Altered gut microbiome composition in nontreated plaque psoriasis patients
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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
- China
- 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
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Psoriasis vulgaris plaque psoriasis,Psoriasis vulgaris,psoriasis vulgaris
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Psoriasis vulgaris
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients diagnosed with Psoriasis vulgaris by two attending dermatologists.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
- Group 1 sample size Number of subjects in the case (exposed) group
- 32
- 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
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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
- Mann-Whitney (Wilcoxon)
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, race, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figures 2d, 2f
Description: Boxplot showing the difference of the relative abundance at the phylum and species level between psoriatic and healthy control samples
Abundance in Group 1: increased abundance in Psoriasis vulgaris
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides uniformis | ||
| Bacteroidota |
Revision editor(s): Anne-mariesharp
Signature 2
Source: Fig 2d - f
Description: Boxplot showing the difference of the relative abundance at the phylum, genus and species level between psoriatic and healthy control samples
Abundance in Group 1: decreased abundance in Psoriasis vulgaris
| NCBI | Quality Control | Links |
|---|---|---|
| Eubacterium | ||
| Roseburia hominis | ||
| Bacillota | ||
| Roseburia |
Revision editor(s): Anne-mariesharp
Experiment 2
Subjects
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Fig 2g
Description: Plot from LEfSe examination revealing enriched bacterial taxa related to either psoriasis individuals (green) or healthy controls (red)
Abundance in Group 1: increased abundance in Psoriasis vulgaris
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides uniformis | ||
| unclassified Escherichia |
Revision editor(s): Anne-mariesharp
Signature 2
Source: Fig 2g
Description: Plot from LEfSe examination revealing enriched bacterial taxa related to either psoriasis individuals (green) or healthy controls (red)
Abundance in Group 1: decreased abundance in Psoriasis vulgaris
| NCBI | Quality Control | Links |
|---|---|---|
| Roseburia hominis |
Revision editor(s): Anne-mariesharp
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy partners(couples or spouses)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Sub group of patients diagnosed with Psoriasis vulgaris by two attending dermatologists.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 17
- Group 1 sample size Number of subjects in the case (exposed) group
- 17
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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
- 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
- Richness Number of species
- unchanged
Signature 1
Source: Fig 3f
Description: Boxplot showing the difference of the relative abundance at the species level between psoriatic and healthy partners' samples
Abundance in Group 1: increased abundance in Psoriasis vulgaris
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes finegoldii |
Revision editor(s): Anne-mariesharp
Signature 2
Source: Fig 3f
Description: Boxplot showing the difference of the relative abundance at the species level between psoriatic and healthy partners' samples
Abundance in Group 1: decreased abundance in Psoriasis vulgaris
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides eggerthii |
Revision editor(s): Anne-mariesharp
Experiment 4
Subjects
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Fig 3g
Description: Plot from LEfSe examination revealing enriched bacterial taxa related to either psoriasis individuals (green) or healthy partners (red).
Abundance in Group 1: increased abundance in Psoriasis vulgaris
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes finegoldii | ||
| Alistipes onderdonkii |
Revision editor(s): Anne-mariesharp
Signature 2
Source: Fig 3g
Description: Plot from LEfSe examination revealing enriched bacterial taxa related to either psoriasis individuals (green) or healthy partners (red).
