Bacteriome analysis of Aggregatibacter actinomycetemcomitans-JP2 genotype-associated Grade C periodontitis in Moroccan adolescents
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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
Authors
Molli VLP, Kissa J, Baraniya D, Gharibi A, Chen T, Al-Hebshi NN, Albandar JM
Journal
Frontiers in oral health
Year
2023
Keywords:
biofilm, dysbiosis, high-throughput nucleotide sequencing, microbiota, periodontitis
BACKGROUND: Grade C (previously aggressive) periodontitis (GCP) in adolescents is prevalent in certain parts of Africa where it is associated with JP2 genotype, a highly virulent strain of Aggregatibacter actinomycetemcomitans. The aim of this study was to characterize the subgingival bacteriome in Moroccan subjects with GCP positive to A. actinomycetemcomitans JP2 genotype. METHODS: Subgingival plaque samples were collected from shallow and deep pockets of 8 subjects with GCP (17.2 ± 1.5 years) and from gingival sulci of 13 controls with no periodontitis (14.6 ± 1.1 years). Identification and genotyping of A. actinomycetemcomitans was performed using PCR analysis of the ltx operon, while bacteriome profiling was done by 16S rRNA gene sequencing (V1-V3 region). Groups were compared in terms of microbial diversity, abundances, and dysbiosis. RESULTS: The shallow and deep pocket sites from GCP cases had a significantly altered microbial composition compared to controls. Species associated with health included Haemophilus parainfluenzae, Lautropia mirabilis, Streptococcus spp., Gemella spp., and Rothia spp. While known periodontal pathogens, including Porphyromonas gingivalis, Tannerella forsythia, Treponema spp. and Fretibacterium spp., were significantly enriched in GCP, non-conventional taxa, including Pseudomonas oral taxon C61 and Enterobacter cloacae were more abundant and showed stronger association with the disease. Less significant differences in abundances of individual taxa were observed between shallow and deep pockets. Overall dysbiosis measured in terms of Subgingival Microbial Dysbiosis Index (SMDI) differentiated between GCP and no-periodontitis with 95% accuracy. CONCLUSIONS: The results suggest that several periodontal pathogens involved in the adult-type periodontitis also play a role in JP2 genotype-associated GCP. The potential role of non-conventional taxa in the pathogenesis of GCP warrants further investigation.
Experiment 1
Needs review
Subjects
- Location of subjects
- Morocco
- 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
- Subgingival dental plaque Subgingival plaque,Subgingival dental plaque,subgingival dental plaque
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Aggressive periodontitis Circumpubertal Periodontitis,Early-Onset Periodontitis,Juvenile Periodontitis,juvenile periodontitis,Periodontitis, Aggressive,periodontitis, aggressive 1,Periodontitis, Aggressive, 1,periodontitis, aggressive, 1,periodontitis, aggressive, type 1,Periodontitis, Circumpubertal,Periodontitis, Juvenile,periodontitis, juvenile,Periodontitis, Prepubertal,periodontitis, prepubertal,Periodontoses,Periodontosis,Prepubertal Periodontitis,Aggressive periodontitis,aggressive periodontitis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Grade C (previously aggressive) Periodontitis- Shallow pocket
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Grade C (previously aggressive) Periodontitis- Shallow pocket refers to the depth of the periodontal pocket(PD ≤ 4 mm), which is the space between the tooth and the surrounding gum tissues. It also indicates mild periodontal disease.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 13
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
- 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
- V1-V3
- 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).
- centered log-ratio
- Statistical test
- MaAsLin2
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.1
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- unchanged
Signature 1
Needs review
Source: Supplementary Table 5,6
Description: Differentially abundant taxa between healthy controls and shallow pocket site.
Abundance in Group 1: increased abundance in Grade C (previously aggressive) Periodontitis- Shallow pocket
Revision editor(s): KateRasheed
Signature 2
Needs review
Source: Supplementary Table 5,6
Description: Differentially abundant taxa between healthy controls and shallow pocket site
Abundance in Group 1: decreased abundance in Grade C (previously aggressive) Periodontitis- Shallow pocket
Revision editor(s): KateRasheed
Experiment 2
Needs review
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Grade C(previously aggressive) Periodontitis- Deep pocket
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Grade C(previously aggressive) Periodontitis- Deep pocket refers to a periodontal pocket with a depth of 6 mm or more (PD ≥ 6 mm). It indicates moderate to severe periodontal disease.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Needs review
Source: Supplementary Table 5,6
Description: Differentially abundant taxa between healthy controls and deep pocket site
Abundance in Group 1: increased abundance in Grade C(previously aggressive) Periodontitis- Deep pocket
Revision editor(s): KateRasheed
Signature 2
Needs review
Source: Supplementary Table 5,6
Description: Differentially abundant taxa between healthy controls and deep pocket site
Abundance in Group 1: decreased abundance in Grade C(previously aggressive) Periodontitis- Deep pocket
Revision editor(s): KateRasheed
Experiment 3
Needs review
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- GCP- Shallow pocket
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- GCP- Deep pocket
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Grade C Periodontitis - Deep pocket refers to a periodontal pocket with a depth of 6 mm or more (PD ≥ 6 mm), indicating moderate to severe periodontal disease.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
Lab analysis
Statistical Analysis
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.25
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Needs review
Source: Supplementary Figure 2A
Description: Differentially abundant taxa between shallow pocket and deep pocket site.
Abundance in Group 1: increased abundance in GCP- Deep pocket
| NCBI | Quality Control | Links |
|---|---|---|
| Treponema | ||
| Atopobium | ||
| Slackia | ||
| Veillonellaceae G1Veillonellaceae G1 | ||
| Tannerella |
Revision editor(s): KateRasheed
Signature 2
Needs review
Source: Supplementary Figure 2A
Description: Differentially abundant taxa between shallow pocket and deep pocket site.
Abundance in Group 1: decreased abundance in GCP- Deep pocket
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacterium | ||
| Abiotrophia | ||
| Granulicatella | ||
| Rothia | ||
| Gemella | ||
| Stenotrophomonas |
Revision editor(s): KateRasheed
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