Targeted Analysis of the Gut Microbiome for Diagnosis, Prognosis and Treatment Individualization in Pediatric 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
- Norway
- 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
- Inflammatory bowel disease autoimmune bowel disorder,Bowel Diseases, Inflammatory,IBD,INFLAMM BOWEL DIS,inflammatory bowel disease,Inflammatory Bowel Diseases,Inflammatory bowel 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
- Inflammatory bowel disease patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients under 18 years old diagnosed with inflammatory bowel disease (Crohn's Disease or ulcerative colitis) from the catchment areas of two university hospitals in three population-based prospective epidemiological studies of treatment-naïve pediatric IBD in South-Eastern Norway between 2005-2015.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 75
- Group 1 sample size Number of subjects in the case (exposed) group
- 107
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Six Months
Lab analysis
- Sequencing type
- PCR
- 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
- RT-qPCR
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)
- 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: Table 2
Description: Bacterial species exhibiting deviating abundances between patient and control groups. IBD vs Healthy.
Abundance in Group 1: decreased abundance in Inflammatory bowel disease patients
Revision editor(s): Yjung24
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy children
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Non-inflammatory bowel disease symptomatic controls
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients under 18 years presented with symptoms of inflammatory bowel disease (Crohn's Disease or ulcerative colitis) but did not meet the criteria for IBD and who had a macroscopically and histologically normal mucosa and normal MRI examination from the catchment areas of two university hospitals in three population-based prospective epidemiological studies of treatment-naïve pediatric IBD in South-Eastern Norway between 2005-2015.
- Group 1 sample size Number of subjects in the case (exposed) group
- 50
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- antibiotics use within the last six months of study for healthy controls (group 0)
Lab analysis
Statistical Analysis
Signature 1
Source: Table 2
Description: Bacterial species exhibiting deviating abundances between patient and control groups. Non-IBD vs. Healthy.
Abundance in Group 1: decreased abundance in Non-inflammatory bowel disease symptomatic controls
Revision editor(s): Yjung24
Signature 2
Source: Table 2
Description: Bacterial species exhibiting deviating abundances between patient and control groups. Non-IBD vs. Healthy.
Abundance in Group 1: increased abundance in Non-inflammatory bowel disease symptomatic controls
| NCBI | Quality Control | Links |
|---|---|---|
| Enterococcus faecium | ||
| Citrobacter koseri |
Revision editor(s): Yjung24
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- non-inflammatory bowel disease symptomatic controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- inflammatory bowel disease patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients under 18 diagnosed with inflammatory bowel disease (Crohn's Disease or ulcerative colitis) from the catchment areas of two university hospitals in three population-based prospective epidemiological studies of treatment-naïve pediatric IBD in South-Eastern Norway between 2005-2015.
- 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
- 110
Lab analysis
Statistical Analysis
Signature 1
Source: Table 2
Description: Bacterial species exhibiting deviating abundances between patient and control groups.
Abundance in Group 1: decreased abundance in inflammatory bowel disease patients
Revision editor(s): Yjung24
Signature 2
Source: Table 2
Description: Bacterial species exhibiting deviating abundances between patient and control groups. IBD vs. Non-IBD.
Abundance in Group 1: increased abundance in inflammatory bowel disease patients
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus parainfluenzae |
Revision editor(s): Yjung24
Experiment 4
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Phenotype Phenotype,phenotype
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Crohn's Disease patients with inflammatory phenotypes
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Crohn's Disease patients with stricturing and/or penetrating phenotypes
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients under 18 diagnosed with Crohn's Disease with stricturing and/or penetrating phenotypes
- Group 0 sample size Number of subjects in the control (unexposed) group
- 53
- Group 1 sample size Number of subjects in the case (exposed) group
- 27
- 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
Signature 1
Source: Section 3.4 (text)
Description: The CD patients had a significantly lower abundance for five bacterial species and a higher abundance for five bacterial species. The CD patients with stricturing and/or penetrating phenotypes had a lower abundance of four species and a higher abundance of Escherichia coli (p = 0.010) compared to the CD patients with an inflammatory phenotype.
