Diagnosis of Crohn's disease and ulcerative colitis using the microbiome
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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: 2024/03/08
Curator: Samreen-19
Revision editor(s): Samreen-19, ChiomaBlessing, Victoria
Subjects
- Location of subjects
- South Korea
- 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 (HC)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Crohn’s disease (CD) patients
- 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
- 50
- Group 1 sample size Number of subjects in the case (exposed) group
- 69
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- None.
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
- MGISEQ-2000
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- Linear Regression
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.0001
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Supplemental. file: Table S5
Description: Differences in the taxonomic composition of the gut microbiome in patients with Crohn's disease (CD) compared to healthy controls (HC)
Abundance in Group 1: increased abundance in Crohn’s disease (CD) patients
Revision editor(s): Samreen-19, ChiomaBlessing
Signature 2
Source: Supplemental. file: Table S5
Description: Differences in the taxonomic composition of the gut microbiome in patients with Crohn's disease (CD) compared to healthy controls (HC)
Abundance in Group 1: decreased abundance in Crohn’s disease (CD) patients
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes finegoldii | ||
| Alistipes shahii |
Revision editor(s): Samreen-19, ChiomaBlessing
Experiment 2
Curated date: 2024/03/09
Curator: Samreen-19
Revision editor(s): Samreen-19, ChiomaBlessing, Victoria
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 (UC) patients
- 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
- 198
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Supplemental. file: Table S8
Description: Differences in the taxonomic composition of the gut microbiome in patients with Ulcerative colitis disease (UC) compared to healthy controls (HC)
Abundance in Group 1: increased abundance in Ulcerative colitis (UC) patients
Revision editor(s): Samreen-19, ChiomaBlessing
Signature 2
Source: Supplemental. file: Table S8
Description: Differences in the taxonomic composition of the gut microbiome in patients with Ulcerative colitis disease (UC) compared to healthy controls (HC)
Abundance in Group 1: decreased abundance in Ulcerative colitis (UC) patients
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes shahii | ||
| Desulfovibrio sp. G11 | ||
| Victivallales bacterium CCUG 44730 | ||
| Odoribacter splanchnicus | ||
| Bradyrhizobium sp. ORS 278 | ||
| Akkermansia muciniphila |
Revision editor(s): Samreen-19, ChiomaBlessing
Experiment 3
Curated date: 2024/03/09
Curator: Samreen-19
Revision editor(s): Samreen-19, ChiomaBlessing, Victoria
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
- Ulcerative colitis (UC) patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Crohn's disease (CD) patients
- 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
- 198
- Group 1 sample size Number of subjects in the case (exposed) group
- 69
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Supplemental. file: Table S2
Description: Differences in the taxonomic composition of the gut microbiome in patients with Crohn's disease (CD) compared to Ulcerative colitis (UC)
Abundance in Group 1: increased abundance in Crohn's disease (CD) patients
Revision editor(s): Samreen-19, ChiomaBlessing
Signature 2
Source: Supplemental. file: Table S2
Description: Differences in the taxonomic composition of the gut microbiome in patients with Crohn's disease (CD) compared to Ulcerative colitis (UC)
Abundance in Group 1: decreased abundance in Crohn's disease (CD) patients
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibacterium prausnitzii | ||
| Lachnospira eligens | ||
| Ligilactobacillus ruminis | ||
| Alicycliphilus denitrificans | ||
| Stigmatella aurantiaca |
Revision editor(s): Samreen-19, ChiomaBlessing
Experiment 4
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
- Health controls (HC)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Crohn's disease patients- Mild group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Crohn's disease in the mild group according to disease activity
- Group 0 sample size Number of subjects in the control (unexposed) group
- 50
- Group 1 sample size Number of subjects in the case (exposed) group
- 49
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Mann-Whitney (Wilcoxon)
- T-Test
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Figure 2J
Description: Differences in the taxonomic composition of the gut microbiome in patients with Crohn's disease (CD)- mild group compared to Healthy controls (HC)
Abundance in Group 1: decreased abundance in Crohn's disease patients- Mild group
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudodesulfovibrio aespoeensis | ||
| Alistipes shahii |
Revision editor(s): ChiomaBlessing
Experiment 5
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Crohn's disease patients- Moderate group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Crohn's disease in the moderate group according to disease activity
- Group 1 sample size Number of subjects in the case (exposed) group
- 19
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Figure 2J
Description: Differences in the taxonomic composition of the gut microbiome in patients with Crohn's disease (CD)- moderate group compared to Healthy controls (HC)
Abundance in Group 1: decreased abundance in Crohn's disease patients- Moderate group
