16S rRNA gene sequencing reveals altered gut microbiota in young adults with schizophrenia and prominent negative symptoms
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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
Curated date: 2024/07/01
Curator:
Revision editor(s):
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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Schizophrenia patients with prominent negative symptoms (SCH-N)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with schizophrenia with prominent negative symptoms (SCH-N) who met the diagnostic criteria of schizophrenia with a total positive and negative syndrome scale (PANSS) score ≥60 according to the Statistical Clinical Interview for DSM-5 by two psychiatrists.
- 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
- 30
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
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
- 3.0
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
Curated date: 2024/07/11
Curator: Jacob A. De Jesus
Revision editor(s): Jacob A. De Jesus, Scholastica, WikiWorks
Source: Figure 2B
Description: Differential species abundance in gut microbiome between healthy controls versus schizophrenia patients with prominent negative symptoms (SCH-N) based on (LEfSe) analysis.
Abundance in Group 1: increased abundance in
Revision editor(s): Jacob A. De Jesus, Scholastica, WikiWorks
Signature 2
Curated date: 2024/07/11
Curator: Jacob A. De Jesus
Revision editor(s): Jacob A. De Jesus, Scholastica, WikiWorks
Source: Figure 2B
Description: Differential species abundance in gut microbiome between healthy controls versus schizophrenia patients with prominent negative symptoms (SCH-N) based on (LEfSe) analysis.
Abundance in Group 1: decreased abundance in
Revision editor(s): Jacob A. De Jesus, Scholastica, WikiWorks
Experiment 2
Curated date: 2024/07/01
Curator: Jacob A. De Jesus
Revision editor(s): Jacob A. De Jesus, Scholastica, WikiWorks
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Schizophrenia patients with prominent negative symptoms (SCH-N)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Schizophrenia patients with prominent positive symptoms (SCH-P)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with schizophrenia with prominent positive symptoms (SCH-P) who met the diagnostic criteria of schizophrenia with a total positive and negative syndrome scale (PANSS) score ≥60; at least three out of seven items of PANSS positive subscale score ≥4, or at least two items score ≥5, and a total PANSS positive subscale score ≥20, and at least 3 points more than the total PANSS negative subscale score.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 30
- Group 1 sample size Number of subjects in the case (exposed) group
- 32
Lab analysis
Statistical Analysis
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 1.5
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
Curated date: 2024/07/11
Curator: Jacob A. De Jesus
Revision editor(s): Jacob A. De Jesus, Scholastica, WikiWorks
Source: Figure 3B
Description: Differential species abundance in gut microbiome between schizophrenia patients with prominent negative (SCH-N) versus positive (SCH-P) symptoms based on (LEfSe) analysis.
Abundance in Group 1: increased abundance in Schizophrenia patients with prominent positive symptoms (SCH-P)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidales | ||
| Brevundimonas | ||
| Pseudomonadales | ||
| Sarcina | ||
| CAG:56CAG:56 |
Revision editor(s): Jacob A. De Jesus, Scholastica, WikiWorks
Signature 2
Curated date: 2024/07/11
Curator: Jacob A. De Jesus
Revision editor(s): Jacob A. De Jesus, Scholastica, WikiWorks
Source: Figure 3B
Description: Differential species abundance in gut microbiome between schizophrenia patients with prominent negative (SCH-N) versus positive (SCH-P) symptoms based on (LEfSe) analysis.
Abundance in Group 1: decreased abundance in Schizophrenia patients with prominent positive symptoms (SCH-P)
| NCBI | Quality Control | Links |
|---|---|---|
| Alphaproteobacteria | ||
| Ezakiella | ||
| Rhizobiaceae | ||
| Sphingomonadaceae | ||
| Sphingomonadales | ||
| Hyphomicrobiales |
Revision editor(s): Jacob A. De Jesus, Scholastica, WikiWorks
