Immunoregulatory role of the gut microbiota in inflammatory depression
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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
- Major depressive disorder major depression,major depressive disorder,recurrent major depression,single major depressive episode,unipolar depression,Major depressive disorder
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls (HC)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Major depressive disorder (MDD)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- First-episode, drug-naïve patients with major depressive disorder (MDD) ages of 18–55.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 85
- Group 1 sample size Number of subjects in the case (exposed) group
- 85
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 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
- LEfSe
- 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
- 2.0
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- 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
- unchanged
- Richness Number of species
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Source: FIG 1 (C)
Description: A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant in patients with major depressive disorder (MDD) compared to healthy controls (HC)
Abundance in Group 1: increased abundance in Major depressive disorder (MDD)
| NCBI | Quality Control | Links |
|---|---|---|
| Adlercreutzia | ||
| Anaerolineae | ||
| Micromonosporaceae | ||
| Myxococcales | ||
| Rhodospirillaceae | ||
| Rhodospirillales | ||
| Thermoleophilia | ||
| Ellin6529Ellin6529 | ||
| iiil_15iiil_15 | ||
| Acidobacteria_6Acidobacteria_6 |
Revision editor(s): Rahila, Scholastica
Signature 2
Source: FIG 1 (C)
Description: A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant in patients with major depressive disorder (MDD) compared to healthy controls (HC)
Abundance in Group 1: decreased abundance in Major depressive disorder (MDD)
| NCBI | Quality Control | Links |
|---|---|---|
| Roseburia | ||
| Clostridiaceae | ||
| Clostridium | ||
| Pasteurellaceae | ||
| Pasteurellales | ||
| Haemophilus | ||
| SMBS3SMBS3 | ||
| Turicibacter | ||
| Turicibacteraceae | ||
| TuricibacteralesTuricibacterales | ||
| Peptostreptococcaceae |
Revision editor(s): Scholastica
Experiment 2
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Gut microbiome measurement Gut microbiome measurement,gut microbiome measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls (HC) and inflammatory depression group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Non-inflammatory depression
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with major depressive disorder (MDD) who had non-inflammatory depression
- Group 0 sample size Number of subjects in the control (unexposed) group
- 127
- Group 1 sample size Number of subjects in the case (exposed) group
- 43
Lab analysis
Statistical Analysis
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2.72
Signature 1
Source: FIG 3 (A1)
Description: A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant among three groups
Abundance in Group 1: increased abundance in Non-inflammatory depression
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Clostridia | ||
| Eubacteriales | ||
| Faecalibacterium | ||
| Haemophilus | ||
| Oscillospiraceae | ||
| Pasteurellaceae | ||
| Pasteurellales |
Revision editor(s): Rahila, Scholastica
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls (HC) and non-inflammatory depression group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Inflammatory depression
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with major depressive disorder (MDD) who had inflammatory depression
- Group 0 sample size Number of subjects in the control (unexposed) group
- 128
- Group 1 sample size Number of subjects in the case (exposed) group
- 42
Lab analysis
Statistical Analysis
Signature 1
Source: FIG 3 (A1)
Description: A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant among three groups
Abundance in Group 1: increased abundance in Inflammatory depression
Revision editor(s): Rahila, Scholastica
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-inflammatory depression
- Group 0 sample size Number of subjects in the control (unexposed) group
- 43
Lab analysis
Statistical Analysis
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2.45
Signature 1
Source: FIG 3 (A1)
Description: A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant in patients with inflammatory versus non-inflammatory depression
Abundance in Group 1: increased abundance in Inflammatory depression
Revision editor(s): Rahila, Scholastica
Signature 2
Source: FIG 3 (A2)
Description: A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant in patients with inflammatory versus non-inflammatory depression
Abundance in Group 1: decreased abundance in Inflammatory depression
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Clostridia | ||
| Clostridiaceae | ||
| Eubacteriales | ||
| Faecalibacterium | ||
| Haemophilus | ||
| Oscillospiraceae | ||
| Pasteurellaceae | ||
| Pasteurellales |
Revision editor(s): Rahila, Scholastica
Experiment 5
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Major depressive disorder major depression,major depressive disorder,recurrent major depression,single major depressive episode,unipolar depression,Major depressive disorder
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls (HC)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
Statistical Analysis
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2.0
Signature 1
Source: FIG 3 (C)
Description: A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant in patients with inflammatory depression compared to healthy controls (HC) at species level using shotgun metagenomic sequencing
Abundance in Group 1: increased abundance in Inflammatory depression
Revision editor(s): Rahila, Scholastica
Signature 2
Source: FIG 3 (C)
Description: A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant in patients with inflammatory depression compared to healthy controls (HC) at species level using shotgun metagenomic sequencing
Abundance in Group 1: decreased abundance in Inflammatory depression
Revision editor(s): Scholastica
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy control (HC)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Inflammatory and non-inflammatory depression
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with major depressive disorder (MDD) grouped into inflammatory and non-inflammatory depression groups
- Group 0 sample size Number of subjects in the control (unexposed) group
- 85
- Group 1 sample size Number of subjects in the case (exposed) group
- 85
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
Statistical Analysis
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2.72
Signature 1
Source: FIG 3 (A1)
Description: A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant among three groups
Abundance in Group 1: decreased abundance in Inflammatory and non-inflammatory depression
| NCBI | Quality Control | Links |
|---|---|---|
| Roseburia | ||
| Clostridiaceae | ||
| Peptostreptococcaceae | ||
| Clostridium | ||
| SMBS3SMBS3 |
Revision editor(s): Rahila, Scholastica
Experiment 7
Subjects
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Mus musculus
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Gut microbiome measurement Gut microbiome measurement,gut microbiome measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low-inflammatory, healthy control and blank groups
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High-inflammatory group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice classified into the high-inflammatory group
- 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
- 20
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- None
Lab analysis
Statistical Analysis
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Not specified
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 4.31
Signature 1
Source: FIG 4 (D3)
Description: A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant among four mice groups
Abundance in Group 1: increased abundance in High-inflammatory group
| NCBI | Quality Control | Links |
|---|---|---|
| Allobaculum | ||
| Erysipelotrichia | ||
| Erysipelotrichaceae | ||
| Erysipelotrichales | ||
| Turicibacteraceae | ||
| Turicibacter | ||
| TuricibacteralesTuricibacterales |
Revision editor(s): Rahila, Scholastica
Experiment 8
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- High-inflammatory, healthy control and blank groups
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Low-inflammatory group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice classified into the low-inflammatory group
- Group 0 sample size Number of subjects in the control (unexposed) group
- 36
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
Lab analysis
Statistical Analysis
Signature 1
Source: FIG 4 (D3)
Description: A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant among four mice groups
Abundance in Group 1: increased abundance in Low-inflammatory group
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridia | ||
| Eubacteriales | ||
| Paracoccus |
Revision editor(s): Rahila, Scholastica
Experiment 9
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy control (HC) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High-inflammatory, low-inflammatory and blank groups
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice classified into the high-inflammatory, low-inflammatory and blank groups
- Group 0 sample size Number of subjects in the control (unexposed) group
- 7
- Group 1 sample size Number of subjects in the case (exposed) group
- 37
Lab analysis
Statistical Analysis
Signature 1
Source: FIG 4 (D3)
Description: A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant among four mice groups
Abundance in Group 1: decreased abundance in High-inflammatory, low-inflammatory and blank groups
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonadota | ||
| Bacteroidaceae | ||
| Bacteroides | ||
| Gammaproteobacteria | ||
| Enterobacteriaceae | ||
| Shigella | ||
| Enterobacterales |
Revision editor(s): Rahila, Scholastica
Experiment 10
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- High-inflammatory, low-inflammatory and healthy control groups
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Blank group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice administered normal saline and classified into the blank group
- Group 0 sample size Number of subjects in the control (unexposed) group
- 35
- Group 1 sample size Number of subjects in the case (exposed) group
- 9
Lab analysis
Statistical Analysis
Signature 1
Source: FIG 4 (D3)
Description: A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant among four mice groups
Abundance in Group 1: increased abundance in Blank group
| NCBI | Quality Control | Links |
|---|---|---|
| Muribaculaceae | ||
| Lachnospiraceae | ||
| Desulfovibrio |
Revision editor(s): Rahila, Scholastica
Experiment 11
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Clostridium butyricum (CB) and normal saline (NS) groups
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High-inflammatory group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice classified into the high-inflammatory group
- Group 0 sample size Number of subjects in the control (unexposed) group
- 13
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
Lab analysis
Statistical Analysis
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 4.22
Signature 1
Source: FIG 6 (C)
Description: A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant among three mice groups
Abundance in Group 1: increased abundance in High-inflammatory group
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridia | ||
| Eubacteriales | ||
| Bacillota | ||
| Lachnospiraceae | ||
| Oscillospiraceae | ||
| Desulfovibrio | ||
| Deltaproteobacteria |
Revision editor(s): Scholastica
Experiment 12
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- High-inflammatory and normal saline (NS) groups
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Clostridium butyricum (CB)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice administered probiotics (Clostridium butyricum)
Lab analysis
Statistical Analysis
Signature 1
Source: FIG 6 (C)
Description: A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant among three mice groups
Abundance in Group 1: increased abundance in Clostridium butyricum (CB)
| NCBI | Quality Control | Links |
|---|---|---|
| Gammaproteobacteria | ||
| Pseudomonadota | ||
| Bacteroidaceae | ||
| Bacteroides | ||
| Enterobacteriaceae | ||
| Enterobacterales | ||
| Shigella | ||
| Butyricimonas | ||
| Odoribacteraceae |
Revision editor(s): Scholastica
Experiment 13
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal saline (NS)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High-inflammatory and Clostridium butyricum (CB) groups
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice administered normal saline (NS)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 6
- Group 1 sample size Number of subjects in the case (exposed) group
- 14
Lab analysis
Statistical Analysis
Signature 1
Source: FIG 6 (C)
Description: A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant among three mice groups
Abundance in Group 1: decreased abundance in High-inflammatory and Clostridium butyricum (CB) groups
| NCBI | Quality Control | Links |
|---|---|---|
| Muribaculaceae | ||
| Bacteroidia | ||
| Bacteroidota | ||
| Bacteroidales |
Revision editor(s): Scholastica
