The gut microbiota is associated with psychiatric symptom severity and treatment outcome among individuals with serious mental illness
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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
- United States of America
- 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
- Unipolar depression Depression,Depression, Emotional,Depression, Endogenous,Depression, Involutional,Depression, Neurotic,Depression, Unipolar,Depressions,Depressions, Emotional,Depressions, Endogenous,Depressions, Neurotic,Depressions, Unipolar,DEPRESSIVE DIS,DEPRESSIVE DIS MAJOR,Depressive Disorder,Depressive Disorder, Major,Depressive Disorders,Depressive Disorders, Major,Depressive Neuroses,Depressive Neurosis,Depressive Symptom,Depressive Symptoms,Depressive Syndrome,Depressive Syndromes,Disorder, Depressive,Disorder, Major Depressive,Disorders, Depressive,Disorders, Major Depressive,Emotional Depression,Emotional Depressions,Endogenous Depression,Endogenous Depressions,Involutional Depression,Involutional Psychoses,Involutional Psychosis,MAJOR DEPRESSIVE DIS,major depressive disorder,Major Depressive Disorders,Neuroses, Depressive,Neurosis, Depressive,Neurotic Depression,Neurotic Depressions,Paraphrenia, Involutional,Psychoses, Involutional,Psychosis, Involutional,Symptom, Depressive,Symptoms, Depressive,Syndrome, Depressive,Syndromes, Depressive,Unipolar Depressions,Unipolar depression,unipolar depression
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- mild depression
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- severe depression
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients in this group were diagnosed with severe depression (The primary patient-reported outcome measures used in this study were the Patient Health Questionnaire – 9 (PHQ-9) and the Patient Health Questionnaire – Generalized Anxiety Disorder screener (GAD-7); they were used to quantify depression severity).
- 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
- 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
- 2
Signature 1
Source: Figure 1A and 1B
Description: Significant bacterial biomarkers among individuals with severe depression VS individuals with mild depression at admission
Abundance in Group 1: increased abundance in severe depression
| NCBI | Quality Control | Links |
|---|---|---|
| Flavonifractor plautii | ||
| Ruminococcus sp. | ||
| Lachnospiraceae bacterium 1_4_56FAA |
Revision editor(s): WikiWorks, Merit, ChiomaBlessing
Signature 2
Curated date: 2021/01/10
Curator: Fatima Zohra
Revision editor(s): WikiWorks, Rukky, ChiomaBlessing, Joan Chuks
Source: Figure 1A and 1B
Description: Significant bacterial biomarkers among individuals with severe depression VS individuals with mild depression at admission
Abundance in Group 1: decreased abundance in severe depression
Revision editor(s): WikiWorks, Rukky, ChiomaBlessing, Joan Chuks
Experiment 2
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- moderate depression
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients in this group were diagnosed with moderate depression (The primary patient-reported outcome measures used in this study were the Patient Health Questionnaire – 9 (PHQ-9) and the Patient Health Questionnaire – Generalized Anxiety Disorder screener (GAD-7); they were used to quantify depression severity).
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 1A and 1B
Description: Significant bacterial biomarkers among individuals with moderate depression VS individuals with mild depression at admission
Abundance in Group 1: increased abundance in moderate depression
| NCBI | Quality Control | Links |
|---|---|---|
| Coprococcus catus | ||
| Flavonifractor | ||
| Streptococcus anginosus | ||
| [Clostridium] symbiosum |
Revision editor(s): WikiWorks, ChiomaBlessing
Experiment 3
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Anxiety disorder anxiety,anxiety disorder,anxiety disorders,anxiety neuroses,anxiety neurosis,anxiety state,anxiety/mood disorders,chronic stress,mood and anxiety disorder,mood and anxiety disorders,neurotic anxiety states,Anxiety disorder
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- mild anxiety
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- severe anxiety
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients in this group were diagnosed with severe anxiety (The primary patient-reported outcome measures used in this study were the Patient Health Questionnaire – 9 (PHQ-9) and the Patient Health Questionnaire – Generalized Anxiety Disorder screener (GAD-7); they were used to quantify anxiety severity).
Lab analysis
Statistical Analysis
Signature 1
Curated date: 2021/01/10
Curator: Fatima Zohra
Revision editor(s): WikiWorks, Atrayees, ChiomaBlessing
Source: Figure 1C and 1D
Description: Significant bacterial biomarkers among individuals with severe anxiety VS individuals with mild anxiety at admission
Abundance in Group 1: increased abundance in severe anxiety
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus anginosus | ||
| Lachnospiraceae bacterium 1_4_56FAA |
Revision editor(s): WikiWorks, Atrayees, ChiomaBlessing
Signature 2
Source: Figure 1C and 1D
Description: Significant bacterial biomarkers among individuals with severe anxiety VS individuals with mild anxiety at admission
Abundance in Group 1: decreased abundance in severe anxiety
Revision editor(s): WikiWorks, Merit, ChiomaBlessing
Experiment 4
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- moderate anxiety
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients in this group were diagnosed with moderate anxiety (The primary patient-reported outcome measures used in this study were the Patient Health Questionnaire – 9 (PHQ-9) and the Patient Health Questionnaire – Generalized Anxiety Disorder screener (GAD-7); they were used to quantify anxiety severity).
Lab analysis
Statistical Analysis
Signature 1
Curated date: 2021/01/10
Curator: Fatima Zohra
Revision editor(s): WikiWorks, Atrayees, ChiomaBlessing
Source: Figure 1C and 1D
Description: Significant bacterial biomarkers among individuals with moderate anxiety VS individuals with mild anxiety at admission
Abundance in Group 1: increased abundance in moderate anxiety
| NCBI | Quality Control | Links |
|---|---|---|
| Lactococcus lactis | ||
| Eggerthella lenta | ||
| Lachnospiraceae bacterium 1_1_57FAA | ||
| Clostridiales bacterium 1_7_47FAA | ||
| unclassified Eggerthella |
Revision editor(s): WikiWorks, Atrayees, ChiomaBlessing
Experiment 5
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Remission disease remission,Remission,remission
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Yes
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants who achieved remission from depression at discharge
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 3A and 3B
Description: Significant bacterial biomarkers among participants who achieved remission from depression (YES) VS participants who did not achieve remission from depression at discharge (NO)
Abundance in Group 1: increased abundance in Yes
Revision editor(s): ChiomaBlessing, Joan Chuks
Signature 2
Source: Figure 3A and 3B
Description: Significant bacterial biomarkers among participants who achieved remission from depression (YES) VS participants who did not achieve remission from depression at discharge (NO)
Abundance in Group 1: decreased abundance in Yes
Revision editor(s): ChiomaBlessing
Experiment 6
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants who achieved remission from anxiety at discharge
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 3C and 3D
Description: Significant bacterial biomarkers among participants who achieved remission from anxiety (YES) VS participants who did not achieve remission from anxiety at discharge (NO)
Abundance in Group 1: increased abundance in Yes
Revision editor(s): ChiomaBlessing, Joan Chuks
Signature 2
Source: Figure 3C and 3D
Description: Significant bacterial biomarkers among participants who achieved remission from anxiety (YES) VS participants who did not achieve remission from anxiety at discharge (NO)
Abundance in Group 1: decreased abundance in Yes
Revision editor(s): ChiomaBlessing
