Fecal microbial dysbiosis in Chinese patients with inflammatory bowel disease
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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
Curated date: 2022/10/20
Curator: Claregrieve1
Revision editor(s): Claregrieve1, Peace Sandy, LGeistlinger
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
- 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 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
- Patients with Crohn's disease
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Crohn's disease (11 with as active disease defined by CDAI > 150, 4 with inactive disease)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 29
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
- 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
- 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
- Kruskall-Wallis
- 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
- 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
- unchanged
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Table 2
Description: Differential microbial abundance between Crohn's patients and healthy controls
Abundance in Group 1: increased abundance in Patients with Crohn's disease
NCBI | Quality Control | Links |
---|---|---|
Abiotrophia | ||
Escherichia | ||
Pseudomonadota | ||
Pseudoramibacter | ||
unidentified rumen bacterium RFN20 |
Revision editor(s): Claregrieve1, Suwaiba
Signature 2
Source: Table 2
Description: Differential microbial abundance between Crohn's patients and healthy controls
Abundance in Group 1: decreased abundance in Patients with Crohn's disease
NCBI | Quality Control | Links |
---|---|---|
Butyricicoccus | ||
Mitsuokella | ||
Haemophilus | ||
Victivallis |
Revision editor(s): Claregrieve1
Experiment 2
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
- Patients with 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
- 14
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- 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: Table 2
Description: Differential microbial abundance between ulcerative colitis patients and healthy controls
Abundance in Group 1: increased abundance in Patients with ulcerative colitis
NCBI | Quality Control | Links |
---|---|---|
Granulicatella | ||
Peptostreptococcus | ||
Schwartzia | ||
Capnocytophaga | ||
Pseudomonadota | ||
Escherichia | ||
Janthinobacterium | ||
Campylobacter | ||
Actinomyces | ||
Eggerthella | ||
Corynebacterium | ||
Spirochaetota |
Revision editor(s): Claregrieve1
Signature 2
Source: Table 2
Description: Differential microbial abundance between ulcerative colitis patients and healthy controls
Abundance in Group 1: decreased abundance in Patients with ulcerative colitis
Revision editor(s): Claregrieve1, Merit
Experiment 3
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 0 name Corresponds to the control (unexposed) group for case-control studies
- Patients with ulcerative colitis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients with Crohn's disease
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Crohn's disease
- Group 0 sample size Number of subjects in the control (unexposed) group
- 14
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
Signature 1
Source: Table 2
Description: Differential abundance between patients with ulcerative colitis vs Crohn's disease
Abundance in Group 1: increased abundance in Patients with Crohn's disease
NCBI | Quality Control | Links |
---|---|---|
Abiotrophia defectiva | ||
Desulfovibrio | ||
Pseudoramibacter | ||
Slackia |
Revision editor(s): Claregrieve1, Suwaiba, Merit
Signature 2
Source: Table 2
Description: Differential abundance between patients with ulcerative colitis vs Crohn's disease
Abundance in Group 1: decreased abundance in Patients with Crohn's disease
NCBI | Quality Control | Links |
---|---|---|
Butyricicoccus | ||
Moryella | ||
Staphylococcus | ||
Capnocytophaga | ||
Haemophilus | ||
Janthinobacterium | ||
Cardiobacterium | ||
Lautropia | ||
Propioniferax innocua | ||
Shewanella | ||
Corynebacterium |
Revision editor(s): Claregrieve1