Oral health and plaque microbial profile in juvenile idiopathic arthritis/Experiment 1
Curated date: 2022/11/10
Curator: Tislam
Revision editor(s): Tislam, WikiWorks, Atrayees, Peace Sandy
Subjects
- Location of subjects
- United States of America
- 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
- Arthritis arthritic joint disease,arthritides,arthritis,inflammation of skeletal joint,inflammatory disorder of joint,skeletal joint inflammation,Arthritis
- 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
- Juvenile Idiopathic Arthritis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Juvenile Idiopathic Arthritis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 11
- Group 1 sample size Number of subjects in the case (exposed) group
- 85
- 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
- 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
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- .05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
- 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
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
Signature 1
Source: Figure 2, text
Description: c Linear discriminant analysis (LDA) through the LefSe tool. Enriched microbial communities between the two groups with a two log-fold difference or greater are shown in the LEfSe plot. d Bacteria genera found to be significantly different between the polyarticular JIA and healthy control groups.*p-value < 0.05
Abundance in Group 1: decreased abundance in Juvenile Idiopathic Arthritis
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Corynebacterium | ||
| Leptotrichia | ||
| Actinomycetaceae |
Revision editor(s): Tislam
Signature 2
Source: Figure 2, text
Description: c Linear discriminant analysis (LDA) through the LefSe tool. Enriched microbial communities between the two groups with a two log-fold difference or greater are shown in the LEfSe plot. d Bacteria genera found to be significantly different between the polyarticular JIA and healthy control groups.*p-value < 0.05
Abundance in Group 1: increased abundance in Juvenile Idiopathic Arthritis
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus | ||
| Haemophilus parainfluenzae | ||
| Leptotrichia | ||
| Haemophilus | ||
| Kingella |
