Compositional changes in fecal microbiota associated with clinical phenotypes and prognosis in Korean 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
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
- 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 control individual
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Ulcerative colitis patient
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients diagnosed with ulcerative colitis from 3 different academic hospitals in Korea.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 100
- Group 1 sample size Number of subjects in the case (exposed) group
- 70
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Patients who used drugs can affect intestinal microbial community, such as probiotics and antibiotics, within a month were excluded.
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
- LEfSe
- 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
- 3.0
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Figure 4a
Description: Taxa list according to linear discriminate analysis values determined from comparisons between HC and UC patients. HC, healthy control individuals; UC, ulcerative colitis.
Abundance in Group 1: increased abundance in Ulcerative colitis patient
Signature 2
Source: Figure 4a
Description: Taxa list according to linear discriminate analysis values determined from comparisons between HC and UC patients. HC, healthy control individuals; UC, ulcerative colitis.
Abundance in Group 1: decreased abundance in Ulcerative colitis patient
Revision editor(s): Yjung24
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 patient
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients diagnosed with Crohn's disease from 3 different academic hospitals in Korea.
- Group 1 sample size Number of subjects in the case (exposed) group
- 39
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Figure 4b
Description: Taxa list according to linear discriminate analysis values determined from comparisons between HC and CD patients. HC, healthy control individuals; CD, Crohn’s disease.
Abundance in Group 1: increased abundance in Crohn's disease patient
Revision editor(s): Yjung24, Peace Sandy
Signature 2
Source: Figure 4b
Description: Taxa list according to linear discriminate analysis values determined from comparisons between HC and CD patients. HC, healthy control individuals; CD, Crohn’s disease.
Abundance in Group 1: decreased abundance in Crohn's disease patient
Revision editor(s): Yjung24, Peace Sandy
Experiment 3
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 0 name Corresponds to the control (unexposed) group for case-control studies
- Patients with mild ulcerative colitis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients with moderate to severe ulcerative colitis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients diagnosed with ulcerative colitis (UC) from 3 different academic hospitals in Korea categorized as moderate to severe forms of UC. The severity of disease was assessed by the Mayo score for UC. Severity was estimated at the time of fecal sampling, and the average follow-up period was 8.0 ± 1.3 years.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 37
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Figure 5a
Description: Taxa list according to linear discriminate analysis values determined from comparisons according to disease severity and extent in ulcerative colitis (UC) patients. Comparisons between moderate to severe and mild UC (A).
Abundance in Group 1: increased abundance in Patients with moderate to severe ulcerative colitis
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridioides difficile | ||
| Ligilactobacillus salivarius |
Revision editor(s): Yjung24
Signature 2
Source: Figure 5a
Description: Taxa list according to linear discriminate analysis values determined from comparisons according to disease severity and extent in ulcerative colitis (UC) patients. Comparisons between moderate to severe and mild UC (A).
Abundance in Group 1: decreased abundance in Patients with moderate to severe ulcerative colitis
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides acidifaciens | ||
| Bacteroides caccae | ||
| Bilophila wadsworthia | ||
| Howardella ureilytica | ||
| Ruminococcus callidus | ||
| Streptococcus pneumoniae | ||
| [Clostridium] innocuum | ||
| Alistipes |
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Patients with remission ulcerative colitis (symptoms of UC are reduced or inapparent)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients diagnosed with ulcerative colitis (UC) from 3 different academic hospitals in Korea categorized as moderate to severe forms of UC. The severity of disease was assessed by the Mayo score for UC. Severity was estimated at the time of fecal sampling, and the average follow-up period was 8.0 ± 1.3 years.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Figure 5b
Description: Taxa list according to linear discriminate analysis values determined from comparisons according to disease severity and extent in ulcerative colitis (UC) patients. Comparisons between moderate to severe UC and remission (B).
Abundance in Group 1: increased abundance in Patients with moderate to severe ulcerative colitis
Revision editor(s): Yjung24
Signature 2
Source: Figure 5b
Description: Taxa list according to linear discriminate analysis values determined from comparisons according to disease severity and extent in ulcerative colitis (UC) patients. Comparisons between moderate to severe UC and remission (B).
