Profiling the Salivary microbiome of the Qatari population/Experiment 7
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
- Coffee consumption caffeine consumption,Coffee consumption,coffee consumption
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-coffee drinkers
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Coffee drinkers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants considered coffee drinkers
- Group 0 sample size Number of subjects in the control (unexposed) group
- 887
- Group 1 sample size Number of subjects in the case (exposed) group
- 110
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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Source: Figure 7c
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 individuals that do not drink coffee (green) and the participants that are considered coffee drinkers (red)
Abundance in Group 1: increased abundance in Coffee drinkers
| NCBI | Quality Control | Links |
|---|---|---|
| Candidatus Saccharibacteria | ||
| Actinomycetota | ||
| Pseudomonadota | ||
| Bacillota | ||
| Lautropia | ||
| Granulicatella | ||
| Haemophilus | ||
| Veillonella | ||
| Streptococcus |
Signature 2
Source: Figure 7c
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 individuals that do not drink coffee (green) and the participants that are considered coffee drinkers (red)
Abundance in Group 1: decreased abundance in Coffee drinkers
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota | ||
| Fusobacteriota | ||
| Prevotella |
Revision editor(s): Suwaiba
