Profiling the Salivary microbiome of the Qatari population/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Atrayees on 2023-6-23
Subjects
- Location of subjects
- Qatar
- 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
- Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Sex design sex_design,Sex design,sex design
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Males
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Females
- Group 0 sample size Number of subjects in the control (unexposed) group
- 555
- Group 1 sample size Number of subjects in the case (exposed) group
- 442
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).
- relative abundances
- Statistical test
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 2
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex, smoking status
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
- Richness Number of species
- increased
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-6-19
Source: Figure 1c
Description: Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in males (green) and females (red)
Abundance in Group 1: decreased abundance in Females
| NCBI | Quality Control | Links |
|---|---|---|
| Bergeyella | ||
| Tannerella | ||
| Bacteroidota |
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-6-19
Source: Figure 1c
Description: Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in males (green) and females (red)
Abundance in Group 1: increased abundance in Females
| NCBI | Quality Control | Links |
|---|---|---|
| Treponema | ||
| Mycoplasma | ||
| Corynebacterium | ||
| Spirochaetota |
