Gut microbiota analyses of inflammatory bowel diseases from a representative Saudi population
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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
- Saudi Arabia
- 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
- 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 diagnosed with inflammatory bowel disease (IBD) through colonoscopy examinations, for ulcerative colitis (UC)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 124
- Group 1 sample size Number of subjects in the case (exposed) group
- 84
- 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
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V9
- 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)?
- No
Signature 1
Source: Supplementary File 14: Table S2
Description: Differential microbial abundance between ulcerative colitis (UC) and healthy controls
Abundance in Group 1: decreased abundance in ulcerative colitis (UC)
Revision editor(s): ChiomaBlessing
Signature 2
Source: Supplementary File 14: Table S2
Description: Differential microbial abundance between ulcerative colitis (UC) and healthy controls
Abundance in Group 1: increased abundance in ulcerative colitis (UC)
Revision editor(s): ChiomaBlessing
Experiment 2
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 diagnosed with inflammatory bowel disease (IBD) through endoscopy examinations, for Crohn's disease (CD)
- Group 1 sample size Number of subjects in the case (exposed) group
- 135
Lab analysis
Statistical Analysis
Signature 1
Source: Supplementary File 15: Table S3
Description: Differential microbial abundance between Crohn's disease (CD) and healthy controls
Abundance in Group 1: decreased abundance in Crohn's disease (CD)
Revision editor(s): ChiomaBlessing
Signature 2
Source: Supplementary File 15: Table S3, Figure 4: left plot
Description: Differential microbial abundance between Crohn's disease (CD) and healthy controls
Abundance in Group 1: increased abundance in Crohn's disease (CD)
Revision editor(s): ChiomaBlessing
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- ulcerative colitis (UC)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 84
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4: right plot
Description: Differential microbial abundance between ulcerative colitis (UC) and Crohn's disease (CD)
Abundance in Group 1: increased abundance in Crohn's disease (CD)
NCBI | Quality Control | Links |
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Turicibacter |
Revision editor(s): ChiomaBlessing
Signature 2
Source: Figure 4, Plot 2
Description: Differential microbial abundance between ulcerative colitis (UC) and Crohn's disease (CD)
Abundance in Group 1: decreased abundance in Crohn's disease (CD)
Revision editor(s): ChiomaBlessing, Peace Sandy