Gut microbial biomarkers for the treatment response in first-episode, drug-naïve schizophrenia: a 24-week follow-up study
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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.
- 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
- Response to risperidone Response to risperidone,response to risperidone
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls (C)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Schizophrenia (SCH) patients at Baseline (S0)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Schizophrenia drug-naïve patients who were newly admitted, and no treatment had begun. Patients had not yet received risperidone.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 107
- Group 1 sample size Number of subjects in the case (exposed) group
- 107
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 30 days
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
- Ion Torrent
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, smoking behavior, education level, sex
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index, smoking behavior, education level, sex, Confounders controlled for: "disease duration" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.disease duration
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
- decreased
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Source: Figure 4c and Supplementary Table 3
Description: Taxa enriched in the gut microbiota of Schizophrenia (SCH) patients at Baseline (S0) and Healthy controls (C).
Abundance in Group 1: increased abundance in Schizophrenia (SCH) patients at Baseline (S0)
NCBI | Quality Control | Links |
---|---|---|
Lachnoclostridium |
Signature 2
Source: Figure 4d and Supplementary Table 3
Description: Taxa enriched in the gut microbiota of Schizophrenia (SCH) patients at Baseline (S0) and Healthy controls (C).
Abundance in Group 1: decreased abundance in Schizophrenia (SCH) patients at Baseline (S0)
Experiment 2
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Schizophrenia (SCH) patients at Week 6 (S1)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Schizophrenia drug-naïve patients who had received 6 weeks of risperidone treatment and were accessed during the treatment.
- Group 1 sample size Number of subjects in the case (exposed) group
- 96
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Source: Figure 4C
Description: Taxa enriched in the gut microbiota of Schizophrenia (SCH) patients at Week 6 (S1) and Healthy controls (C).
Abundance in Group 1: decreased abundance in Schizophrenia (SCH) patients at Week 6 (S1)
NCBI | Quality Control | Links |
---|---|---|
Romboutsia |
Revision editor(s): MyleeeA
Experiment 3
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Schizophrenia (SCH) patients at Week 12 (S2)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Schizophrenia drug-naïve patients who had received 12 weeks of risperidone treatment and were accessed during the treatment.
- Group 1 sample size Number of subjects in the case (exposed) group
- 74
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 30 Days
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Source: Figure 4C
Description: Taxa enriched in the gut microbiota of SCH patients at Week 12 (S2) and Healthy controls (C).
Abundance in Group 1: decreased abundance in Schizophrenia (SCH) patients at Week 12 (S2)
NCBI | Quality Control | Links |
---|---|---|
Romboutsia |
Revision editor(s): MyleeeA
Experiment 4
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Schizophrenia (SCH) patients at Week 24 (S3)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Schizophrenia drug-naïve patients who had received 24 weeks of risperidone treatment and were accessed after the treatment.
- Group 1 sample size Number of subjects in the case (exposed) group
- 60
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 30 days
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index, education level, sex, smoking behavior, Confounders controlled for: "disease duration" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.disease duration
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Source: Figure 4d
Description: Taxa enriched in the gut microbiota of SCH patients at Week 24 (S3) and Healthy controls (C).
Abundance in Group 1: decreased abundance in Schizophrenia (SCH) patients at Week 24 (S3)
NCBI | Quality Control | Links |
---|---|---|
Romboutsia |
Revision editor(s): Aleru Divine
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Schizophrenia (SCH) patients at Baseline (S0)
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 30 Days
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
Signature 1
Source: Supplementary Figure S5
Description: Taxa enriched in the gut microbiota of Schizophrenia (SCH) patients at Baseline(S0) and After treatment at Week 24 (S3)
Abundance in Group 1: increased abundance in Schizophrenia (SCH) patients at Week 24 (S3)
Revision editor(s): MyleeeA
Signature 2
Source: Supplementary Figure 5 and Figure 4c
Description: Taxa enriched in the gut microbiota of Schizophrenia patients at Baseline(S0) and After treatment at Week 24 (S3)
Abundance in Group 1: decreased abundance in Schizophrenia (SCH) patients at Week 24 (S3)
NCBI | Quality Control | Links |
---|---|---|
Lachnoclostridium |
Revision editor(s): Aleru Divine, MyleeeA