Enteric nervous system damage caused by abnormal intestinal butyrate metabolism may lead to 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
- Group 1
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Group 2
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Low risk people for Functional constipation (FC) whose defecation frequency was 1 time/day
- Group 0 sample size Number of subjects in the control (unexposed) group
- 38
- Group 1 sample size Number of subjects in the case (exposed) group
- 360
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- BGISEQ-500 Sequencing
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- DESeq2
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Figure 1E, Table S4, Figure S3a, Figure S5e, Figure S5f
Description: Significant different bacteria genus, species among the four groups obtained via Deseq2 in the comparison between groups 1 and 2
Abundance in Group 1: increased abundance in Group 2
Signature 2
Source: Figure 1E, Table S4, Figure S3a, Figure S5e, Figure S5f
Description: Significant different bacteria genus, species among the four groups obtained via Deseq2 in the comparison between groups 1 and 2
Abundance in Group 1: decreased abundance in Group 2
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Group 2
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Group 3
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- High risk people for Functional constipation (FC) whose defecation frequency was 1 time/2 days
- Group 0 sample size Number of subjects in the control (unexposed) group
- 360
- Group 1 sample size Number of subjects in the case (exposed) group
- 52
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
Source: Figure 1E, Table S4, Figure S3b
Description: Significant different bacteria genus, species among the four groups obtained via Deseq2 in the comparison between groups 2 and 3
Abundance in Group 1: increased abundance in Group 3
Signature 2
Source: Figure 1E, Table S4, Figure S3b
Description: Significanf different bacteria genus, species among the four groups obtained via Deseq2 in the comparison between groups 2 and 3
Abundance in Group 1: decreased abundance in Group 3
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Group 3
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Group 4
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Functional constipation (FC) whose defecation frequency was 1 time/3 days
- Group 0 sample size Number of subjects in the control (unexposed) group
- 52
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Figure 1E, Table S4, Figure S3C
Description: Significant different bacteria genus, species among the four groups obtained via Deseq2 in the comparison between groups 3 and 4
Abundance in Group 1: increased abundance in Group 4
Signature 2
Source: Figure 1E, Table S4, Figure S3C
Description: Significant different bacteria genus, species among the four groups obtained via Deseq2 in the comparison between groups 3 and 4
Abundance in Group 1: decreased abundance in Group 4
Experiment 4
Subjects
- 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
- Functional constipation (FC) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Functional constipation (FC)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 6
- Group 1 sample size Number of subjects in the case (exposed) group
- 6
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- LEfSe
- 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
- 2.5
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Figure 3E, Table S5
Description: Significant differential taxa between Healthy controls (HC) and Functional Constipation (FC) group using LeFse analysis
Abundance in Group 1: increased abundance in Functional constipation (FC) group
Revision editor(s): Tosin
Signature 2
Source: Figure 3E, Table S5
Description: Significant differential taxa between Healthy controls (HC) and Functional Constipation (FC) group using LeFse analysis
Abundance in Group 1: decreased abundance in Functional constipation (FC) group
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium paraputrificum | ||
| Fusobacterium ulcerans | ||
| Fusobacterium mortiferum | ||
| Eubacterium sp. CAG:38 | ||
| Clostridium disporicum |
Revision editor(s): Tosin
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Group 2
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- FCHR (Functional constipation high-risk) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Combination of High risk people for Functional constipation (FC) whose defecation frequency was 1 time/2 days and High risk people for Functional constipation (FC) whose defecation frequency was 1 time/3 days.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 360
- Group 1 sample size Number of subjects in the case (exposed) group
- 62
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- DESeq2
- 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
Signature 1
Source: Figure S5e, Figure S5f
Description: Significant different bacterias among the three groups obtained by Deseq2, FC=log2 fold change at the genus and species levels.
Abundance in Group 1: increased abundance in FCHR (Functional constipation high-risk) group
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium sp. CAG:226 | ||
| Clostridium sp. CAG:417 | ||
| Clostridium sp. CAG:798 | ||
| Mycoplasma |
Revision editor(s): Tosin
Signature 2
Source: Figure S5e, Figure S5f
Description: Significant different bacterias among the three groups obtained by Deseq2, FC=log2 fold change at the genus and species levels.
Abundance in Group 1: increased abundance in FCHR (Functional constipation high-risk) group
Revision editor(s): Tosin
