Oral microbiome dysbiosis among cigarette smokers and smokeless tobacco users compared to non-users
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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 States of America
- 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
- Buccal epithelium Buccal epithelium,buccal epithelium
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Smoking behaviour measurement Smoking behaviour measurement,smoking behaviour measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Cigarettes users (CG ) + Smokeless tobacco users (ST)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Non-tobacco users (NU)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Users had never used tobacco products in their lifetime.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 42
- Group 1 sample size Number of subjects in the case (exposed) group
- 43
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 6 Months.
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-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
- Statistical test
- Kruskall-Wallis
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- Matched on Factors on which subjects have been matched on in a case-control study
- age, race, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Fig. 4, S8 and S9
Description: Box plots of relative abundance of the top 14 bacterial genera by user group: cigarette user (CG, orange), smokeless tobacco user (ST, green), and non-user (NU). (*) represents p-value < 0.05.
Abundance in Group 1: increased abundance in Non-tobacco users (NU)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota | ||
| Pseudomonadota | ||
| Actinomycetota | ||
| Fusobacteriota | ||
| Granulicatella | ||
| Actinomyces | ||
| Prevotella | ||
| Oribacterium |
Revision editor(s): Shulamite
Signature 2
Source: Fig. 4, S8 and S9
Description: Box plots of relative abundance of the top 14 bacterial genera by user group: cigarette user (CG, orange), smokeless tobacco user (ST, green), and non-user (NU). (*) represents p-value < 0.05.
Abundance in Group 1: decreased abundance in Non-tobacco users (NU)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota |
Revision editor(s): Shulamite
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Cigarettes users (CG )
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Users had never used tobacco products.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 24
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 6 Months
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- race, sex, age
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Fig 4.
Description: Box plots of relative abundance of the top 14 bacterial genera by user group: cigarette user (CG, orange), smokeless tobacco user (ST, green), and non-user (NU). (*) represents p-value < 0.05.
Abundance in Group 1: increased abundance in Non-tobacco users (NU)
| NCBI | Quality Control | Links |
|---|---|---|
| Neisseria | ||
| Veillonella |
Revision editor(s): Shulamite
Experiment 3
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Smokeless tobacco users (ST)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Users who had used tobacco at least once per week for the previous whole year.
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- age, race, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Fig 4
Description: Box plots of relative abundance of the top 14 bacterial genera by user group: cigarette user (CG, orange), smokeless tobacco user (ST, green), and non-user (NU). (*) represents p-value < 0.05.
Abundance in Group 1: increased abundance in Smokeless tobacco users (ST)
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonas |
Revision editor(s): Shulamite
Signature 2
Source: fig 4
Description: Box plots of relative abundance of the top 14 bacterial genera by user group: cigarette user (CG, orange), smokeless tobacco user (ST, green), and non-user (NU). (*) represents p-value < 0.05.
Abundance in Group 1: decreased abundance in Smokeless tobacco users (ST)
| NCBI | Quality Control | Links |
|---|---|---|
| Leptotrichia |
Revision editor(s): Shulamite
Experiment 4
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Non-tobacco users (NU)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Users who had never used tobacco product in their life time.
- Group 1 sample size Number of subjects in the case (exposed) group
- 43
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Fig 5A
Description: Relative abundance of bacterial OTUs in buccal swab samples that were statistically significantly different (α = 0.001) between (a) non-users (NU) and cigarette users (CG) and (b) non-users (NU) and smokeless tobacco users (ST).
Abundance in Group 1: increased abundance in Non-tobacco users (NU)
| NCBI | Quality Control | Links |
|---|---|---|
| Abiotrophia | ||
| Streptococcus anginosus | ||
| Actinomyces |
Revision editor(s): Shulamite
Signature 2
Source: Fig 5A
Description: Relative abundance of bacterial OTUs in buccal swab samples that were statistically significantly different (α = 0.001) between (a) non-users (NU) and cigarette users (CG) and (b) non-users (NU) and smokeless tobacco users (ST).
Abundance in Group 1: decreased abundance in Non-tobacco users (NU)
| NCBI | Quality Control | Links |
|---|---|---|
| Aggregatibacter | ||
| Leptotrichiaceae |
Revision editor(s): Shulamite
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-tobacco users (NU)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Cigarette users (CG)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Users had smoked more than six cigarettes on a typical day for the previous 3 years.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 43
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Fig 5A
Description: Relative abundance of bacterial OTUs in buccal swab samples that were statistically significantly different (α = 0.001) between (a) non-users (NU) and cigarette users (CG) and (b) non-users (NU) and smokeless tobacco users (ST).
