Immunoregulatory role of the gut microbiota in inflammatory depression
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Liu P, Liu Z, Wang J, Wang J, Gao M, Zhang Y, Yang C, Zhang A, Li G, Li X, Liu S, Liu L, Sun N, Zhang K
Journal
Nature communications
Year
2024
Inflammatory depression is a treatment-resistant subtype of depression. A causal role of the gut microbiota as a source of low-grade inflammation remains unclear. Here, as part of an observational trial, we first analyze the gut microbiota composition in the stool, inflammatory factors and short-chain fatty acids (SCFAs) in plasma, and inflammatory and permeability markers in the intestinal mucosa of patients with inflammatory depression (ChiCTR1900025175). Gut microbiota of patients with inflammatory depression exhibits higher Bacteroides and lower Clostridium, with an increase in SCFA-producing species with abnormal butanoate metabolism. We then perform fecal microbiota transplantation (FMT) and probiotic supplementation in animal experiments to determine the causal role of the gut microbiota in inflammatory depression. After FMT, the gut microbiota of the inflammatory depression group shows increased peripheral and central inflammatory factors and intestinal mucosal permeability in recipient mice with depressive and anxiety-like behaviors. Clostridium butyricum administration normalizes the gut microbiota, decreases inflammatory factors, and displays antidepressant-like effects in a mouse model of inflammatory depression. These findings suggest that inflammatory processes derived from the gut microbiota can be involved in neuroinflammation of inflammatory depression.
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 , Blood , Colonic mucosa 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,Portion of blood,Vertebrate blood,Whole blood,Blood,blood,Colon mucosa,Colon mucous membrane,Colonic mucosa,Colonic mucous membrane,Large bowel mucosa,Mucosa of colon,Mucosa of large bowel,colonic mucosa
- 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 (HCs)
- 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
- Patients who had Major depressive disorder (MDD)
- 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)
- three 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) between MDD patients and HCs
Abundance in Group 1: increased abundance in Major depressive disorder (MDD)
| NCBI | Quality Control | Links |
|---|---|---|
| Micromonosporaceae | ||
| Adlercreutzia | ||
| Thermoleophilia | ||
| Rhodospirillales | ||
| Acidobacteriota | ||
| Rhodospirillaceae | ||
| Myxococcales | ||
| Anaerolineae | ||
| Ellin6529Ellin6529 | ||
| iiil_15iiil_15 |
Revision editor(s): Rahila
Experiment 2
Differences from previous experiment shown
Subjects
- 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 who belongs to non-inflammatory depression group
- 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
- 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: The LEfSe analysis was performed among three groups and found that compared with Non-inflammatory depression group and HCs.
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
Experiment 3
Differences from previous experiment shown
Subjects
- 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 who belongs to inflammatory depression group
- Group 1 sample size Number of subjects in the case (exposed) group
- 42
Lab analysis
Statistical Analysis
Signature 1
Source: FIG 3 (A1)
Description: The LEfSe analysis was performed among three groups and found that compared with inflammatory depression group and HCs.
Abundance in Group 1: increased abundance in inflammatory depression
Revision editor(s): Rahila
Experiment 4
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) 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 who belongs to the inflammatory depression group
- 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: The LEfSe analysis was performed among three groups and found that compared with inflammatory depression group and Non-inflammatory depression group.
Abundance in Group 1: increased abundance in inflammatory depression
Revision editor(s): Rahila
Signature 2
Source: FIG 3 (A2)
Description: The LEfSe analysis was performed among three groups and found that compared with Non-inflammatory depression group and inflammatory depression group.
Abundance in Group 1: decreased abundance in inflammatory depression
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Clostridia | ||
| Eubacteriales | ||
| Faecalibacterium | ||
| Oscillospiraceae | ||
| Clostridiaceae | ||
| Haemophilus | ||
| Pasteurellaceae | ||
| Pasteurellales |
Revision editor(s): Rahila
Experiment 5
Differences from previous experiment shown
Subjects
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy controls (HCs)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients who belongs to inflammatory depression group
- 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: The LEfSe analysis between gut microbiota of inflammatory depression group (n = 20) and HCs (n = 20).
Abundance in Group 1: increased abundance in inflammatory depression
Revision editor(s): Rahila
Experiment 6
Differences from previous experiment shown
Subjects
- 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 , Blood , Colonic mucosa , Brain 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,Portion of blood,Vertebrate blood,Whole blood,Blood,blood,Colon mucosa,Colon mucous membrane,Colonic mucosa,Colonic mucous membrane,Large bowel mucosa,Mucosa of colon,Mucosa of large bowel,colonic mucosa,Encephalon,Suprasegmental levels of nervous system,Suprasegmental structures,Synganglion,The brain,Brain,brain
- 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
- high-inflammatory
- 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
- 7
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- NONE
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
- 4.31
Alpha Diversity
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Source: FIG 4 (D3)
Description: The LEfSe analysis between the High-inflammatory group(Mice) and HC group(Mice).
