Dysbiosis in the Gut Microbiota in Patients with Inflammatory Bowel Disease during Remission
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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
- Malta
- 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
- 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 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
- Ulcerative colitis (UC)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Ulcerative colitis (UC) in a state of remission
- Group 0 sample size Number of subjects in the control (unexposed) group
- 97
- Group 1 sample size Number of subjects in the case (exposed) group
- 66
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V2
- 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).
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index, sex
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- decreased
Signature 1
Source: Appendix Table 5
Description: Analyses of differential abundances at lower taxonomic levels with respect to IBD status/health condition
Abundance in Group 1: increased abundance in Ulcerative colitis (UC)
Revision editor(s): Samreen-19
Signature 2
Source: Appendix Table 5
Description: Analyses of differential abundances at lower taxonomic levels with respect to IBD status/health condition
Abundance in Group 1: decreased abundance in Ulcerative colitis (UC)
Revision editor(s): Samreen-19
Experiment 2
Subjects
- 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 (CD) in a state of remission
- Group 1 sample size Number of subjects in the case (exposed) group
- 32
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- decreased
Signature 1
Source: Appendix Table 5
Description: Analyses of differential abundances at lower taxonomic levels with respect to IBD status/health condition
Abundance in Group 1: increased abundance in Crohn’s disease (CD)
Revision editor(s): Samreen-19
Signature 2
Source: Appendix Table 5
Description: Analyses of differential abundances at lower taxonomic levels with respect to IBD status/health condition
Abundance in Group 1: decreased abundance in Crohn’s disease (CD)
Revision editor(s): Samreen-19
Experiment 3
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Gut microbiome measurement Gut microbiome measurement,gut microbiome measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Crohn's disease (CD)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Ulcerative colitis (UC)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Ulcerative colitis (UC) in a state of remission
- Group 0 sample size Number of subjects in the control (unexposed) group
- 32
- Group 1 sample size Number of subjects in the case (exposed) group
- 66
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- decreased
Signature 1
Source: Appendix Table 5
Description: Analyses of differential abundances at lower taxonomic levels with respect to IBD status/health condition
Abundance in Group 1: increased abundance in Ulcerative colitis (UC)
NCBI | Quality Control | Links |
---|---|---|
unclassified Parabacteroides | ||
unclassified Faecalibacterium | ||
unclassified Parasutterella |
Revision editor(s): Samreen-19
Signature 2
Source: Appendix Table 5
Description: Analyses of differential abundances at lower taxonomic levels with respect to IBD status/health condition
Abundance in Group 1: decreased abundance in Ulcerative colitis (UC)
NCBI | Quality Control | Links |
---|---|---|
unclassified Dorea | ||
unclassified Subdoligranulum | ||
unclassified Escherichia |
Revision editor(s): Samreen-19
Experiment 4
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Smoking behavior smoking,Smoking behavior,smoking behavior
- 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
- Patients with Inflammatory Bowel Disease (IBD) who are smokers
- Group 0 sample size Number of subjects in the control (unexposed) group
- 63
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- decreased
Signature 1
Source: Appendix Table 9
Description: Differential abundance analysis for smoking behaviour
Abundance in Group 1: increased abundance in Yes
NCBI | Quality Control | Links |
---|---|---|
unclassified Lachnospiraceae | ||
unclassified Bacteroides | ||
unclassified Faecalibacterium | ||
unclassified Sutterella |
Revision editor(s): Samreen-19
Signature 2
Source: Appendix Table 9
Description: Differential abundance analysis for smoking behaviour
Abundance in Group 1: decreased abundance in Yes
Revision editor(s): Samreen-19
Experiment 5
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Ex
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Inflammatory Bowel Disease (IBD) who were ex-smokers (had stopped smoking for at least 6 months).
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- decreased
Signature 1
Source: Appendix Table 9
Description: Differential abundance analysis for smoking behaviour
Abundance in Group 1: increased abundance in Ex
NCBI | Quality Control | Links |
---|---|---|
Phocaeicola dorei | ||
unclassified Lachnospiraceae | ||
unclassified Bacteroides | ||
unclassified Parasutterella | ||
unclassified Faecalibacterium |
Revision editor(s): Samreen-19
Signature 2
Source: Appendix Table 9
Description: Differential abundance analysis for smoking behaviour
Abundance in Group 1: decreased abundance in Ex
Revision editor(s): Samreen-19
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Ex
- 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
- Patients with Inflammatory Bowel Disease (IBD) who are smokers
- Group 0 sample size Number of subjects in the control (unexposed) group
- 25
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- decreased
Signature 1
Source: Appendix Table 9
Description: Differential abundance analysis for smoking behaviour
Abundance in Group 1: increased abundance in Yes
NCBI | Quality Control | Links |
---|---|---|
unclassified Bilophila | ||
unclassified Faecalibacterium | ||
unclassified Bacteroides | ||
unclassified Sutterella |
Revision editor(s): Samreen-19
Signature 2
Source: Appendix Table 9
Description: Differential abundance analysis for smoking behavior
Abundance in Group 1: decreased abundance in Yes
Revision editor(s): Samreen-19