Abundance in Group 1: increased abundance in Cigarette users (CG)
| NCBI | Quality Control | Links |
|---|---|---|
| uncultured Peptostreptococcaceae bacterium | ||
| uncultured Anaerovorax sp. | ||
| uncultured Rhodococcus sp. | ||
| Solobacterium moorei | ||
| Streptococcus infantis |
Revision editor(s): Shulamite
Signature 2
Source: Fig 5A
Description: Relative abundance of bacterial OTUs in buccal swab samples that were statistically significantly different (α = 0.001) between (a) non-users (NU) and cigarette users (CG) and (b) non-users (NU) and smokeless tobacco users (ST).
Abundance in Group 1: decreased abundance in Cigarette users (CG)
Revision editor(s): Shulamite
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Smokeless tobacco user (ST).
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Non-tobacco users (NU)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Users who had never used a tobacco product in their lifetime.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 18
- Group 1 sample size Number of subjects in the case (exposed) group
- 43
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Fig 5B
Description: Relative abundance of bacterial OTUs in buccal swab samples that were statistically significantly different (α = 0.001) between (a) non-users (NU) and cigarette users (CG) and (b) non-users (NU) and smokeless tobacco users (ST).
Abundance in Group 1: increased abundance in Non-tobacco users (NU)
| NCBI | Quality Control | Links |
|---|---|---|
| uncultured Streptococcus sp. | ||
| uncultured Actinomyces sp. | ||
| uncultured Mogibacteriaceaeuncultured Mogibacteriaceae | ||
| uncultured Oribacterium sp. | ||
| uncultured Peptostreptococcus sp. |
Revision editor(s): Shulamite
Signature 2
Source: Fig 5B
Description: Relative abundance of bacterial OTUs in buccal swab samples that were statistically significantly different (α = 0.001) between (a) non-users (NU) and cigarette users (CG) and (b) non-users (NU) and smokeless tobacco users (ST).
Abundance in Group 1: decreased abundance in Non-tobacco users (NU)
| NCBI | Quality Control | Links |
|---|---|---|
| uncultured Neisseria sp. | ||
| uncultured Achromobacter sp. | ||
| Neisseria subflava | ||
| Haemophilus parainfluenzae |
Revision editor(s): Shulamite
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-tobacco users (NU)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Smokeless tobacco users (ST)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Users who had used tobacco at least once a week for the previous whole year.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 43
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Fig 5B
Description: Relative abundance of bacterial OTUs in buccal swab samples that were statistically significantly different (α = 0.001) between (a) non-users (NU) and cigarette users (CG) and (b) non-users (NU) and smokeless tobacco users (ST).
Abundance in Group 1: increased abundance in Smokeless tobacco users (ST)
| NCBI | Quality Control | Links |
|---|---|---|
| uncultured Coprococcus sp. |
Revision editor(s): Shulamite
Experiment 8
Subjects
- 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
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Cigarette users (CG)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Users who had smoked more than six cigarettes on a typical day for the previous 3 years.
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Fig. 6A
Description: Relative abundance of bacterial OTUs in saliva samples that was statistically significantly different (α = 0.001) between (a) non-users (NU) and cigarette users (CG) and (b) non-users (NU) and smokeless tobacco users (ST).
Abundance in Group 1: increased abundance in Cigarette users (CG)
Revision editor(s): Shulamite
Signature 2
Source: Fig. 6B
Description: Relative abundance of bacterial OTUs in saliva samples that was statistically significantly different (α = 0.001) between (a) non-users (NU) and cigarette users (CG) and (b) non-users (NU) and smokeless tobacco users (ST).
Abundance in Group 1: decreased abundance in Cigarette users (CG)
Revision editor(s): Shulamite
Experiment 9
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Cigarettes users (CG )
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Non-tobacco users (NU)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Users who had never used a tobacco product in their lifetime.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 24
- Group 1 sample size Number of subjects in the case (exposed) group
- 43
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Fig. 6A
Description: Relative abundance of bacterial OTUs in saliva samples that was statistically significantly different (α = 0.001) between (a) non-users (NU) and cigarette users (CG) and (b) non-users (NU) and smokeless tobacco users (ST).
Abundance in Group 1: increased abundance in Non-tobacco users (NU)
Revision editor(s): Shulamite
Signature 2
Source: Fig. 6A
Description: Relative abundance of bacterial OTUs in saliva samples that was statistically significantly different (α = 0.001) between (a) non-users (NU) and cigarette users (CG) and (b) non-users (NU) and smokeless tobacco users (ST).
