Gut Microbiota Associated with Clinical Relapse in Patients with Quiescent Ulcerative Colitis
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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
- Japan
- 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
- quiescent ulcerative colitis patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- consecutive recruitment of patients with quiescent UC in our outpatient clinic from November 2016 to September 2017. Clinical remission was defined as a Lichtiger index score of ≤4.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 59
- Group 1 sample size Number of subjects in the case (exposed) group
- 59
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- no history of antibiotic use within three months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-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
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 4
- 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
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Figure 1f
Description: linear discriminant analysis effect size (LEfSe) analysis identified taxa that characterized each group. Cladogram of LEfSe analysis results. Yellow-shaded areas indicate taxa that characterize UC, and green-shaded areas indicate taxa that characterize HCs. Linear discriminant analysis (LDA) scores for identified taxa of patient of UCs (7 taxa) and HC (6 taxa) was shown. ** p < 0.01.
Abundance in Group 1: increased abundance in quiescent ulcerative colitis patients
| NCBI | Quality Control | Links |
|---|---|---|
| Acidimicrobiia | ||
| Actinomycetota | ||
| Bacilli | ||
| Bifidobacteriaceae | ||
| Bifidobacteriales | ||
| Bifidobacterium | ||
| Lactobacillales |
Revision editor(s): Yjung24, Peace Sandy
Signature 2
Source: Figure 1f
Description: linear discriminant analysis effect size (LEfSe) analysis identified taxa that characterized each group. Cladogram of LEfSe analysis results. Yellow-shaded areas indicate taxa that characterize UC, and green-shaded areas indicate taxa that characterize HCs. Linear discriminant analysis (LDA) scores for identified taxa of patient of UCs (7 taxa) and HC (6 taxa) was shown. ** p < 0.01.
Abundance in Group 1: decreased abundance in quiescent ulcerative colitis patients
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidales | ||
| Bacteroidia | ||
| Bacteroidota | ||
| Clostridia | ||
| Eubacteriales |
Revision editor(s): Yjung24, Peace Sandy
Experiment 2
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Disease progression measurement Disease progression measurement,disease progression measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- sustained remission of ulcerative colitis group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- relapsed ulcerative colitis group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients who had clinically relapsed during the 3.5 year-long follow-up period. Clinical relapse was defined as clinical or endoscopic deterioration requiring therapeutic modification.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 40
- Group 1 sample size Number of subjects in the case (exposed) group
- 19
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Not specified
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- 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
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 2g
Description: linear discriminant analysis effect size (LEfSe) analysis identified taxa that characterized each group. Cladogram of LEfSe analysis results. Red-shaded areas indicate taxathat characterize relapse group, and blue-shaded areas indicate taxa that characterize SusRem group. Linear discriminant analysis (LDA) scores for identified taxa of SusRem (2 taxa) and Relapse (6 taxa)
Abundance in Group 1: increased abundance in relapsed ulcerative colitis group
| NCBI | Quality Control | Links |
|---|---|---|
| Acidimicrobiia | ||
| Actinomycetota | ||
| Bifidobacteriaceae | ||
| Bifidobacteriales | ||
| Bifidobacterium | ||
| Faecalibacterium |
Revision editor(s): Yjung24, Peace Sandy
Signature 2
Source: Figure 2g
Description: linear discriminant analysis effect size (LEfSe) analysis identified taxa that characterized each group. Cladogram of LEfSe analysis results. Red-shaded areas indicate taxa that characterize relapse group, and blue-shaded areas indicate taxa that characterize SusRem group. Linear discriminant analysis (LDA) scores for identified taxa of SusRem (2 taxa) and Relapse (6 taxa)
Abundance in Group 1: decreased abundance in relapsed ulcerative colitis group
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella | ||
| Prevotellaceae |
Revision editor(s): Yjung24, Peace Sandy
