The gut microbiome and metabolites are altered and interrelated in patients with functional constipation
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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
- Chronic constipation Chronic constipation,Infrequent bowel movements,chronic constipation
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Functional Constipation
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients diagnosed with Functional Constipation by physicians according to the Rome IV diagnostic criteria.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 21
- Group 1 sample size Number of subjects in the case (exposed) group
- 21
- 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
- T-Test
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
Source: Figure 1E and Table S1
Description: Differential microbiome of the FC (Functional constipation) and HC (Healthy control) groups at the genus levels
Abundance in Group 1: increased abundance in Functional Constipation
Signature 2
Source: Figure 1E and Table S1
Description: Differential microbiome of the FC (Functional constipation) and HC (Healthy control) groups at the genus levels
Abundance in Group 1: decreased abundance in Functional Constipation
| NCBI | Quality Control | Links |
|---|---|---|
| ML635J40_aquatic_groupML635J40_aquatic_group |
Experiment 2
Subjects
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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
Source: Figure 2A, 2B
Description: LDA score diagram and Phylogenetic tree in the cladogram showing significantly differential taxa
Abundance in Group 1: increased abundance in Functional Constipation
Revision editor(s): Anne-mariesharp
Signature 2
Source: Figure 2A, 2B
Description: LDA score diagram and Phylogenetic tree in the cladogram showing significantly differential taxa
Abundance in Group 1: decreased abundance in Functional Constipation
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes | ||
| Gilliamella | ||
| Muribaculaceae | ||
| Orbaceae | ||
| Orbales | ||
| ML635J_40_aquatic_groupML635J_40_aquatic_group |
Revision editor(s): Anne-mariesharp, Tosin
Experiment 3
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Bowel dysfunction disease of lower digestive tract,lower digestive tract disease,Bowel dysfunction,bowel dysfunction
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low levels of complete spontaneous bowel movements (CSBMs)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High levels of complete spontaneous bowel movements (CSBMs)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with high levels of complete spontaneous bowel movements
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
Lab analysis
Statistical Analysis
- Statistical test
- Spearman Correlation
- 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
- Not specified
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
Signature 1
Source: Table S2
Description: The correlations between differential genera and clinical parameters.
Abundance in Group 1: increased abundance in High levels of complete spontaneous bowel movements (CSBMs)
| NCBI | Quality Control | Links |
|---|---|---|
| Gilliamella | ||
| ML635J_40_aquatic_groupML635J_40_aquatic_group |
Signature 2
Source: Table S2
Description: The correlations between differential genera and clinical parameters.
Abundance in Group 1: decreased abundance in High levels of complete spontaneous bowel movements (CSBMs)
Experiment 4
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Complicated disease course CDC,Complicated disease course,complicated disease course
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low course of disease
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High course of disease
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with high course of the disease (Functional Constipation)
Lab analysis
Statistical Analysis
Signature 1
Source: Table S2
Description: The correlations between differential genera and clinical parameters
Abundance in Group 1: increased abundance in High course of disease
Revision editor(s): Anne-mariesharp
Signature 2
Source: Table S2
Description: The correlations between differential genera and clinical parameters
Abundance in Group 1: decreased abundance in High course of disease
| NCBI | Quality Control | Links |
|---|---|---|
| Gilliamella | ||
| ML635J_40_aquatic_groupML635J_40_aquatic_group |
Revision editor(s): Anne-mariesharp, Tosin
Experiment 5
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Constipation Constipation,Costiveness,Dyschezia,constipation
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low level of straining during defecation
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High level of straining during defecation
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with high level of straining during defecation
Lab analysis
Statistical Analysis
Signature 1
Source: Table S2
