Gastrointestinal Dysmotility Predisposes to Colitis through Regulation of Gut Microbial Composition and Linoleic Acid Metabolism
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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.
- Mus musculus
- 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
- Colitis Colitides,colitis,colitis (disease),colon inflammation,inflammation of colon,Colitis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Wild Type (WT) Mice
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Kit wsh/wsh mice
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- c-Kit receptor dysfunction-based ICC-deficient murine model (Kitwsh/wsh) before Dextran Sulfate Sodium (DSS) treatment. Kitwsh/wsh C57BL/6J mice were from Jackson Laboratory (BarHarbor, ME).
- 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
- 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
- 2.5
- Matched on Factors on which subjects have been matched on in a case-control study
- age, 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
Signature 1
Source: Figure 3C
Description: Differences in microbial taxa at species levels between Wild Type (WT) and Kit wsh/wsh mice were calculated by LDA effect size (LEfSe).
Abundance in Group 1: increased abundance in Kit wsh/wsh mice
Revision editor(s): MyleeeA
Signature 2
Source: Figure 3C
Description: Differences in microbial taxa at species levels between Wild Type (WT) and Kit wsh/wsh mice were calculated by LDA effect size (LEfSe).
Abundance in Group 1: decreased abundance in Kit wsh/wsh mice
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium sp. Culture-54 | ||
| Ligilactobacillus animalis | ||
| Mucispirillum schaedleri | ||
| Parabacteroides goldsteinii | ||
| Adlercreutzia mucosicola | ||
| Lachnospiraceae bacterium A4 |
Revision editor(s): MyleeeA
Experiment 2
Subjects
Lab analysis
Statistical Analysis
- Statistical test
- T-Test
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Figure 3D
Description: Differences in microbial taxa at the genus and species levels between Wild Type (WT) and Kit wsh/wsh mice.
Abundance in Group 1: increased abundance in Kit wsh/wsh mice
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia | ||
| Akkermansia muciniphila |
Revision editor(s): MyleeeA
Signature 2
Source: Figure 3D
Description: Differences in microbial taxa at the genus and species levels between Wild Type (WT) and Kit wsh/wsh mice.
Abundance in Group 1: decreased abundance in Kit wsh/wsh mice
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus | ||
| Ligilactobacillus animalis | ||
| Lactobacillus johnsonii |
Revision editor(s): MyleeeA
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Wild Type (WT) Mice (No DSS)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Kit wsh/wsh mice (No DSS)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- c-Kit receptor dysfunction-based ICC-deficient murine model (Kitwsh/wsh) without Dextran Sulfate Sodium (DSS) treatment. Kitwsh/wsh C57BL/6J mice were from Jackson Laboratory (BarHarbor, ME).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Figure 3E
Description: Differences in microbial taxa at the species levels between Wild Type (WT) and Kit wsh/wsh mice not treated with DSS.
Abundance in Group 1: increased abundance in Kit wsh/wsh mice (No DSS)
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia muciniphila |
Revision editor(s): MyleeeA
Signature 2
Source: Figure 3E
Description: Differences in microbial taxa at the species levels between Wild Type (WT) and Kit wsh/wsh mice not treated with DSS.
Abundance in Group 1: decreased abundance in Kit wsh/wsh mice (No DSS)
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus johnsonii | ||
| Ligilactobacillus animalis |
Revision editor(s): MyleeeA
Experiment 4
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Response to transplant Response to transplant,response to transplant
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls - Fecal Microbiota Transplantation (HC-FMT)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Chronic Constipation - Fecal Microbiota Transplantation (CC-FMT)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Fecal microbiota transplant (FMT), recipient mice were pre-treated with a cocktail of antibiotics (ABX) in drinking water for 2 weeks. Mice were administered filtered donor fecal homogenate by oral gavage (300 μl per mouse) one day after ABX treatment every other day over a period of 10 days.
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
Signature 1
Source: Figure 8F
Description: Differences in microbial taxa significant between Chronic Constipation - Fecal Microbiota Transplantation (CC-FMT) and Healthy controls - Fecal Microbiota Transplantation (HC-FMT).
Abundance in Group 1: increased abundance in Chronic Constipation - Fecal Microbiota Transplantation (CC-FMT)
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia muciniphila |
Revision editor(s): MyleeeA
Signature 2
Source: Figure 8F
Description: Differences in microbial taxa significant between Chronic Constipation - Fecal Microbiota Transplantation (CC-FMT) and Healthy controls - Fecal Microbiota Transplantation (HC-FMT).
Abundance in Group 1: decreased abundance in Chronic Constipation - Fecal Microbiota Transplantation (CC-FMT)
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus |
Revision editor(s): MyleeeA
Experiment 5
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Treatment Treatment,treatment
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Wild Type (WT) Mice (DSS)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Kit wsh/wsh mice (DSS)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- c-Kit receptor dysfunction-based ICC-deficient murine model (Kitwsh/wsh) with Dextran Sulfate Sodium (DSS) treatment. Kitwsh/wsh C57BL/6J mice were from Jackson Laboratory (BarHarbor, ME).
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- age, 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
Signature 1
Source: Figure 3E
Description: Differences in microbial taxa at the species levels between Wild Type (WT) and Kit wsh/wsh mice treated with DSS.