Abundance in Group 1: decreased abundance in Crohn's Disease patients with stricturing and/or penetrating phenotypes
| NCBI | Quality Control | Links |
|---|---|---|
| Christensenella minuta | ||
| [Clostridium] scindens | ||
| Lachnospira eligens | ||
| Roseburia hominis |
Revision editor(s): Yjung24
Signature 2
Source: Section 3.4 (text)
Description: The CD patients had a significantly lower abundance for five bacterial species and a higher abundance for five bacterial species. The CD patients with stricturing and/or penetrating phenotypes had a lower abundance of four species and a higher abundance of Escherichia coli (p = 0.010) compared to the CD patients with an inflammatory phenotype.
Abundance in Group 1: increased abundance in Crohn's Disease patients with stricturing and/or penetrating phenotypes
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia coli |
Revision editor(s): Yjung24
Experiment 5
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Treatment Treatment,treatment
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Inflammatory bowel disease patients treated with conventional therapy
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Inflammatory bowel disease patients treated with biological therapy
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- 58% of inflammatory bowel disease patients were later treated with biologic therapy due to failure to induce remission with conventional treatments or relapse after primary induction.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 46
- Group 1 sample size Number of subjects in the case (exposed) group
- 64
Lab analysis
Statistical Analysis
Signature 1
Source: Table 3
Description: Bacterial species exhibiting deviating abundances between medical therapy groups and between groups with high and low calprotectin levels.
Abundance in Group 1: decreased abundance in Inflammatory bowel disease patients treated with biological therapy
Revision editor(s): Yjung24
Signature 2
Source: Table 3
Description: Bacterial species exhibiting deviating abundances between medical therapy groups and between groups with high and low calprotectin levels.
Abundance in Group 1: increased abundance in Inflammatory bowel disease patients treated with biological therapy
| NCBI | Quality Control | Links |
|---|---|---|
| Mediterraneibacter gnavus | ||
| Phocaeicola vulgatus |
Revision editor(s): Yjung24
Experiment 6
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Increased inflammatory response Increased inflammatory response,increased inflammatory response
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Inflammatory bowel disease patients with fecal calprotectin levels < 1000 mg/kg
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Inflammatory bowel disease patients with fecal calprotectin levels > 1000 mg/kg
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Inflammatory bowel disease patients with higher fecal protectin levels (31 with CD and 12 with UC had above 1000 mg/kg).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 67
- Group 1 sample size Number of subjects in the case (exposed) group
- 43
Lab analysis
Statistical Analysis
Signature 1
Source: Table 3
Description: Bacterial species exhibiting deviating abundances between medical therapy groups and between groups with high and low calprotectin levels.
Abundance in Group 1: decreased abundance in Inflammatory bowel disease patients with fecal calprotectin levels > 1000 mg/kg
| NCBI | Quality Control | Links |
|---|---|---|
| Roseburia hominis | ||
| Roseburia inulinivorans | ||
| Roseburia intestinalis | ||
| Alistipes finegoldii | ||
| Barnesiella intestinihominis |
Revision editor(s): Yjung24
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Inflammatory bowel disease patients receiving one biologic or conventional therapy
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Inflammatory bowel disease patients receiving second class of biologic drug
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- A subset of the IBD patients receiving biologic therapy needed further treatment escalation to a second class of biologics.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 88
- Group 1 sample size Number of subjects in the case (exposed) group
- 22
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- antibiotics use within the last six months of study for healthy controls (group 0)
Lab analysis
Statistical Analysis
Signature 1
Source: Text: Page 6 Paragraph 2
Description: A subset of the IBD patients receiving biologic therapy needed further treatment escalation to a second class of biologics. These patients had a significantly lower abundance of Bifidobacterium bifidum, Roseburia hominis and Bacteroides xylanisolvens compared to the IBD patients who received one biologic or conventional therapy.
Abundance in Group 1: decreased abundance in Inflammatory bowel disease patients receiving second class of biologic drug
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium bifidum | ||
| Roseburia hominis | ||
| Bacteroides xylanisolvens |
Revision editor(s): Yjung24