Abundance in Group 1: decreased abundance in Psoriasis vulgaris
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides eggerthii |
Revision editor(s): Anne-mariesharp
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients diagnosed with Psoriasis vulgaris by two attending dermatologists.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
- Group 1 sample size Number of subjects in the case (exposed) group
- 32
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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
- Not specified
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, race, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Fig 4d
Description: Boxplot showing the difference of the relative abundance at the phylum level between psoriatic and healthy controls samples
Abundance in Group 1: increased abundance in Psoriasis vulgaris
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota |
Revision editor(s): Anne-mariesharp
Signature 2
Source: Fig 4d - f
Description: Boxplot showing the difference of the relative abundance at the phylum, genus and species level between psoriatic and healthy controls samples
Abundance in Group 1: decreased abundance in Psoriasis vulgaris
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Coprococcus | ||
| Eubacterium | ||
| Lachnospira eligens | ||
| Lachnospiraceae bacterium 8_1_57FAA | ||
| Phocaeicola coprophilus | ||
| Roseburia | ||
| Roseburia intestinalis |
Revision editor(s): Anne-mariesharp
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy partners(couples or spouses) & Healthy controls
- Group 0 sample size Number of subjects in the control (unexposed) group
- 32
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Fig 4g
Description: Plot from LEfSe examination revealing enriched bacterial taxa related to either psoriasis individuals (pink) or healthy partners (green) or healthy controls (red)
Abundance in Group 1: increased abundance in Psoriasis vulgaris
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia coli |
Revision editor(s): Anne-mariesharp
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls & Psoriasis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Healthy partners(couples or spouses)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Healthy partners of Psoriasis patients
- Group 0 sample size Number of subjects in the control (unexposed) group
- 47
- Group 1 sample size Number of subjects in the case (exposed) group
- 17
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Fig 4g
Description: Plot from LEfSe examination revealing enriched bacterial taxa related to either psoriasis individuals (pink) or healthy partners (green) or healthy controls (red)
Abundance in Group 1: increased abundance in Healthy partners(couples or spouses)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides eggerthii | ||
| Bacteroides sp. 3_1_19 | ||
| Flavonifractor plautii | ||
| Hungatella hathewayi | ||
| Solobacterium moorei |
Revision editor(s): Anne-mariesharp
Experiment 8
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy partners(couples or spouses) & Psoriasis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Healthy controls
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Healthy controls(participants) with no Psoriasis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 49
- 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
- Richness Number of species
- unchanged
Signature 1
Source: Fig 4g
Description: Plot from LEfSe examination revealing enriched bacterial taxa related to either psoriasis individuals (pink) or healthy partners (green) or healthy controls (red).
Abundance in Group 1: increased abundance in Healthy controls
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnospira eligens | ||
| Lachnospiraceae bacterium 8_1_57FAA | ||
| Roseburia intestinalis | ||
| Ligilactobacillus ruminis |
Revision editor(s): Anne-mariesharp
Experiment 9
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Healthy partners(couples or spouses)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Healthy partners(couples or spouses) with no psoriasis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
- Group 1 sample size Number of subjects in the case (exposed) group
- 17
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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
- 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
- Richness Number of species
- unchanged
Signature 1
Source: Fig 5e, 5f
Description: Boxplot showing the difference of the relative abundance at the genus and species level between healthy controls and healthy partners samples
Abundance in Group 1: increased abundance in Healthy partners(couples or spouses)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Bacteroides eggerthii | ||
| Escherichia | ||
| Escherichia coli | ||
| Parasutterella excrementihominis |
Revision editor(s): Anne-mariesharp
Signature 2
Source: Fig 5e, 5f
Description: Boxplot showing the difference of the relative abundance at the genus and species level between healthy controls and healthy partners samples
Abundance in Group 1: decreased abundance in Healthy partners(couples or spouses)
| NCBI | Quality Control | Links |
|---|---|---|
| Candida albicans | ||
| Coprococcus | ||
| Lachnospira eligens | ||
| Roseburia intestinalis | ||
| unclassified Peptostreptococcaceae |
Revision editor(s): Anne-mariesharp
Experiment 10
Subjects
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Fig 5g
Description: Plot from LEfSe examination revealing enriched bacterial taxa related to either healthy partners (green) or healthy controls(red)
