31, 2017
A Comparison of Endodontic Microbiomes Associated With Symptomatic and Asymptomatic Apical Periodontitis by
David Donnermeyer1,2, Edgar Schäfer3, Daniel Hagenfeld2
1Department of Restorative, Preventive and Pediatric Dentistry, School of Dental Medicine, University of Bern, Bern, Switzerland.
Aim:
This cross-sectional study aimed to compare the endodontic microbiome assessed from root canals of teeth associated with either symptomatic or asymptomatic apical periodontitis and analysed by 16S rDNA gene sequencing.
Methodology:
60 teeth presenting clinical and radiographic signs of symptomatic or asymptomatic apical periodontitis (n = 30) were included in this cross-sectional study after participants had given their written informed consent. After isolation with rubber dam, disinfection and access cavity preparation, glide paths were prepared using C-Pilot Files and K-Files under electronic root canal length control. Microbial samples were collected from a total of 120 root canals (symptomatic apical periodontitis, SAP: n = 62, asymptomatic apical periodontitis, AAP: n = 58) each with a sterile file (size 20/0.06) in a single length technique. Only one specimen per tooth was included in the analysis; in multi-rooted teeth, the specimen with highest sequencing depth. After DNA extraction, the hypervariable region V4 of the bacterial 16 S rRNA gene was amplified and sequenced (Illumina MiSeq). Taxonomy was assigned based on the expanded Human Oral Microbiome Database (eHOMD). Statistical analysis of diversity parameters comprised Mann-Whitney U tests and PERMANOVA. Compositional differences were evaluated by differential abundance analyses using DESeq2, LinDA, and ANCOM-BC2 methods.
Results:
No differences were observed in richness and diversity (Shannon diversity index) on the genus or ASV level (p > 0.05). According to PERMANOVA, SAP and AAP microbiomes did not differ significantly both on genus and ASV levels (p > 0.05). Among highly abundant genera, Fusobacterium was indicated to be more abundant in SAP samples whereas Actinomyces was more abundant in AAP samples.
Conclusions:
The expression of clinical symptoms in apical periodontitis does not appear to be determined by specific microorganisms but may instead reflect shifts of the relative abundance of the microbial community.
