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
- Response to antidepressant Response to antidepressant,response to antidepressant
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Chronic Unpredictable Mild Stress (CUMS), CUMS + Xiaoyaosan (XYS) and CUMS + fluoxetine (FLX) groups
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Control Group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples collected from the mice groups without any intervention or drug administration.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 18
- 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
- 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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 4
Signature 1
Source: Figure 4F and Figure S2d
Description: LEfSe analysis of the microbiome data showing differentially abundant bacterial taxa in the control, CUMS, (CUMS + XYS) and (CUMS + FLX) groups.
Abundance in Group 1: increased abundance in Control Group
| NCBI | Quality Control | Links |
|---|---|---|
| Acidimicrobiia | ||
| Actinomycetota | ||
| Armatimonadota | ||
| Bacillales | ||
| Bacillota | ||
| Chloroflexota | ||
| Deinococcota | ||
| Gemmatimonadota | ||
| Staphylococcaceae | ||
| Staphylococcus |
Revision editor(s): Aleru Divine
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control, (CUMS + XYS) and (CUMS + FLX) groups
- 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)
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4F and Figure S2d
Description: LEfSe analysis of the microbiome data showing differentially abundant bacterial taxa in the control, CUMS, (CUMS + XYS) and (CUMS + FLX) groups.
Abundance in Group 1: increased abundance in CUMS group
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidaceae | ||
| Bacteroidales | ||
| Bacteroides | ||
| Bacteroidia | ||
| Enterobacterales | ||
| Enterobacteriaceae | ||
| Fusobacteriota | ||
| Gammaproteobacteria | ||
| Klebsiella | ||
| Pseudomonadota | ||
| Verrucomicrobiota |
Revision editor(s): Aleru Divine
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control, CUMS, and (CUMS + XYS) groups
- 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 fluoxetine (FLX).
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4F and Figure S2d
Description: LEfSe analysis of the microbiome data showing differentially abundant bacterial taxa in the control, CUMS, (CUMS + XYS) and (CUMS + FLX) groups.
Abundance in Group 1: increased abundance in CUMS + FLX group
| NCBI | Quality Control | Links |
|---|---|---|
| Acidobacteriota | ||
| Allobaculum | ||
| Atribacterota | ||
| Bacteroidota | ||
| Chlorobiota | ||
| Cyanobacteriota | ||
| Deferribacterota | ||
| Erysipelotrichaceae | ||
| Erysipelotrichales | ||
| Erysipelotrichia | ||
| Planctomycetota |
Revision editor(s): Aleru Divine
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control, CUMS, and (CUMS + FLX) groups
- 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 Xiaoyaosan (XYS).
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4F and Figure S2d
Description: LEfSe analysis of the microbiome data showing differentially abundant bacterial taxa in the control, CUMS, (CUMS + XYS) and (CUMS + FLX) groups.
Abundance in Group 1: increased abundance in CUMS + XYS group
| NCBI | Quality Control | Links |
|---|---|---|
| Bacilli | ||
| Bacillota | ||
| Lactobacillaceae | ||
| Lactobacillales | ||
| Lactobacillus | ||
| Mycoplasmatota |
Revision editor(s): Aleru Divine
Experiment 5
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Environmental stress treatment environmental stress,EnvironmentalStress,Environmental stress treatment,environmental stress treatment
- 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)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 6
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: LEfSe analysis of the microbiome data showing differentially abundant bacterial taxa in the control and CUMS group
Abundance in Group 1: increased abundance in CUMS Group
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella | ||
| unclassified Paraprevotella |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 8G
Description: LEfSe analysis of the microbiome data showing differentially abundant bacterial taxa in the control and CUMS group
Abundance in Group 1: decreased abundance in CUMS Group
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteria | ||
| Faecalibacterium |
Revision editor(s): Aleru Divine
Experiment 6
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Response to transplant Response to transplant,response to transplant
- 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 that received fecal microbiota transplantation from host induced with chronic unpredictable mild stress (CUMS).
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: LEfSe analysis of the microbiome data showing differentially abundant bacterial taxa in the control and Control + FMT(CUMS) group.
Abundance in Group 1: increased abundance in Control + FMT(CUMS) group
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 8i
Description: LEfSe analysis of the microbiome data showing differentially abundant bacterial taxa in the control and Control + FMT(CUMS) group.
Abundance in Group 1: decreased abundance in Control + FMT(CUMS) group
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota |
Revision editor(s): Aleru Divine
Experiment 7
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 + FMT(XYS) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice group that received fecal microbiota transplantation from host treated with Xiaoyaosan (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 8K
Description: LEfSe analysis of the microbiome data showing differentially abundant bacterial taxa in the control and CUMS + FMT(XYS) group.
