Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study/Experiment 5
From BugSigDB
Reviewed Marked as Reviewed by ChiomaBlessing on 2023-12-11
Curated date: 2023/12/05
Curator: ChiomaBlessing
Revision editor(s): ChiomaBlessing, Tosin, WikiWorks
Subjects
- Location of subjects
- United Arab Emirates
- 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
- SalivaSaliva
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Cotinine negative
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Cotinine positive
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Subjects with positive cotinine result
- Group 0 sample size Number of subjects in the control (unexposed) group
- 225
- Group 1 sample size Number of subjects in the case (exposed) group
- 22
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).
- raw counts
- Statistical test
- DESeq2
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Signature 1
Needs review
Source: Supplemental. Table S4
Description: Differentially abundant taxa at all taxonomical levels in the contrasts between cotinine positive versus cotinine negative.
Abundance in Group 1: decreased abundance in Cotinine positive
Revision editor(s): ChiomaBlessing, WikiWorks
Signature 2
Needs review
Source: Supplemental. Table S4
Description: Differentially abundant taxa at all taxonomical levels in the contrasts between cotinine positive versus cotinine negative.
Abundance in Group 1: increased abundance in Cotinine positive
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium | ||
| Campylobacter | ||
| Desulfobulbus | ||
| Filifactor | ||
| Megasphaera | ||
| Mycoplasma | ||
| Paludibacter | ||
| Treponema | ||
| uncultured Synergistes sp. | ||
| unclassified Paraprevotella | ||
| Spirochaetia |
Revision editor(s): ChiomaBlessing, WikiWorks