Abundance in Group 1: increased abundance in high-inflammatory
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidaceae | ||
| Bacteroides | ||
| Enterobacteriaceae | ||
| Gammaproteobacteria | ||
| Shigella | ||
| Enterobacterales | ||
| Pseudomonadota |
Revision editor(s): Rahila
Experiment 7
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- low-inflammatory
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
Lab analysis
Statistical Analysis
Alpha Diversity
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Source: FIG 4 (D3)
Description: The LEfSe analysis between the High-inflammatory group(Mice) and Low-inflammatory group(Mice).
Abundance in Group 1: increased abundance in high-inflammatory
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidaceae | ||
| Bacteroides | ||
| Enterobacteriaceae | ||
| Gammaproteobacteria | ||
| Shigella | ||
| Pseudomonadota | ||
| Enterobacterales |
Revision editor(s): Rahila
Signature 2
Source: FIG 4 (D3)
Description: The LEfSe analysis between the High-inflammatory group(Mice) and Low-inflammatory group(Mice).
Abundance in Group 1: decreased abundance in high-inflammatory
| NCBI | Quality Control | Links |
|---|---|---|
| S24_7S24_7 | ||
| Lachnospiraceae | ||
| Desulfovibrio |
Revision editor(s): Rahila
Experiment 8
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- blank group
- Group 0 sample size Number of subjects in the control (unexposed) group
- 9
Lab analysis
Statistical Analysis
Alpha Diversity
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Source: FIG 4 (D3)
Description: The LEfSe analysis between the High-inflammatory group(Mice) and Blank group(Mice).
Abundance in Group 1: increased abundance in high-inflammatory
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidaceae | ||
| Bacteroides | ||
| Enterobacteriaceae | ||
| Gammaproteobacteria | ||
| Shigella | ||
| Enterobacterales | ||
| Pseudomonadota |
Revision editor(s): Rahila
Signature 2
Source: FIG 4 (D3)
Description: The LEfSe analysis between the High-inflammatory group(Mice) and Blank group(Mice).
Abundance in Group 1: decreased abundance in high-inflammatory
| NCBI | Quality Control | Links |
|---|---|---|
| Allobaculum | ||
| Erysipelotrichaceae | ||
| Erysipelotrichales | ||
| Turicibacter | ||
| Turicibacteraceae | ||
| TuricibacteralesTuricibacterales | ||
| Erysipelotrichia |
Revision editor(s): Rahila
Experiment 9
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- High inflammatory
- 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 classified into the Clostridium butyricum (CB)group
- 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
- 7
Lab analysis
Statistical Analysis
- 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
- 4.22
Alpha Diversity
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
Source: FIG 6 (C)
Description: The LEfSe analysis between the CB group (Mice) and High-inflammatory group(Mice).
Abundance in Group 1: increased abundance in Clostridium butyricum (CB)
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridia | ||
| Eubacteriales | ||
| Bacillota | ||
| Lachnospiraceae | ||
| Oscillospiraceae | ||
| Desulfovibrio | ||
| Deltaproteobacteria |
Revision editor(s): Rahila
Signature 2
Source: FIG 6 (C)
Description: The LEfSe analysis between the CB group (Mice) and High-inflammatory group(Mice).
Abundance in Group 1: decreased abundance in Clostridium butyricum (CB)
| NCBI | Quality Control | Links |
|---|---|---|
| Gammaproteobacteria | ||
| Pseudomonadota | ||
| Bacteroidaceae | ||
| Bacteroides | ||
| Enterobacteriaceae | ||
| Enterobacterales | ||
| Shigella | ||
| Butyricimonas | ||
| Odoribacteraceae |
Revision editor(s): Rahila
Experiment 10
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal saline (NS)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 6
Lab analysis
Statistical Analysis
Alpha Diversity
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: FIG 6 (C)
Description: The LEfSe analysis between the CB group (Mice) and NS group(Mice).
Abundance in Group 1: increased abundance in Clostridium butyricum (CB)
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridia | ||
| Eubacteriales | ||
| Bacillota | ||
| Oscillospiraceae | ||
| Lachnospiraceae | ||
| Desulfovibrio | ||
| Deltaproteobacteria |
Revision editor(s): Rahila
Signature 2
Source: FIG 6 (C)
Description: The LEfSe analysis between the CB group (Mice) and NS group(Mice).
Abundance in Group 1: decreased abundance in Clostridium butyricum (CB)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidales | ||
| Bacteroidia | ||
| S24_7S24_7 |
Revision editor(s): Rahila
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