Abundance in Group 1: increased abundance in CUMS + FMT(XYS) group
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteria | ||
| Prevotella | ||
| unclassified Paraprevotella |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 8K
Description: LEfSe analysis of the microbiome data showing differentially abundant bacterial taxa in the control and CUMS + FMT(XYS) 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
Experiment 8
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
- Control + FMT(CUMS) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice group that received fecal microbiota transplantation (FMT) from host induced with chronic unpredictable mild stress (CUMS).
Lab analysis
Statistical Analysis
- Statistical test
- Pearson Correlation
- 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
- 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 S5F
Description: Gut microbiota change at genus level (Control versus Control+FMT(CUMS))
Abundance in Group 1: increased abundance in Control + FMT(CUMS) group
| NCBI | Quality Control | Links |
|---|---|---|
| Allobaculum | ||
| Prevotella | ||
| Parabacteroides | ||
| Sutterella | ||
| Bacteroides |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure S5F
Description: Gut microbiota change at genus level (Control versus Control+FMT(CUMS))
Abundance in Group 1: decreased abundance in Control + FMT(CUMS) group
Revision editor(s): Aleru Divine
Experiment 9
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 + FMT(XYS) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice group that received fecal microbiota transplantation from host treated with Xiaoyaosan (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 S5d
Description: Gut microbiota change at genus level (CUMS versus CUMS+FMT(XYS)).
Abundance in Group 1: increased abundance in CUMS + FMT(XYS) group
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia | ||
| Lactobacillus | ||
| Sutterella | ||
| Prevotella | ||
| Parabacteroides | ||
| Bacteroides |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure S5d
Description: Gut microbiota change at genus level (CUMS versus CUMS+FMT(XYS)).
Abundance in Group 1: decreased abundance in CUMS + FMT(XYS) group
Revision editor(s): Aleru Divine
Experiment 10
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Environmental stress treatment environmental stress,EnvironmentalStress,Environmental stress treatment,environmental stress treatment
- 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)
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 S5E
Description: Gut microbiota change at genus level (Control versus CUMS).
Abundance in Group 1: increased abundance in CUMS Group
| NCBI | Quality Control | Links |
|---|---|---|
| Allobaculum | ||
| Oscillospira | ||
| Clostridium | ||
| Prevotella | ||
| Gardnerella | ||
| Parabacteroides | ||
| Helicobacter | ||
| Akkermansia | ||
| Prevotella sp. |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure S5E
Description: Gut microbiota change at genus level (Control versus CUMS).
Abundance in Group 1: decreased abundance in CUMS Group
| NCBI | Quality Control | Links |
|---|---|---|
| Candidatus Arthromitus | ||
| Bacteroides | ||
| Lactobacillus | ||
| Ruminococcus | ||
| Staphylococcus | ||
| Coprococcus | ||
| unidentified | ||
| Sutterella | ||
| Roseburia | ||
| Faecalibacterium | ||
| Blautia |
Revision editor(s): Aleru Divine
Experiment 11
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Depressive disorder depression,melancholia,melancholias,mental depression,syndrome, depressive,syndromes, depressive,Depressive disorder,depressive disorder
- 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.
Lab analysis
Statistical Analysis
- Statistical test
- Kruskall-Wallis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Figure 4(G-I)
Description: The relative abundances of selected bacterial signatures in the control, CUMS, (CUMS + XYS) and (CUMS + FLX) groups.
Abundance in Group 1: increased abundance in CUMS group
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Klebsiella |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 4(G-I)
Description: The relative abundances of selected bacterial signatures in the control, CUMS, (CUMS + XYS) and (CUMS + FLX) groups.
Abundance in Group 1: decreased abundance in CUMS group
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus |
Revision editor(s): Aleru Divine
Experiment 12
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Response to antidepressant Response to antidepressant,response to antidepressant
- 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 Xiaoyaosan (XYS).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Figure 4(G-I)
Description: The relative abundances of selected bacterial signatures in the control, CUMS, (CUMS + XYS) and (CUMS + FLX) groups.
Abundance in Group 1: increased abundance in CUMS + XYS group
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 4(G-I)
Description: The relative abundances of selected bacterial signatures in the control, CUMS, (CUMS + XYS) and (CUMS + FLX) groups.
Abundance in Group 1: decreased abundance in CUMS + XYS group
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Klebsiella |
Revision editor(s): Aleru Divine
Experiment 13
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 fluoxetine (FLX).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Figure 4(G-I)
Description: The relative abundances of selected bacterial signatures in the control, CUMS, (CUMS + XYS) and (CUMS + FLX) groups.
Abundance in Group 1: decreased abundance in CUMS + FLX group
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Klebsiella |
Revision editor(s): Aleru Divine
