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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
- Qatar
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Females
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Males
- Group 0 sample size Number of subjects in the control (unexposed) group
- 555
- Group 1 sample size Number of subjects in the case (exposed) group
- 442
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V3
- 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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex, smoking status
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- increased
Signature 1
Source: Figure 1c
Description: Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in males (green) and females (red)
Abundance in Group 1: increased abundance in Males
| NCBI | Links |
|---|---|
| Spirochaetota | |
| Bergeyella | |
| Tannerella � |
Revision editor(s): Suwaiba
Signature 2
Source: Figure 1c
Description: Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in males (green) and females (red)
Abundance in Group 1: decreased abundance in Males
| NCBI | Links |
|---|---|
| Bacteroidota | |
| Treponema � | |
| Mycoplasma � | |
| Corynebacterium � |
Revision editor(s): Suwaiba
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Adults
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Elderly
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- People older than 65years of age
- Group 0 sample size Number of subjects in the control (unexposed) group
- 979
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
Lab analysis
Statistical Analysis
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.001
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex
Alpha Diversity
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Figure 2c
Description: Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in Elderly (green) and Adults (red).
Abundance in Group 1: increased abundance in Elderly
| NCBI | Links |
|---|---|
| Bacteroidota | |
| Spirochaeta | |
| Prevotella � | |
| Treponema � | |
| g__Saccharibacteria_TM7__G_3_g__Saccharibacteria_TM7__G_3_ |
Revision editor(s): Suwaiba
Signature 2
Source: Figure 2c
Description: Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in Elderly (green) and Adults (red).
Abundance in Group 1: decreased abundance in Elderly
Revision editor(s): Suwaiba
Experiment 3
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Gingival bleeding Bleeding gums,Gingival haemorrhage,Gingival hemorrhage,Gingivorrhagia,Gingival bleeding
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Participants without gingivitis bleeding
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Participants with gingival bleeding
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants reported suffering from a bleeding gum
- Group 0 sample size Number of subjects in the control (unexposed) group
- 913
- Group 1 sample size Number of subjects in the case (exposed) group
- 84
Lab analysis
Statistical Analysis
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.01
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Not specified
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Not specified
Alpha Diversity
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Figure 3c
Description: Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in individuals that did not report bleeding (green) and the participants that reported bleeding gums (red)
Abundance in Group 1: increased abundance in Participants with gingival bleeding
| NCBI | Links |
|---|---|
| Bacteroidota | |
| Capnocytophaga � | |
| Prevotella � |
Revision editor(s): Suwaiba
Signature 2
Source: Figure 3c
Description: Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in individuals that did not report bleeding (green) and the participants that reported bleeding gums (red)
Abundance in Group 1: decreased abundance in Participants with gingival bleeding
Revision editor(s): Suwaiba
Experiment 4
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Oral ulcer Mouth sore,Mouth ulcer,Oral mucosal ulceration,Oral ulcer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Participants without oral ulcers
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Participants with oral ulcers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants who reported suffering from oral ulcers
- Group 0 sample size Number of subjects in the control (unexposed) group
- 960
- Group 1 sample size Number of subjects in the case (exposed) group
- 37
Lab analysis
Statistical Analysis
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.001
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Alpha Diversity
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Figure 4c
Description: Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in individuals that did not report any mouth ulcer (green) and the participants that reported having mouth ulcers (red)
Abundance in Group 1: increased abundance in Participants with oral ulcers
| NCBI | Links |
|---|---|
| Bacteroidota | |
| Capnocytophaga � | |
| Prevotella � |
Revision editor(s): Suwaiba
Signature 2
Source: Figure 4c
Description: Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in individuals that did not report any mouth ulcer (green) and the participants that reported having mouth ulcers (red)