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudodesulfovibrio aespoeensis | ||
| Alistipes shahii |
Revision editor(s): ChiomaBlessing
Signature 2
Source: Figure 2J
Description: Differences in the taxonomic composition of the gut microbiome in patients with Crohn's disease (CD)- moderate group compared to Healthy controls (HC)
Abundance in Group 1: increased abundance in Crohn's disease patients- Moderate group
| NCBI | Quality Control | Links |
|---|---|---|
| Polynucleobacter wuianus |
Revision editor(s): ChiomaBlessing
Experiment 6
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 disease patients- Mild, moderate and severe groups
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Ulcerative colitis disease in the mild, moderate and severe groups according to disease activity
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Figure 3J
Description: Differences in the taxonomic composition of the gut microbiome in patients with Ulcerative colitis disease (UC)- mild, moderate and severe groups compared to Healthy controls (HC)
Abundance in Group 1: decreased abundance in Ulcerative colitis disease patients- Mild, moderate and severe groups
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia muciniphila | ||
| Porphyromonas asaccharolytica | ||
| Alistipes shahii |
Revision editor(s): ChiomaBlessing
Signature 2
Source: Figure 3J
Description: Differences in the taxonomic composition of the gut microbiome in patients with Ulcerative colitis disease (UC)- mild, moderate and severe groups compared to Healthy controls (HC)
Abundance in Group 1: increased abundance in Ulcerative colitis disease patients- Mild, moderate and severe groups
| NCBI | Quality Control | Links |
|---|---|---|
| Candidatus Pantoea carbekii |
Revision editor(s): ChiomaBlessing
Experiment 7
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
- Ulcerative colitis disease patients- Mild group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Ulcerative colitis disease patients- Severe group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Ulcerative colitis disease in the severe group according to disease activity
- Group 0 sample size Number of subjects in the control (unexposed) group
- 162
- Group 1 sample size Number of subjects in the case (exposed) group
- 11
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Figure 3J
Description: Differences in the taxonomic composition of the gut microbiome in patients with Ulcerative colitis disease (UC)- severe group compared to Ulcerative colitis disease (UC)- mild group (Mann-Whitney and T-test)
Abundance in Group 1: decreased abundance in Ulcerative colitis disease patients- Severe group
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia muciniphila | ||
| Porphyromonas asaccharolytica | ||
| Alistipes shahii |
Revision editor(s): ChiomaBlessing
Signature 2
Source: Figure 3J
Description: Differences in the taxonomic composition of the gut microbiome in patients with Ulcerative colitis disease (UC)- severe group compared to Ulcerative colitis disease (UC)- mild group (Mann-Whitney and T-test)
Abundance in Group 1: increased abundance in Ulcerative colitis disease patients- Severe group
| NCBI | Quality Control | Links |
|---|---|---|
| Candidatus Pantoea carbekii |
Revision editor(s): ChiomaBlessing
Experiment 8
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Ulcerative colitis disease patients- Moderate group
- Group 0 sample size Number of subjects in the control (unexposed) group
- 25
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Figure 3J
Description: Differences in the taxonomic composition of the gut microbiome in patients with Ulcerative colitis disease (UC)- severe group compared to Ulcerative colitis disease (UC)- moderate group
Abundance in Group 1: decreased abundance in Ulcerative colitis disease patients- Severe group
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes shahii |
Revision editor(s): ChiomaBlessing
Signature 2
Source: Figure 3J
Description: Differences in the taxonomic composition of the gut microbiome in patients with Ulcerative colitis disease (UC)- severe group compared to Ulcerative colitis disease (UC)- moderate group
Abundance in Group 1: increased abundance in Ulcerative colitis disease patients- Severe group
| NCBI | Quality Control | Links |
|---|---|---|
| Candidatus Pantoea carbekii |
Revision editor(s): ChiomaBlessing
Experiment 9
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Ulcerative colitis disease patients- Mild group
- Group 0 sample size Number of subjects in the control (unexposed) group
- 162
Lab analysis
Statistical Analysis
- Statistical test
- Linear Regression
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.01
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Supplemental. Table S9
Description: Differences in the taxonomic composition of the gut microbiome in patients with Ulcerative colitis disease (UC)- severe group compared to Ulcerative colitis disease (UC)- mild group
Abundance in Group 1: decreased abundance in Ulcerative colitis disease patients- Severe group
| NCBI | Quality Control | Links |
|---|---|---|
| Desulfarculus baarsii | ||
| Denitrobacterium detoxificans |
Revision editor(s): ChiomaBlessing
Signature 2
Source: Supplemental. Table S9
Description: Differences in the taxonomic composition of the gut microbiome in patients with Ulcerative colitis disease (UC)- severe group compared to Ulcerative colitis disease (UC)- mild group
Abundance in Group 1: increased abundance in Ulcerative colitis disease patients- Severe group
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillus sp. SJ-10 | ||
| Blattella germanica |
Revision editor(s): ChiomaBlessing
