Smoking and salivary microbiota: a cross-sectional analysis of an Italian alpine population
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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
- Italy
- 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
- Mouth Adult mouth,Cavital oralis,Cavitas oris,Cavum oris,Mouth cavity,Oral region,Oral vestibule,Regio oralis,Rima oris,Stoma,Stomatodaeum,Trophic apparatus,Vestibule of mouth,Vestibulum oris,Mouth
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- smoking status measurement smoking status measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Never smokers
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Current smokers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Individuals who reported being smokers at the day of examination with daily smoking intensity at least 1 month prior to the visit.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 880
- Group 1 sample size Number of subjects in the case (exposed) group
- 326
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 12 weeks
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
- 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
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: figure 1
Description: Heatmap of the 44 genera diferentially abundant between Current and Never smokers
Abundance in Group 1: increased abundance in Current smokers
Revision editor(s): OdigiriGreat, Folakunmi
Signature 2
Source: figure 1
Description: Result of the Heatmap of the 44 genera diferentially abundant between Current and Never smokers.
Abundance in Group 1: decreased abundance in Current smokers
Revision editor(s): OdigiriGreat, Folakunmi
Experiment 2
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Former smokers (0-1 year)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Former smokers who quit smoking 0-1 year prior to study
- Group 0 sample size Number of subjects in the control (unexposed) group
- 656
- Group 1 sample size Number of subjects in the case (exposed) group
- 21
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 3
Description: The salivary microbiota of individuals who quit smoking (n=369) showed multiple-year perturbation and tends to resemble Never smokers’ profles within 5 years. (A) Heatmap of the relationship between the years since quitting smoking and the mean relative abundance of genera previously found signifcantly associated with smoking
Abundance in Group 1: increased abundance in Former smokers (0-1 year)
| NCBI | Quality Control | Links |
|---|---|---|
| Abiotrophia | ||
| Aggregatibacter | ||
| Bulleidia | ||
| Cryptobacterium | ||
| Dialister | ||
| Fretibacterium | ||
| Kingella | ||
| Mycoplasma | ||
| uncultured Peptostreptococcus sp. |
Revision editor(s): OdigiriGreat, Folakunmi
Signature 2
Source: Figure 3
Description: The salivary microbiota of individuals who quit smoking (n=369) showed multiple-year perturbation and tends to resemble Never smokers’ profles within 5 years. (A) Heatmap of the relationship between the years since quitting smoking and the mean relative abundance of genera previously found signifcantly associated with smoking
Abundance in Group 1: decreased abundance in Former smokers (0-1 year)
Revision editor(s): OdigiriGreat, Folakunmi
Experiment 3
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Former smokers (2-3 year)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Former smokers who quit smoking 2-3 year prior to study
- Group 1 sample size Number of subjects in the case (exposed) group
- 30
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 3
Description: The salivary microbiota of individuals who quit smoking (n=369) showed multiple-year perturbation and tends to resemble Never smokers’ profles within 5 years. (A) Heatmap of the relationship between the years since quitting smoking and the mean relative abundance of genera previously found signifcantly associated with smoking
Abundance in Group 1: increased abundance in Former smokers (2-3 year)
| NCBI | Quality Control | Links |
|---|---|---|
| Bergeyella | ||
| Cardiobacterium | ||
| Haemophilus |
Revision editor(s): OdigiriGreat
Signature 2
Source: Figure 3
Description: The salivary microbiota of individuals who quit smoking (n=369) showed multiple-year perturbation and tends to resemble Never smokers’ profles within 5 years. (A) Heatmap of the relationship between the years since quitting smoking and the mean relative abundance of genera previously found signifcantly associated with smoking
Abundance in Group 1: decreased abundance in Former smokers (2-3 year)
Revision editor(s): OdigiriGreat, Folakunmi
Experiment 4
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Former smokers (4-5 year)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Former smokers who quit smoking 4-5year prior to study
- Group 1 sample size Number of subjects in the case (exposed) group
- 25
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 3
Description: The salivary microbiota of individuals who quit smoking (n=369) showed multiple-year perturbation and tends to resemble Never smokers’ profles within 5 years. (A) Heatmap of the relationship between the years since quitting smoking and the mean relative abundance of genera previously found signifcantly associated with smoking
Abundance in Group 1: increased abundance in Former smokers (4-5 year)
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Atopobium | ||
| Bifidobacterium | ||
| Catonella | ||
| Leptotrichia | ||
| Megasphaera | ||
| Mitsuokella | ||
| Veillonella | ||
| uncultured Peptostreptococcus sp. | ||
| Bacteroides sp. |
Revision editor(s): OdigiriGreat, Folakunmi
Signature 2
Source: Figure 3
Description: The salivary microbiota of individuals who quit smoking (n=369) showed multiple-year perturbation and tends to resemble Never smokers’ profles within 5 years. (A) Heatmap of the relationship between the years since quitting smoking and the mean relative abundance of genera previously found signifcantly associated with smoking
Abundance in Group 1: decreased abundance in Former smokers (4-5 year)
Revision editor(s): OdigiriGreat, Folakunmi
Experiment 5
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Former smokers (5-10 years)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Former smokers who quit smoking 5-10 years prior to study
- Group 1 sample size Number of subjects in the case (exposed) group
- 35
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 3
Description: The salivary microbiota of individuals who quit smoking (n=369) showed multiple-year perturbation and tends to resemble Never smokers’ profles within 5 years. (A) Heatmap of the relationship between the years since quitting smoking and the mean relative abundance of genera previously found signifcantly associated with smoking
Abundance in Group 1: increased abundance in Former smokers (5-10 years)
| NCBI | Quality Control | Links |
|---|---|---|
| Candidatus Absconditabacteria | ||
| Ottowia | ||
| Lautropia | ||
| Candidatus Gracilibacteria | ||
| Peptostreptococcus | ||
| Lactobacillus | ||
| Alloscardovia | ||
| Stomatobaculum | ||
| Filifactor | ||
| Treponema | ||
| Mycoplasma |
Revision editor(s): OdigiriGreat
Signature 2
Source: Figure 3
Description: The salivary microbiota of individuals who quit smoking (n=369) showed multiple-year perturbation and tends to resemble Never smokers’ profles within 5 years. (A) Heatmap of the relationship between the years since quitting smoking and the mean relative abundance of genera previously found signifcantly associated with smoking
Abundance in Group 1: decreased abundance in Former smokers (5-10 years)
Revision editor(s): OdigiriGreat
Experiment 6
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Former smokers (11-62 year)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Former smokers who quit smoking 11-62 years prior to study
- Group 1 sample size Number of subjects in the case (exposed) group
- 145
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 3
Description: The salivary microbiota of individuals who quit smoking (n=369) showed multiple-year perturbation and tends to resemble Never smokers’ profles within 5 years. (A) Heatmap of the relationship between the years since quitting smoking and the mean relative abundance of genera previously found signifcantly associated with smoking
Abundance in Group 1: increased abundance in Former smokers (11-62 year)
| NCBI | Quality Control | Links |
|---|---|---|
| Porphyromonas | ||
| Capnocytophaga | ||
| Neisseria |
Revision editor(s): OdigiriGreat
Signature 2
Source: Figure 3
Description: The salivary microbiota of individuals who quit smoking (n=369) showed multiple-year perturbation and tends to resemble Never smokers’ profles within 5 years. (A) Heatmap of the relationship between the years since quitting smoking and the mean relative abundance of genera previously found signifcantly associated with smoking
Abundance in Group 1: decreased abundance in Former smokers (11-62 year)
Revision editor(s): OdigiriGreat
