Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Vallès Y, Inman CK, Peters BA, Ali R, Wareth LA, Abdulle A, Alsafar H, Anouti FA, Dhaheri AA, Galani D, Haji M, Hamiz AA, Hosani AA, Houqani MA, Junaibi AA, Kazim M, Kirchhoff T, Mahmeed WA, Maskari FA, Alnaeemi A, Oumeziane N, Ramasamy R, Schmidt AM, Weitzman M, Zaabi EA, Sherman S, Hayes RB, Ahn J
Journal
Scientific reports
Year
2018
Cigarette smoking alters the oral microbiome; however, the effect of alternative tobacco products remains unclear. Middle Eastern tobacco products like dokha and shisha, are becoming globally widespread. We tested for the first time in a Middle Eastern population the hypothesis that different tobacco products impact the oral microbiome. The oral microbiome of 330 subjects from the United Arab Emirates Healthy Future Study was assessed by amplifying the bacterial 16S rRNA gene from mouthwash samples. Tobacco consumption was assessed using a structured questionnaire and further validated by urine cotinine levels. Oral microbiome overall structure and specific taxon abundances were compared, using PERMANOVA and DESeq analyses respectively. Our results show that overall microbial composition differs between smokers and nonsmokers (p = 0.0001). Use of cigarettes (p = 0.001) and dokha (p = 0.042) were associated with overall microbiome structure, while shisha use was not (p = 0.62). The abundance of multiple genera were significantly altered (enriched/depleted) in cigarette smokers; however, only Actinobacillus, Porphyromonas, Lautropia and Bifidobacterium abundances were significantly changed in dokha users whereas no genera were significantly altered in shisha smokers. For the first time, we show that smoking dokha is associated to oral microbiome dysbiosis, suggesting that it could have similar effects as smoking cigarettes on oral health.
Experiment 1
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-4
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
- 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).
- 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
- 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
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-4
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 | Quality Control | Links |
|---|---|---|
| Atopobium | ||
| Bifidobacterium | ||
| Campylobacter | ||
| Dialister | ||
| Enhydrobacter | ||
| Megasphaera | ||
| Mycoplasma | ||
| Paludibacter | ||
| Prevotella | ||
| Treponema | ||
| uncultured Synergistes sp. |
Revision editor(s): Adi13, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-4
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
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-4
Differences from previous experiment shown
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
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-4
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 Control | Links |
|---|---|---|
| Bifidobacterium |
Revision editor(s): Adi13, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-4
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 Control | Links |
|---|---|---|
| Lautropia | ||
| Porphyromonas |
Revision editor(s): Adi13, ChiomaBlessing
Experiment 3
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-4
Differences from previous experiment shown
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 2
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-4
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 Shisha Smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Candidatus Gracilibacteria bacterium GN02-872 | ||
| Cyanobacteriota | ||
| candidate division SR1 bacterium |
Revision editor(s): Adi13, ChiomaBlessing
Experiment 4
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-4
Differences from previous experiment shown
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
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-4
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 Mutiple Smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Campylobacter | ||
| Enhydrobacter | ||
| Mycoplasma | ||
| Paludibacter | ||
| Treponema | ||
| uncultured Synergistes sp. |
Revision editor(s): Adi13, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-4
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 Mutiple Smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Actinobacillus | ||
| Eikenella | ||
| Gemella | ||
| Haemophilus | ||
| Lautropia | ||
| Neisseria | ||
| Vagococcus |
Revision editor(s): Adi13, ChiomaBlessing
Experiment 5
Reviewed Marked as Reviewed by ChiomaBlessing on 2023-12-11
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Cotinine measurement Cotinine measurement,cotinine measurement
- 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 1 sample size Number of subjects in the case (exposed) group
- 22
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2023-12-11
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
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2023-12-11
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
Experiment 6
Reviewed Marked as Reviewed by ChiomaBlessing on 2023-12-11
Differences from previous experiment shown
Subjects
- 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 1 sample size Number of subjects in the case (exposed) group
- 105
Lab analysis
Statistical Analysis
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
Experiment 7
Reviewed Marked as Reviewed by ChiomaBlessing on 2023-12-11
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Dokha
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- CIigarettes
- 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
- 16
- Group 1 sample size Number of subjects in the case (exposed) group
- 33
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Experiment 8
Reviewed Marked as Reviewed by ChiomaBlessing on 2023-12-11
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Shisha
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2023-12-11
Source: Supplemental. Table S3
Description: Differentially abundant taxa at all taxonomical levels between Cigarettes and Shisha
Abundance in Group 1: decreased abundance in CIigarettes
| NCBI | Quality Control | Links |
|---|---|---|
| Actinobacillus | ||
| Butyrivibrio | ||
| Capnocytophaga | ||
| Comamonadaceae | ||
| Fusobacteriia | ||
| Gemellaceae | ||
| Weeksellaceae |
Revision editor(s): ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2023-12-11
Source: Supplemental. Table S3
Description: Differentially abundant taxa at all taxonomical levels between Cigarettes and Shisha
Abundance in Group 1: increased abundance in CIigarettes
| NCBI | Quality Control | Links |
|---|---|---|
| Paludibacter | ||
| Treponema | ||
| uncultured Synergistes sp. | ||
| Mycoplasma |
Revision editor(s): ChiomaBlessing
Experiment 9
Reviewed Marked as Reviewed by ChiomaBlessing on 2023-12-11
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Dokha
- 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
- 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
Reviewed Marked as Reviewed by ChiomaBlessing on 2023-12-11
Source: Supplemental. Table S3
Description: Differentially abundant taxa at all taxonomical levels between Dokha and Shisha
Abundance in Group 1: decreased abundance in Dokha
| NCBI | Quality Control | Links |
|---|---|---|
| Actinobacillus | ||
| Weeksellaceae | ||
| Gemellaceae |
Revision editor(s): ChiomaBlessing
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