Microbiome differences between trauma- and caries-derived periapical lesions using next-generation sequencing
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI Uniform resource identifier for web resources.
Authors
Zhan J., Huang Y., Meng X., Wang Y., Liang J., Zhu F., She R., Huang S., Huo L.
Journal
Journal of oral microbiology
Year
2025
Keywords:
Trauma teeth, campylobacter, microbiome, next-generation sequencing, periapical lesions
BACKGROUND: While the microbiome of caries-derived periapical lesions has been extensively characterized, the microbial profile of trauma-derived periapical lesions remains poorly understood. This study aimed to characterize the apical microbiome of trauma-derived periapical lesions and identify taxonomic differences between trauma- and caries-derived periapical lesions. METHODS: Twenty patients with periapical lesions were enrolled, comprising 10 trauma-derived cases (trauma group) and 10 caries-derived cases (caries group). Microbial samples were collected using sterile paper points inserted into the root canal exudate, followed by DNA extraction and Illumina sequencing of the hypervariable V3-V4 regions of the 16S rRNA gene. Bioinformatic analyses included α-diversity, β-diversity based on Bray-Curtis distance and differential abundance testing (LEfSe method with LDA score ≥ 2.0). RESULTS: Sequencing revealed 36 bacterial phyla and 587 genera across all samples. Trauma group showed significantly greater relative abundance of Campylobacter (P = 0.002) compared to caries group, whereas Prevotella (P = 0.008), Vibrio (P = 0.041) and Filifactor (P = 0.006) exhibited reduced abundance. The core microbiota in the trauma group included Phocaeicola, Porphyromonas and Pyramidobacter, based on relative abundance. LEfSe analysis identified Campylobacter as a biomarker for the trauma group. CONCLUSIONS: Trauma-derived periapical lesions exhibited reduced microbial diversity compared to caries-derived periapical lesions, with Campylobacter identified as a potential pathognomonic taxon for trauma-derived periapical lesions.
Experiment 1
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Dental pulp Dental pulp cell,Pulp of tooth,Tooth pulp,Dental pulp,dental pulp
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Periapical Periodontitis apical periodontitis,periapical periodontitis,Periapical Periodontitis,periapical Periodontitis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Caries
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Trauma
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients suffering from chronic apical periodontitis due to trauma
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Mann-Whitney (Wilcoxon)
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Source: Figure 5A
Description: Differential abundance between caries and trauma group
Abundance in Group 1: increased abundance in Trauma
| NCBI | Quality Control | Links |
|---|---|---|
| Campylobacterota |
Revision editor(s): EniolaAde
Signature 2
Source: Figure 5B and 5C
Description: Differential abundance between caries group and trauma group
Abundance in Group 1: decreased abundance in Trauma
| NCBI | Quality Control | Links |
|---|---|---|
| Filifactor | ||
| Filifactor villosus | ||
| Oribacterium | ||
| Prevotella | ||
| Segatella oris | ||
| Vibrio 678715Vibrio 678715 |
Revision editor(s): EniolaAde
Experiment 2
Differences from previous experiment shown
Subjects
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Source: Figure 6A and 6B
Description: Taxa differing in abundance between caries group and trauma as determined by Linear discriminant analysis Effect Size (LEFSe)
Abundance in Group 1: increased abundance in Trauma
| NCBI | Quality Control | Links |
|---|---|---|
| Campylobacter | ||
| Campylobacter showae | ||
| Campylobacterota | ||
| Campylobacteraceae | ||
| campylobacteriacampylobacteria | ||
| Campylobacterales |
Revision editor(s): EniolaAde
Signature 2
Source: Figure 6A and 6B
Description: Taxa differing in abundance between caries group and trauma as determined by Linear discriminant analysis Effect Size (LEFSe)
Abundance in Group 1: decreased abundance in Trauma
Revision editor(s): EniolaAde
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