Fecal Microbiota in Patients with Irritable Bowel Syndrome Compared with Healthy Controls Using Real-Time Polymerase Chain Reaction: An Evidence of Dysbiosis
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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: 2021/06/04
Curator: Kwekuamoo
Revision editor(s): LGeistlinger, Kwekuamoo, Claregrieve1, WikiWorks
Subjects
- Location of subjects
- India
- Host species Species from which microbiome was sampled (if applicable)
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- irritable bowel syndrome [X]Psychogenic IBS,Adaptive colitis,Colitides, Mucous,Colitis, Mucous,Colon spasm,Colon, Irritable,Functional bowel disease,IBD,IBS,IBS - Irritable bowel syndrome,IC - Irritable colon,Irritable bowel,Irritable bowel - IBS,irritable bowel syndrome,Irritable Bowel Syndromes,Irritable Colon,irritable colon,Irritable colon (disorder),Irritable colon - Irritable bowel syndrome,Irritable colon syndrome,Membranous colitis,Mucous Colitides,Mucous colitis,mucus colitis,Nervous colitis,Psychogenic IBS,psychogenic IBS,Spastic colitis,Spastic colon,spastic colon,Syndrome, Irritable Bowel,Syndromes, Irritable Bowel
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy Control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- IBS
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with IBS diagnosed using Rome III. Patients were classified into three sub-types
using Rome III criteria: constipation predominant IBS (IBS-C), diarrhea predominant (IBS-D), and un-subtyped (IBS-U). All participants.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 30
- Group 1 sample size Number of subjects in the case (exposed) group
- 47
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 4 weeks
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- RT-qPCR
Statistical Analysis
- 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
Signature 1
Source: Table 3.
Description: Relative difference in 16S rRNA copy number of fecal bacteria between patients with IBS and healthy controls
Abundance in Group 1: increased abundance in IBS
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia | ||
| Blautia coccoides | ||
| Veillonella | ||
| Bacteroides | ||
| Pseudomonas aeruginosa |
Revision editor(s): Kwekuamoo
Signature 2
Source: Table 3.
Description: Relative difference in 16S rRNA copy number of fecal bacteria between patients with IBS and healthy controls
Abundance in Group 1: decreased abundance in IBS
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium |
Revision editor(s): Kwekuamoo
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Health Control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- IBS-C
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with IBS diagnosed using Rome III. Patients were classified into three sub-types
using Rome III criteria: constipation predominant IBS (IBS-C).
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Patients who had prior history of gastrointestinal surgery, inflammatory bowel disease, and celiac disease were excluded. Patients with IBS who used antibiotics, probiotics, or prokinetics within last 4 weeks of inclusion into the study were also excluded.
Lab analysis
Statistical Analysis
Signature 1
Source: Table 4.
Description: Relative difference in 16S rRNA copy number of fecal bacteria in subgroups of patients with IBS and healthy controls.
Abundance in Group 1: increased abundance in IBS-C
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Blautia | ||
| Blautia coccoides | ||
| Lactobacillus | ||
| Pseudomonas aeruginosa | ||
| Veillonella |
Revision editor(s): Kwekuamoo
Signature 2
Source: Table 4.
Description: Relative difference in 16S rRNA copy number of fecal bacteria in subgroups of patients with IBS and healthy controls.
Abundance in Group 1: decreased abundance in IBS-C
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium catenulatum |
Revision editor(s): Kwekuamoo
Experiment 3
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- IBS-D
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with IBS diagnosed using Rome III. Patients were classified into three sub-types
using Rome III criteria: diarrhea predominant IBS (IBS-D).
Lab analysis
Statistical Analysis
Signature 1
Source: Table 4.
Description: Relative difference in 16S rRNA copy number of fecal bacteria in subgroups of patients with IBS and healthy controls.
Abundance in Group 1: increased abundance in IBS-D
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia | ||
| Blautia coccoides | ||
| Veillonella | ||
| Bacteroides | ||
| Pseudomonas aeruginosa |
Revision editor(s): Kwekuamoo
Signature 2
Source: Table 4.
Description: Relative difference in 16S rRNA copy number of fecal bacteria in subgroups of patients with IBS and healthy controls.
Abundance in Group 1: decreased abundance in IBS-D
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus | ||
| Bifidobacterium catenulatum |
Revision editor(s): Kwekuamoo
Experiment 4
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- IBS-U
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with IBS diagnosed using Rome III. Patients were classified into three sub-types
using Rome III criteria: un-subtyped (IBS-U).
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
Lab analysis
Statistical Analysis
Signature 1
Source: Table 4.
Description: Relative difference in 16S rRNA copy number of fecal bacteria in subgroups of patients with IBS and healthy controls.
Abundance in Group 1: increased abundance in IBS-U
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium catenulatum | ||
| Bacteroides | ||
| Pseudomonas aeruginosa |
Revision editor(s): Kwekuamoo
Signature 2
Source: Table 4.
Description: Relative difference in 16S rRNA copy number of fecal bacteria in subgroups of patients with IBS and healthy controls.
Abundance in Group 1: decreased abundance in IBS-U
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus | ||
| Blautia | ||
| Blautia coccoides | ||
| Veillonella |
Revision editor(s): Kwekuamoo
