Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Subjects
- Location of subjects
- United Arab Emirates
- Host species Species from which microbiome was sampled (if applicable)
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- smoking behavior smoking,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
- Cigarette 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 cigarettes (CS)
- 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
- 33
- 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).
- relative abundances
- 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
Source: Table 2
Description: Differentially abundant taxa at selected taxonomical levels by type of tobacco use, compared to nonsmokers
Abundance in Group 1: increased abundance in Cigarette Smokers
NCBI | Links |
---|---|
Atopobium � | |
Bifidobacterium � | |
Campylobacter � | |
Dialister � | |
Enhydrobacter ⚠� | |
Megasphaera � | |
Mycoplasma � | |
Paludibacter | |
Prevotella � | |
Treponema � |
Revision editor(s): Adi13
Signature 2
Source: Table 2
Description: Differentially abundant taxa at selected taxonomical levels by type of tobacco use, compared to nonsmokers
Abundance in Group 1: decreased abundance in Cigarette Smokers
Revision editor(s): Adi13
Experiment 2
Subjects
- 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 1 sample size Number of subjects in the case (exposed) group
- 16
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Table 2
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 | Links |
---|---|
Atopobium � | |
Bifidobacterium � | |
Campylobacter � | |
Dialister � | |
Enhydrobacter ⚠� | |
Megasphaera � | |
Mycoplasma � | |
Paludibacter | |
Prevotella � | |
Treponema � |
Revision editor(s): Adi13
Signature 2
Source: Table 2
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
Revision editor(s): Adi13
Experiment 3
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Shisha 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 shisha (SS)
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Table 2
Description: Differentially abundant taxa at selected taxonomical levels by type of tobacco use, compared to nonsmokers
Abundance in Group 1: increased abundance in Shisha Smokers
Revision editor(s): Adi13
Signature 2
Source: Table 2
Description: Differentially abundant taxa at selected taxonomical levels by type of tobacco use, compared to nonsmokers
Abundance in Group 1: decreased abundance in Shisha Smokers
NCBI | Links |
---|---|
Fusobacterium � | |
Haemophilus � | |
Lautropia � | |
Neisseria � | |
Paludibacter | |
Peptostreptococcus � | |
Porphyromonas � | |
Vagococcus � | |
Treponema � |
Revision editor(s): Adi13
Experiment 4
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mutiple Smokers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- People consuming tobacco in multiple forms out of cigarettes (CS), dokha (DS) and shisha (SS)
- Group 1 sample size Number of subjects in the case (exposed) group
- 41
Lab analysis
Statistical Analysis
Signature 1
Source: Table 2
Description: Differentially abundant taxa at selected taxonomical levels by type of tobacco use, compared to nonsmokers
Abundance in Group 1: increased abundance in Mutiple Smokers
NCBI | Links |
---|---|
Bifidobacterium � | |
Campylobacter � | |
Dialister � | |
Enhydrobacter ⚠� | |
Leptotrichia � | |
Mycoplasma � | |
Paludibacter | |
Treponema � |
Revision editor(s): Adi13
Signature 2
Source: Table 2
Description: Differentially abundant taxa at selected taxonomical levels by type of tobacco use, compared to nonsmokers
Abundance in Group 1: decreased abundance in Mutiple Smokers
Revision editor(s): Adi13