Description: The correlations between differential genera and clinical parameters
Abundance in Group 1: increased abundance in High level of straining during defecation
Revision editor(s): Anne-mariesharp
Signature 2
Source: Table S2
Description: The correlations between differential genera and clinical parameters
Abundance in Group 1: decreased abundance in High level of straining during defecation
| NCBI | Quality Control | Links |
|---|---|---|
| Gilliamella | ||
| ML635J_40_aquatic_groupML635J_40_aquatic_group |
Revision editor(s): Anne-mariesharp, Tosin
Experiment 6
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Anxiety Anxiety,anxiety
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low level of self-rating anxiety scale (SAS)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High level of self-rating anxiety scale (SAS)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with high level of self-rating anxiety scale (SAS)
Lab analysis
Statistical Analysis
Signature 1
Source: Table S2
Description: The correlations between differential genera and clinical parameters
Abundance in Group 1: increased abundance in High level of self-rating anxiety scale (SAS)
Revision editor(s): Anne-mariesharp
Signature 2
Source: Table S2
Description: The correlations between differential genera and clinical parameters
Abundance in Group 1: decreased abundance in High level of self-rating anxiety scale (SAS)
| NCBI | Quality Control | Links |
|---|---|---|
| Gilliamella | ||
| ML635J_40_aquatic_groupML635J_40_aquatic_group |
Revision editor(s): Anne-mariesharp, Tosin
Experiment 7
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Depressive disorder depression,melancholia,melancholias,mental depression,syndrome, depressive,syndromes, depressive,Depressive disorder,depressive disorder
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low self-rating depression scale (SDS)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High self-rating depression scale (SDS)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with high self-rating depression scale (SDS)
Lab analysis
Statistical Analysis
Signature 1
Source: Table S2
Description: The correlations between differential genera and clinical parameters
Abundance in Group 1: increased abundance in High self-rating depression scale (SDS)
Revision editor(s): Anne-mariesharp, Tosin
Signature 2
Source: Table S2
Description: The correlations between differential genera and clinical parameters
Abundance in Group 1: decreased abundance in High self-rating depression scale (SDS)
| NCBI | Quality Control | Links |
|---|---|---|
| Gilliamella | ||
| ML635J_40_aquatic_groupML635J_40_aquatic_group |
Revision editor(s): Anne-mariesharp, Tosin
Experiment 8
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Chronic constipation Chronic constipation,Infrequent bowel movements,chronic constipation
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low levels of bristol stool form scale (BSFS)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High levels of bristol stool form scale (BSFS)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with high levels of bristol stool form scale
Lab analysis
Statistical Analysis
Signature 1
Source: Table S2
Description: The correlations between differential genera and clinical parameters.
Abundance in Group 1: increased abundance in High levels of bristol stool form scale (BSFS)
| NCBI | Quality Control | Links |
|---|---|---|
| Gilliamella | ||
| ML635J_40_aquatic_groupML635J_40_aquatic_group |
Revision editor(s): Daberechi
Signature 2
Source: Table S2
Description: The correlations between differential genera and clinical parameters.
Abundance in Group 1: decreased abundance in High levels of bristol stool form scale (BSFS)
Experiment 9
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Health-related quality of life measurement HRQOL,Health-related quality of life measurement,health-related quality of life measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low levels of patient assessment of constipation quality of life (PAC-QOL) index
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High levels of patient assessment of constipation quality of life (PAC-QOL) index
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with high levels of patient assessment of constipation quality of life (PAC-QOL) index
Lab analysis
Statistical Analysis
Signature 1
Source: Table S2
Description: The correlations between differential genera and clinical parameters
Abundance in Group 1: increased abundance in High levels of patient assessment of constipation quality of life (PAC-QOL) index
| NCBI | Quality Control | Links |
|---|---|---|
| Gilliamella | ||
| ML635J_40_aquatic_groupML635J_40_aquatic_group |
Revision editor(s): Daberechi
Signature 2
Source: Table S2
Description: The correlations between differential genera and clinical parameters
Abundance in Group 1: decreased abundance in High levels of patient assessment of constipation quality of life (PAC-QOL) index
