Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study/Experiment 2

From BugSigDB


Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-4

Curated date: 2023/03/17

Curator: Adi13

Revision editor(s): Adi13, Claregrieve1, ChiomaBlessing

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
Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Smoking behavior smoking,Smoking behavior,smoking behavior
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Nonsmokers
Group 1 name Corresponds to the case (exposed) group for case-control studies
Dokha Smokers
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
People consuming tobacco in the form of dokha (DS)
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
16
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
None

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

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-4

Curated date: 2023/03/18

Curator: Adi13

Revision editor(s): Adi13, ChiomaBlessing

Source: Supplemental. Table S2

Description: Differentially abundant taxa at selected taxonomical levels by type of tobacco use, compared to nonsmokers

Abundance in Group 1: increased abundance in Dokha Smokers

NCBI Quality ControlLinks
Bifidobacterium

Revision editor(s): Adi13, ChiomaBlessing

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-4

Curated date: 2023/03/18

Curator: Adi13

Revision editor(s): Adi13, ChiomaBlessing

Source: Supplemental. Table S2

Description: Differentially abundant taxa at selected taxonomical levels by type of tobacco use, compared to nonsmokers

Abundance in Group 1: decreased abundance in Dokha Smokers

NCBI Quality ControlLinks
Lautropia
Porphyromonas

Revision editor(s): Adi13, ChiomaBlessing