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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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Shukla R, Ghoshal U, Dhole TN, Ghoshal UC
Journal
Digestive diseases and sciences
Year
2015
Keywords:
Dysbiosis, Functional gastrointestinal disorder, Gastrointestinal microbiota, Quantitative real-time polymerase chain reaction
BACKGROUND: Dysbiosis may play a role in irritable bowel syndrome (IBS), hitherto an enigmatic disorder. We evaluated selected fecal microbes in IBS patients and healthy controls (HC). METHODS: Fecal 16S rRNA copy number of selected bacteria was studied using qPCR in 47 patients with IBS (Rome III) and 30 HC. RESULTS: Of 47 patients, 20 had constipation (IBS-C), 20 diarrhea (IBS-D), and seven unclassified IBS (IBS-U). Relative difference in 16S rRNA copy number of Bifidobacterium (P = 0.042) was lower, while those of Ruminococcus productus-Clostridium coccoides (P = 0.016), Veillonella (P = 0.008), Bacteroides thetaiotamicron (P < 0.001), Pseudomonas aeruginosa (P < 0.001), and Gram-negative bacteria (GNB, P = 0.001) were higher among IBS patients than HC. Number of Lactobacillus (P = 0.002) was lower, while that of Bacteroides thetaiotamicron (P < 0.001) and segmented filamentous bacteria (SFB, P < 0.001) was higher among IBS-D than IBS-C. Numbers of Bacteroides thetaiotamicron (P < 0.001), P. aeruginosa (P < 0.001), and GNB (P < 0.01) were higher among IBS-C and IBS-D than HC. Quantity of SFB was higher among IBS-D (P = 0.011) and lower among IBS-C (P = 0.002) than HC. Number of Veillonella species was higher among IBS-C than HC (P = 0.002). P. aeruginosa was frequently detected among IBS than HC (46/47 [97.9 %] vs. 10/30 [33.3 %], P < 0.001). Abdominal distension (n = 34/47) was associated with higher number of Bacteroides thetaiotamicron, Clostridium coccoides, P. aeruginosa, SFB, and GNB; bloating (n = 22/47) was associated with Clostridium coccoides and GNB. Microbial flora was different among IBS than HC on principal component analysis. CONCLUSION: Fecal microbiota was different among IBS than HC, and different sub-types were associated with different microbiota. P. aeruginosa was more frequent and higher in number among IBS patients.
Experiment 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-9
Curated date: 2021/06/04
Curator: Kwekuamoo
Revision editor(s): WikiWorks, LGeistlinger, Claregrieve1, Kwekuamoo, Peace Sandy, Folakunmi, MyleeeA, Tosin
Subjects
- Location of subjects
- India
- 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
- 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)
- 1 month
Lab analysis
- Sequencing type
- 16S
- 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)?
- Yes
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
Signature 1
Needs review
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 |
|---|---|---|
| Bacteroides | ||
| Blautia coccoides | ||
| Blautia producta | ||
| Pseudomonas aeruginosa | ||
| Veillonella |
Experiment 2
Reviewed Marked as Reviewed by Folakunmi on 2024-2-9
Differences from previous experiment shown
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
Signature 1
Needs review
Source: Table 4.
Description: Relative difference in 16S rRNA copy number of fecal bacteria in subgroups of patients with IBS-C and healthy controls.
Abundance in Group 1: increased abundance in IBS-C
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Blautia coccoides | ||
| Blautia producta | ||
| Lactobacillus | ||
| Pseudomonas aeruginosa | ||
| Veillonella |
Experiment 3
Reviewed Marked as Reviewed by Folakunmi on 2024-2-9
Differences from previous experiment shown
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
Needs review
Source: Table 4.
Description: Relative difference in 16S rRNA copy number of fecal bacteria in subgroups of patients with IBS-D and healthy controls.
Abundance in Group 1: increased abundance in IBS-D
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Candidatus Arthromitus sp. SFB-mouse | ||
| Pseudomonas aeruginosa |
Experiment 4
Reviewed Marked as Reviewed by Folakunmi on 2024-2-9
Differences from previous experiment shown
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 sub-types: un-subtyped (IBS-U).
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
Lab analysis
Statistical Analysis
Experiment 5
Reviewed Marked as Reviewed by Folakunmi on 2024-2-9
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Irritable Bowel Syndrome, diarrhea predominant (IBS-D)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Irritable Bowel Syndrome, constipation predominant (IBS-C)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients were classified into three sub-types using Rome III criteria: diarrhea predominant IBS (IBS-D).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
Signature 1
Needs review
Source: Table 4
Description: Relative difference in 16S rRNA copy number of fecal bacteria in subgroups of patients with IBS-C and IBS-D
Abundance in Group 1: increased abundance in Irritable Bowel Syndrome, constipation predominant (IBS-C)
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus |
Signature 2
Source: Table 4
Description: Relative difference in 16S rRNA copy number of fecal bacteria in subgroups of patients with IBS-C and IBS-D
Abundance in Group 1: decreased abundance in Irritable Bowel Syndrome, constipation predominant (IBS-C)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Candidatus Arthromitus sp. SFB-mouse |
Experiment 6
Reviewed Marked as Reviewed by Folakunmi on 2024-2-9
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No Visible abdominal distension
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Visible abdominal distension
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with IBS showing Visible abdominal distension as symptoms
- Group 0 sample size Number of subjects in the control (unexposed) group
- 13
- Group 1 sample size Number of subjects in the case (exposed) group
- 34
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-9
Source: Table 5
Description: Association of IBS symptoms in relation to bacterial load
Abundance in Group 1: increased abundance in Visible abdominal distension
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia coccoides | ||
| Candidatus Arthromitus sp. SFB-mouse | ||
| Pseudomonas aeruginosa | ||
| Bacteroides thetaiotaomicron |
Experiment 7
Reviewed Marked as Reviewed by Folakunmi on 2024-2-9
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No Abdominal Bloating
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Abdominal Bloating
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with IBS showing Abdominal Bloating/Abdominal discomfort as symptoms
- Group 0 sample size Number of subjects in the control (unexposed) group
- 25
- Group 1 sample size Number of subjects in the case (exposed) group
- 22
Lab analysis
Statistical Analysis
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