Abundance in Group 1: increased abundance in Kit wsh/wsh mice (DSS)
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia muciniphila |
Revision editor(s): MyleeeA
Signature 2
Source: Figure 3E
Description: Differences in microbial taxa at the species levels between Wild Type (WT) and Kit wsh/wsh mice treated with DSS.
Abundance in Group 1: decreased abundance in Kit wsh/wsh mice (DSS)
| NCBI | Quality Control | Links |
|---|---|---|
| Ligilactobacillus animalis | ||
| Lactobacillus johnsonii |
Revision editor(s): MyleeeA
Experiment 6
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Diet measurement Diet measurement,diet measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control Diet (CD) mice
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Low-carbohydrate and high-protein diet (LCHD) mice
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- WT mice fed with an isocaloric low-carbohydrate and high-protein diet (LCHD, 28.9% carbohydrate, 60.0% protein, and 11.1% fat as percentages of calories) for 4 weeks
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
Signature 1
Source: Supplementary Figure 4C
Description: Differences in microbial taxa significant between mice fed with Low-carbohydrate and high-protein diet (LCHD) and Control Diet (CD).
Abundance in Group 1: increased abundance in Low-carbohydrate and high-protein diet (LCHD) mice
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia muciniphila |
Revision editor(s): MyleeeA
Signature 2
Source: Supplementary Figure 4C
Description: Differences in microbial taxa significant between mice fed with Low-carbohydrate and high-protein diet (LCHD) and Control Diet (CD).
Abundance in Group 1: decreased abundance in Low-carbohydrate and high-protein diet (LCHD) mice
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus |
Revision editor(s): MyleeeA
Experiment 7
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Colitis Colitides,colitis,colitis (disease),colon inflammation,inflammation of colon,Colitis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Wild Type (WT) Mice
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Kit wsh/wsh Mice
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- c-Kit receptor dysfunction-based ICC-deficient murine model (Kitwsh/wsh). Kitwsh/wsh C57BL/6J mice were from Jackson Laboratory (BarHarbor, ME).
- 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
- Statistical test
- ANOVA
- Matched on Factors on which subjects have been matched on in a case-control study
- age, 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
Signature 1
Source: Supplementary Figure 5A
Description: Differences in microbial taxa at the species levels between Wild Type (WT) and Kit wsh/wsh mice.
Abundance in Group 1: increased abundance in Kit wsh/wsh Mice
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia muciniphila |
Revision editor(s): MyleeeA
Signature 2
Source: Supplementary Figure 5A
Description: Differences in microbial taxa at the species levels between Wild Type (WT) and Kit wsh/wsh mice.
Abundance in Group 1: decreased abundance in Kit wsh/wsh Mice
| NCBI | Quality Control | Links |
|---|---|---|
| Ligilactobacillus animalis | ||
| Lactobacillus johnsonii |
Revision editor(s): MyleeeA
Experiment 8
Subjects
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- 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 controls (HC)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Chronic Constipation (CC)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Chronic Constipation
- 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
- 30
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 2 months
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
Signature 1
Source: Figure 8C
Description: Relative abundance of microbial taxa in stool samples from Chronic constipation patients (CC) and Healthy controls (HC).
Abundance in Group 1: increased abundance in Chronic Constipation (CC)
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia muciniphila |
Revision editor(s): MyleeeA
Signature 2
Source: Figure 8C
Description: Relative abundance of microbial taxa in stool samples from Chronic constipation patients (CC) and Healthy controls (HC).
Abundance in Group 1: decreased abundance in Chronic Constipation (CC)
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus |
Revision editor(s): MyleeeA
Experiment 9
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Crohn's disease Colitis, Granulomatous,CROHN DIS,Crohn Disease,Crohn disease,Crohn's associated gastritis,Crohn's disease,Crohn's disease of colon,Crohn's disease of large bowel,CROHNS DIS,Crohns Disease,Enteritis, Granulomatous,Enteritis, Regional,Gastritis Associated with Crohn Disease,Gastritis Associated with Crohn's Disease,granulomatous colitis,Ileitis, Regional,Ileitis, Terminal,Ileocolitis,pediatric Crohn's disease,regional enteritis,crohn disease,crohn's disease
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Crohn's Disease (CD)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Crohn's disease
- Group 1 sample size Number of subjects in the case (exposed) group
- 32
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 8C
Description: Relative abundance of microbial taxa in stool samples from Crohn's Disease patients (CD) and Healthy controls (HC).
Abundance in Group 1: decreased abundance in Crohn's Disease (CD)
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus |
Revision editor(s): MyleeeA
Experiment 10
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Ulcerative colitis colitis ulcerative,Colitis, Ulcerative,Left-sided ulcerative (chronic) colitis,Left-sided ulcerative colitis,left-sided ulcerative colitis,Other ulcerative colitis,Other ulcerative colitis (disorder),UC - ulcerative colitis,ulcerative colitis,ulcerative colitis (disease),ulcerative colitis (disorder),Ulcerative colitis, unspecified,ULCERATVE COLITIS UNSPCF,Ulcerative colitis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Ulcerative colitis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Ulcerative colitis
- Group 1 sample size Number of subjects in the case (exposed) group
- 25
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 8C
Description: Relative abundance of microbial taxa in stool samples from Ulcerative colitis patients (UC) and Healthy controls (HC).
Abundance in Group 1: decreased abundance in Ulcerative colitis
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus |
Revision editor(s): MyleeeA
