Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study/Experiment 6

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Reviewed Marked as Reviewed by ChiomaBlessing on 2023-12-11

Curated date: 2023/12/10

Curator: ChiomaBlessing

Revision editor(s): 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

Non-smokers

Group 1 name Corresponds to the case (exposed) group for case-control studies

Smokers

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

People consuming tobacco (in any form; cigarettes, dokha, shisha)

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

105

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

increased

Chao1 Abundance-based estimator of species richness

increased

Simpson Estimator of species richness and species evenness: more weight on species evenness

increased

Richness Number of species

increased