Fecal Microbiota in Patients with Irritable Bowel Syndrome Compared with Healthy Controls Using Real-Time Polymerase Chain Reaction: An Evidence of Dysbiosis
From BugSigDB
Jump to:navigation, search
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 Uniform resource identifier for web resources.
Authors
Shukla R, Ghoshal U, Dhole TN, Ghoshal UC
Journal
Digestive diseases and sciences
Year
2015
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
Needs review
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 | 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 | Links |
|---|---|
| Bifidobacterium |
Revision editor(s): Kwekuamoo
Experiment 2
Needs review
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
- 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 0 sample size Number of subjects in the control (unexposed) group
- 30
- 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
- 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 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 | 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 | Links |
|---|---|
| Bifidobacterium catenulatum |
Revision editor(s): Kwekuamoo
Experiment 3
Needs review
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
- Health Control
- 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).
- 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
- 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
- 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 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 | 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 | Links |
|---|---|
| Lactobacillus | |
| Bifidobacterium catenulatum |
Revision editor(s): Kwekuamoo
Experiment 4
Needs review
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
- Health Control
- 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 0 sample size Number of subjects in the control (unexposed) group
- 30
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
- 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
- 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 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 | 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 | Links |
|---|---|
| Lactobacillus | |
| Blautia | |
| Blautia coccoides | |
| Veillonella |
Revision editor(s): Kwekuamoo
Retrieved from "https://bugsigdb.org/w/index.php?title=Study_443&oldid=82414"
Hidden category:
