Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3
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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.
- Mus musculus
- 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
- Control group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- CUMS group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice group induced with chronic unpredictable mild stress (CUMS) for 8 weeks.
- 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
- 6
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 4
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Figure 4F and Figure S2d
Description: LEfSe analysis of the differentially abundant taxa in each groups.
Abundance in Group 1: increased abundance in CUMS group
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacterales | ||
| Enterobacteriaceae | ||
| Klebsiella | ||
| Gammaproteobacteria | ||
| Pseudomonadota | ||
| Bacteroides | ||
| Bacteroidaceae | ||
| Bacteroidia | ||
| Bacteroidales | ||
| Fusobacteriia | ||
| Verrucomicrobiota |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 4F and Figure S2d
Description: LEfSe analysis of the differentially abundant taxa in each groups.
Abundance in Group 1: decreased abundance in CUMS group
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillales | ||
| Actinomycetota | ||
| Staphylococcaceae | ||
| Staphylococcus | ||
| Chloroflexia | ||
| Bacillota | ||
| Gemmatimonadetes | ||
| ThermiThermi | ||
| Armatimonadota |
Revision editor(s): Aleru Divine
Experiment 2
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- CUMS + XYS group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice group induced with chronic unpredictable mild stress (CUMS) for 8 weeks, followed by daily oral administration of XYS.
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
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 4F and Figure S2d
Description: LEfSe analysis of the differentially abundant taxa in each groups.
Abundance in Group 1: increased abundance in CUMS + XYS group
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Lactobacillus | ||
| Bacilli | ||
| Lactobacillales | ||
| Lactobacillaceae | ||
| Mycoplasmatota |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 4F and Figure S2d
Description: LEfSe analysis of the differentially abundant taxa in each groups.
Abundance in Group 1: decreased abundance in CUMS + XYS group
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Armatimonadota | ||
| Bacillales | ||
| Bacillota | ||
| Chloroflexia | ||
| Gemmatimonadetes | ||
| Staphylococcaceae | ||
| Staphylococcus | ||
| ThermiThermi |
Revision editor(s): Aleru Divine
Experiment 3
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- CUMS + FLX group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice group induced with chronic unpredictable mild stress (CUMS) for 8 weeks, followed by daily oral administration of FLX.
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
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 4F and Figure S2d
Description: LEfSe analysis of the differentially abundant taxa in each groups.
Abundance in Group 1: increased abundance in CUMS + FLX group
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 4F and Figure S2d
Description: LEfSe analysis of the differentially abundant taxa in each groups.
Abundance in Group 1: decreased abundance in CUMS + FLX group
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Armatimonadota | ||
| Bacillales | ||
| Bacillota | ||
| Chloroflexia | ||
| Gemmatimonadetes | ||
| Staphylococcaceae | ||
| Staphylococcus | ||
| ThermiThermi |
Revision editor(s): Aleru Divine
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- CUMS group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- CUMS + XYS group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice group induced with chronic unpredictable mild stress (CUMS) for 8 weeks, followed by daily oral administration of XYS.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- increased
Signature 1
Source: Figure 4F and Figure S2d
Description: LEfSe analysis of the differentially abundant taxa in each groups.
Abundance in Group 1: increased abundance in CUMS + XYS group
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Lactobacillus | ||
| Bacilli | ||
| Lactobacillales | ||
| Lactobacillaceae | ||
| Mycoplasmatota |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 4F and Figure S2d
Description: LEfSe analysis of the differentially abundant taxa in each groups.
Abundance in Group 1: decreased abundance in CUMS + XYS group
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacterales | ||
| Enterobacteriaceae | ||
| Klebsiella | ||
| Gammaproteobacteria | ||
| Pseudomonadota | ||
| Bacteroides | ||
| Bacteroidaceae | ||
| Bacteroidia | ||
| Bacteroidales | ||
| Fusobacteriia | ||
| Verrucomicrobiota |
Revision editor(s): Aleru Divine
Experiment 5
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- CUMS + FLX group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice group induced with chronic unpredictable mild stress (CUMS) for 8 weeks, followed by daily oral administration of FLX.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- increased
Signature 1
Source: Figure 4F and Figure S2d
Description: LEfSe analysis of the differentially abundant taxa in each groups.
Abundance in Group 1: increased abundance in CUMS + FLX group
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 4F and Figure S2d
Description: LEfSe analysis of the differentially abundant taxa in each groups.
Abundance in Group 1: decreased abundance in CUMS + FLX group
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacterales | ||
| Enterobacteriaceae | ||
| Klebsiella | ||
| Gammaproteobacteria | ||
| Pseudomonadota | ||
| Bacteroides | ||
| Bacteroidaceae | ||
| Bacteroidia | ||
| Bacteroidales | ||
| Fusobacteriia | ||
| Verrucomicrobiota |
Revision editor(s): Aleru Divine
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- CUMS + XYS group
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
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 4F and Figure S2d
Description: LEfSe analysis of the differentially abundant taxa in each groups.
Abundance in Group 1: increased abundance in CUMS + FLX group
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 4F and Figure S2d
Description: LEfSe analysis of the differentially abundant taxa in each groups.
Abundance in Group 1: decreased abundance in CUMS + FLX group
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Lactobacillus | ||
| Bacilli | ||
| Lactobacillales | ||
| Lactobacillaceae | ||
| Mycoplasmatota |
Revision editor(s): Aleru Divine
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- CUMS
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice group induced with chronic unpredictable mild stress (CUMS) for 8 weeks.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- 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
- unchanged
Signature 1
Source: Figure 8G
Description: The representation of the differentially abundant taxa between the CUMS and the control group.
Abundance in Group 1: increased abundance in CUMS
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella | ||
| ParaprevotellaceaeParaprevotellaceae |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 8G
Description: The representation of the differentially abundant taxa between CUMS and control.
Abundance in Group 1: decreased abundance in CUMS
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteria | ||
| Faecalibacterium |
Revision editor(s): Aleru Divine
Experiment 8
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Control + FMT(CUMS) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice group with no stress stimulation for 8 weeks, followed by daily FMT (feces from CUMS group in the first experiment.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- 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
- unchanged
Signature 1
Source: Figure 8i
Description: The representation of the differentially abundant taxa between the Control + FMT(CUMS) group and the control group.
Abundance in Group 1: increased abundance in Control + FMT(CUMS) group
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 8i
Description: The representation of the differentially abundant taxa between the Control + FMT(CUMS) group and the control group.
Abundance in Group 1: decreased abundance in Control + FMT(CUMS) group
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota |
Revision editor(s): Aleru Divine
Experiment 9
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- CUMS + FMT(XYS) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice group induced with chronic unpredictable mild stress (CUMS) for 8 weeks, followed by daily FMT (feces from CUMS + XYS group in the first experiment) for 4 weeks.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- 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
- unchanged
Signature 1
Source: Text and Figure S5f
Description: Differential abundance in the Control group and the CUMS + FMT(XYS) group
Abundance in Group 1: increased abundance in CUMS + FMT(XYS) group
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus | ||
| Akkermansia |
Revision editor(s): Aleru Divine
Experiment 10
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- CUMS group
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
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 8K
Description: The representation of the differentially abundant taxa between the CUMS and the CUMS + FMT(XYS) group.
Abundance in Group 1: increased abundance in CUMS + FMT(XYS) group
| NCBI | Quality Control | Links |
|---|---|---|
| ParaprevotellaceaeParaprevotellaceae | ||
| Prevotella | ||
| Bacteria |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 8K
Description: The representation of the differentially abundant taxa between the Control + FMT(CUMS) group and the CUMS group.
Abundance in Group 1: decreased abundance in CUMS + FMT(XYS) group
| NCBI | Quality Control | Links |
|---|---|---|
| Candidatus Arthromitus | ||
| Dialister | ||
| Ruminococcus |
Revision editor(s): Aleru Divine
