Immunoregulatory role of the gut microbiota in inflammatory depression/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2024-8-5
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
Reviewed Marked as Reviewed by Svetlana up on 2024-8-5
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
Reviewed Marked as Reviewed by Svetlana up on 2024-8-5
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