Abundance in Group 1: decreased abundance in Participants with oral ulcers
| NCBI | Links |
|---|---|
| Bacillota | |
| Fusobacteriota | |
| Gemella � | |
| Granulicatella � | |
| Haemophilus � | |
| Leptotrichia � | |
| Megasphaera � | |
| Neisseria � | |
| Pseudomonadota | |
| Streptococcus � | |
| Veillonella � | |
| Actinomycetota |
Revision editor(s): Suwaiba
Experiment 5
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- dentures false teeth,dentures
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Participants without dentures
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Participants with dentures
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants who reported using dentures
- Group 0 sample size Number of subjects in the control (unexposed) group
- 861
- Group 1 sample size Number of subjects in the case (exposed) group
- 136
Lab analysis
Statistical Analysis
Alpha Diversity
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Figure 5c
Description: Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in individuals that did not use dentures (green) and the participants that reported using dentures (red)
Abundance in Group 1: increased abundance in Participants with dentures
| NCBI | Links |
|---|---|
| Actinomycetota | |
| Pseudomonadota | |
| Pseudoramibacter ⚠� | |
| Neisseria � | |
| Streptococcus � |
Revision editor(s): Suwaiba
Signature 2
Source: Figure 5c
Description: Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in individuals that did not use dentures (green) and the participants that reported using dentures (red)
Abundance in Group 1: decreased abundance in Participants with dentures
| NCBI | Links |
|---|---|
| Campylobacter � | |
| g__Ruminococcaceae__G_2_g__Ruminococcaceae__G_2_ |
Revision editor(s): Suwaiba
Experiment 6
Subjects
- 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
- 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
- Participants classified as smokers
- Group 0 sample size Number of subjects in the control (unexposed) group
- 733
- Group 1 sample size Number of subjects in the case (exposed) group
- 264
Lab analysis
Statistical Analysis
- 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)?
- Not specified
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Figure 6c
Description: Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in smokers (green) and non- smokers (red)
Abundance in Group 1: increased abundance in Smokers
| NCBI | Links |
|---|---|
| Bacteroidota | |
| Prevotella � |
Revision editor(s): Suwaiba
Signature 2
Source: Figure 6c
Description: Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in smokers (green) and non- smokers (red)
Abundance in Group 1: decreased abundance in Smokers
| NCBI | Links |
|---|---|
| Pseudomonadota | |
| Synergistota | |
| Lactococcus � | |
| Corynebacterium � | |
| Gemella � | |
| Capnocytophaga � | |
| Streptococcus � |
Revision editor(s): Suwaiba
Experiment 7
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- coffee consumption caffeine consumption,coffee consumption
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-coffee drinkers
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Coffee drinkers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants considered coffee drinkers
- Group 0 sample size Number of subjects in the control (unexposed) group
- 887
- Group 1 sample size Number of subjects in the case (exposed) group
- 110
Lab analysis
Statistical Analysis
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.001
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex
Alpha Diversity
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Source: Figure 7c
Description: Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in individuals that do not drink coffee (green) and the participants that are considered coffee drinkers (red)
Abundance in Group 1: increased abundance in Coffee drinkers
Revision editor(s): Suwaiba
Signature 2
Source: Figure 7c
Description: Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in individuals that do not drink coffee (green) and the participants that are considered coffee drinkers (red)
Abundance in Group 1: decreased abundance in Coffee drinkers
| NCBI | Links |
|---|---|
| Bacteroidota | |
| Fusobacteriota | |
| Prevotella � |
Revision editor(s): Suwaiba
Experiment 8
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Not specified
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non tea drinkers
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Tea drinkers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants considered tea drinkers
- Group 0 sample size Number of subjects in the control (unexposed) group
- 229
- Group 1 sample size Number of subjects in the case (exposed) group
- 768
Lab analysis
Statistical Analysis
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Not specified
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Not specified
Alpha Diversity
- Richness Number of species
- increased
Signature 1
Source: Figure 8c
Description: Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. Features with LDA scores ≥ 2 are presented
Abundance in Group 1: decreased abundance in Tea drinkers
| NCBI | Links |
|---|---|
| Capnocytophaga � |
Revision editor(s): Suwaiba