Abundance in Group 1: decreased abundance in Patients with moderate to severe ulcerative colitis
Experiment 5
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Distal colitis , Pancolitis distal colitis,inflammation of left colon,left colon inflammation,Distal colitis,pan-ulcerative colitis,pancolitis,universal colitis,Pancolitis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- patients with proctitis ulcerative colitis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- patients with left sided or extensive ulcerative colitis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients diagnosed with ulcerative colitis (UC) from 3 different academic hospitals in Korea defined as left sided (distal colitis) or extensive (pancolitis).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 21
- Group 1 sample size Number of subjects in the case (exposed) group
- 28
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Figure 5c
Description: Taxa list according to linear discriminate analysis values determined from comparisons according to disease severity and extent in ulcerative colitis (UC) patients. Comparisons between left sided or extensive UC and proctitis.
Abundance in Group 1: increased abundance in patients with left sided or extensive ulcerative colitis
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium bifidum | ||
| Intestinibacter bartlettii | ||
| Flavonifractor plautii | ||
| Anaerostipes hadrus | ||
| Lacticaseibacillus paracasei | ||
| Mediterraneibacter gnavus |
Revision editor(s): Yjung24
Signature 2
Source: Figure 5c
Description: Taxa list according to linear discriminate analysis values determined from comparisons according to disease severity and extent in ulcerative colitis (UC) patients. Comparisons between left sided or extensive UC and proctitis.
Abundance in Group 1: decreased abundance in patients with left sided or extensive ulcerative colitis
Experiment 6
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 remission Crohn's disease
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- patients with active Crohn's disease
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients diagnosed with Crohn's disease (CD) from 3 different academic hospitals in Korea. The severity of disease was assessed by the Crohn’s Disease Activity Index CD. Active status including mild, moderate, severe forms of CD. Severity was estimated at the time of fecal sampling, and the average follow-up period was 8.0 ± 1.3 years.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 24
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 6a
Description: Taxa list according to linear discriminate analysis values determined from comparisons according to disease severity and extent in Crohn’s disease (CD) patients. Comparisons between remission and active CD (A).
Abundance in Group 1: increased abundance in patients with active Crohn's disease
| NCBI | Quality Control | Links |
|---|---|---|
| Phascolarctobacterium succinatutens | ||
| Ligilactobacillus salivarius | ||
| Limosilactobacillus mucosae | ||
| Porphyromonas asaccharolytica | ||
| Coprococcus catus |
Revision editor(s): Yjung24
Signature 2
Source: Figure 6a
Description: Taxa list according to linear discriminate analysis values determined from comparisons according to disease severity and extent in Crohn’s disease (CD) patients. Comparisons between remission and active CD (A).
Abundance in Group 1: decreased abundance in patients with active Crohn's disease
Revision editor(s): Yjung24
Experiment 7
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Ileocolitis ileal crohn's,ileocolic Crohn's,ileocolitis,Ileocolitis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- patients with small bowel Crohn's disease
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- patients with ileocolonic Crohn's disease
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients diagnosed with ileocolonic Crohn's disease (CD) from 3 different academic hospitals in Korea.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 17
- Group 1 sample size Number of subjects in the case (exposed) group
- 17
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 6b
Description: Taxa list according to linear discriminate analysis values determined from comparisons according to disease severity and extent in Crohn’s disease (CD) patients. Comparisons between ileocolonic and small bowel CD (B).
Abundance in Group 1: increased abundance in patients with ileocolonic Crohn's disease
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus gasseri | ||
| Bacteroides ovatus | ||
| Weissella confusa |
Revision editor(s): Yjung24
Signature 2
Source: Figure 6b
Description: Taxa list according to linear discriminate analysis values determined from comparisons according to disease severity and extent in Crohn’s disease (CD) patients. Comparisons between ileocolonic and small bowel CD (B).
Abundance in Group 1: decreased abundance in patients with ileocolonic Crohn's disease
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia coccoides | ||
| Bilophila wadsworthia | ||
| Enterocloster clostridioformis |
Revision editor(s): Yjung24