Abundance in Group 1: increased abundance in Healthy partners(couples or spouses)
Revision editor(s): Anne-mariesharp
Signature 2
Source: Fig 5g
Description: Plot from LEfSe examination revealing enriched bacterial taxa related to either healthy partners (green) or healthy controls(red)
Abundance in Group 1: decreased abundance in Healthy partners(couples or spouses)
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerobutyricum hallii | ||
| Candida albicans | ||
| Dasheen mosaic virus | ||
| Lachnospira eligens | ||
| Lachnospiraceae bacterium 8_1_57FAA | ||
| Roseburia intestinalis | ||
| unclassified Peptostreptococcaceae |
Revision editor(s): Anne-mariesharp
Experiment 11
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Mild psoriasis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Moderate to severe psoriasis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients identified as having moderate to severe psoriasis based on a Psoriasis Area and Severity Index PASI score ≥10.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 21
- Group 1 sample size Number of subjects in the case (exposed) group
- 11
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Fig 6e, 6f
Description: Boxplot showing the difference of the relative abundance at the genus and species level between mild psoriasis and moderate-to-severe psoriasis
Abundance in Group 1: increased abundance in Moderate to severe psoriasis
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacter | ||
| Enterobacter cloacae | ||
| Paraprevotella | ||
| Paraprevotella sp. |
Revision editor(s): Anne-mariesharp
Signature 2
Source: Fig 6e, 6f
Description: Boxplot showing the difference of the relative abundance at the genus and species level between mild psoriasis and moderate-to-severe psoriasis
Abundance in Group 1: decreased abundance in Moderate to severe psoriasis
| NCBI | Quality Control | Links |
|---|---|---|
| Gemella | ||
| Parabacteroides goldsteinii | ||
| Roseburia intestinalis | ||
| Streptococcus_mitis_oralis_pneumoniaeStreptococcus_mitis_oralis_pneumoniae |
Revision editor(s): Anne-mariesharp
Experiment 12
Subjects
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Fig 6g
Description: Plot from LEfSe examination revealing enriched bacterial taxa related to either mild psoriasis (red) or moderate-to-severe psoriasis(green).
Abundance in Group 1: increased abundance in Moderate to severe psoriasis
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacter cloacae | ||
| Paraprevotella sp. |
Revision editor(s): Anne-mariesharp
Signature 2
Source: Fig 6g
Description: Plot from LEfSe examination revealing enriched bacterial genera related to either mild psoriasis (red) or moderate-to-severe individuals(green).
Abundance in Group 1: decreased abundance in Moderate to severe psoriasis
| NCBI | Quality Control | Links |
|---|---|---|
| Parabacteroides goldsteinii | ||
| Roseburia intestinalis | ||
| Streptococcus_mitis_oralis_pneumoniaeStreptococcus_mitis_oralis_pneumoniae |
Revision editor(s): Anne-mariesharp
Experiment 13
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Healthy partners(couples or spouses)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Healthy partners of psoriasis patients
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
- Group 1 sample size Number of subjects in the case (exposed) group
- 17
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Fig 4d
Description: Boxplot showing the difference of the relative abundance at the phylum level between healthy partners and healthy controls samples
Abundance in Group 1: increased abundance in Healthy partners(couples or spouses)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota | ||
| Bacteroides eggerthii |
Revision editor(s): Anne-mariesharp, Aleru Divine
Signature 2
Source: Fig 4d - f
Description: Boxplot showing the difference of the relative abundance at the phylum, genus and species level between healthy partners and healthy controls samples
Abundance in Group 1: decreased abundance in Healthy partners(couples or spouses)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Roseburia | ||
| Coprococcus | ||
| Eubacterium | ||
| Roseburia intestinalis | ||
| Lachnospiraceae bacterium 8_1_57FAA | ||
| Lachnospira eligens | ||
| Phocaeicola coprophilus |
Revision editor(s): Anne-mariesharp
Experiment 14
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy partners(couples or spouses)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Psoriasis vulgaris
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients diagnosed with Psoriasis vulgaris by two attending dermatologists.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 17
- Group 1 sample size Number of subjects in the case (exposed) group
- 32
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Fig 4d, 4f
Description: Boxplot showing the difference of the relative abundance at the phylum and species level between psoriatic and healthy partners samples
Abundance in Group 1: increased abundance in Psoriasis vulgaris
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota | ||
| Roseburia intestinalis |
Revision editor(s): Anne-mariesharp, Aleru Divine
Signature 2
Source: Fig 4d - f
Description: Boxplot showing the difference of the relative abundance at the phylum, genus and species level between psoriatic and healthy partners samples
Abundance in Group 1: decreased abundance in Psoriasis vulgaris
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Bacteroides eggerthii | ||
| Eubacterium | ||
| Roseburia | ||
| Lachnospira eligens |
Revision editor(s): Anne-mariesharp, Aleru Divine
