Bacteriome analysis of Aggregatibacter actinomycetemcomitans-JP2 genotype-associated Grade C periodontitis in Moroccan adolescents/Experiment 3
From BugSigDB
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
- 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
- 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)
- 0.25
- 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
- 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