Abundance in Group 1: decreased abundance in Non-tobacco users (NU)
Revision editor(s): Shulamite
Experiment 10
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Smokeless tobacco user (ST).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 18
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Fig 6B
Description: Relative abundance of bacterial OTUs in saliva samples that was statistically significantly different (α = 0.001) between (a) non-users (NU) and cigarette users (CG) and (b) non-users (NU) and smokeless tobacco users (ST).
Abundance in Group 1: increased abundance in Non-tobacco users (NU)
| NCBI | Quality Control | Links |
|---|---|---|
| uncultured Corynebacterium sp. | ||
| uncultured Actinomyces sp. |
Revision editor(s): Shulamite
Signature 2
Source: Fig. 6B
Description: Relative abundance of bacterial OTUs in saliva samples that was statistically significantly different (α = 0.001) between (a) non-users (NU) and cigarette users (CG) and (b) non-users (NU) and smokeless tobacco users (ST).
Abundance in Group 1: decreased abundance in Non-tobacco users (NU)
| NCBI | Quality Control | Links |
|---|---|---|
| uncultured Prevotella sp. | ||
| uncultured Neisseria sp. | ||
| Escherichia coli |
Revision editor(s): Shulamite
Experiment 11
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-tobacco users (NU)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Smokeless tobacco users (ST)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Users who had used tobacco at least once a week for the previous whole year.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 43
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Fig. 6B
Description: Relative abundance of bacterial OTUs in saliva samples that was statistically significantly different (α = 0.001) between (a) non-users (NU) and cigarette users (CG) and (b) non-users (NU) and smokeless tobacco users (ST).
Abundance in Group 1: increased abundance in Smokeless tobacco users (ST)
| NCBI | Quality Control | Links |
|---|---|---|
| uncultured Streptococcaceae bacterium | ||
| uncultured Streptococcus sp. |
Revision editor(s): Shulamite
Signature 2
Source: Fig. 6B
Description: Relative abundance of bacterial OTUs in saliva samples that was statistically significantly different (α = 0.001) between (a) non-users (NU) and cigarette users (CG) and (b) non-users (NU) and smokeless tobacco users (ST).
Abundance in Group 1: decreased abundance in Smokeless tobacco users (ST)
| NCBI | Quality Control | Links |
|---|---|---|
| uncultured Leptotrichia sp. | ||
| Treponema amylovorum | ||
| Porphyromonas endodontalis |
Revision editor(s): Shulamite
Experiment 12
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Cigarettes users (CG )
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Non-tobacco users (NU)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Users who had never used a tobacco product in their lifetime.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 24
- Group 1 sample size Number of subjects in the case (exposed) group
- 43
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Fig. 4, S8 and S9
Description: Box plots of relative abundance of the top 14 bacterial genera by user group: cigarette user (CG, orange), smokeless tobacco user (ST, green), and non-user (NU). (*) represents p-value < 0.05.
Abundance in Group 1: increased abundance in Non-tobacco users (NU)
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacterium | ||
| Haemophilus | ||
| Pseudomonas | ||
| Rothia | ||
| Actinomycetota | ||
| Pseudomonadota |
Revision editor(s): Shulamite
Experiment 13
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Smokeless tobacco users (ST)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Users who had used tobacco at least once a week for the previous whole year.
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Fig. 4, S8 and S9
Description: Box plots of relative abundance of the top 14 bacterial genera by user group: cigarette user (CG, orange), smokeless tobacco user (ST, green), and non-user (NU). (*) represents p-value < 0.05.
Abundance in Group 1: increased abundance in Smokeless tobacco users (ST)
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonadota | ||
| Fusobacterium | ||
| Granulicatella | ||
| Neisseria | ||
| Leptotrichia | ||
| Oribacterium | ||
| Porphyromonas | ||
| Rothia | ||
| Haemophilus |
Revision editor(s): Shulamite
Signature 2
Source: Fig. 4, S8 and S9
Description: Box plots of relative abundance of the top 14 bacterial genera by user group: cigarette user (CG, orange), smokeless tobacco user (ST, green), and non-user (NU). (*) represents p-value < 0.05.
Abundance in Group 1: decreased abundance in Smokeless tobacco users (ST)
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus | ||
| Actinomyces | ||
| Veillonella | ||
| Prevotella | ||
| Bacteroidia | ||
| Bacillota | ||
| Actinomycetota |
Revision editor(s): Shulamite
