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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Reviewed Marked as Reviewed by Claregrieve1 on 2022/12/26
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


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
Not specified
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

Needs review

Curated date: 2021/06/28

Curator: Kwekuamoo

Revision editor(s): Kwekuamoo

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 ControlLinks
Blautia
Blautia coccoides
Veillonella
Bacteroides
Pseudomonas aeruginosa

Revision editor(s): Kwekuamoo

Signature 2

Needs review

Curated date: 2021/07/18

Curator: Kwekuamoo

Revision editor(s): Kwekuamoo

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 ControlLinks
Bifidobacterium

Revision editor(s): Kwekuamoo

Experiment 2


Needs review

Curated date: 2021/07/18

Curator: Kwekuamoo

Revision editor(s): LGeistlinger, Kwekuamoo, WikiWorks

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
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

Needs review

Curated date: 2021/07/18

Curator: Kwekuamoo

Revision editor(s): Kwekuamoo

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 ControlLinks
Bacteroides
Blautia
Blautia coccoides
Lactobacillus
Pseudomonas aeruginosa
Veillonella

Revision editor(s): Kwekuamoo

Signature 2

Needs review

Curated date: 2021/07/18

Curator: Kwekuamoo

Revision editor(s): Kwekuamoo

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 ControlLinks
Bifidobacterium catenulatum

Revision editor(s): Kwekuamoo

Experiment 3


Needs review

Curated date: 2021/07/18

Curator: Kwekuamoo

Revision editor(s): LGeistlinger, Kwekuamoo, WikiWorks

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

Curated date: 2021/07/18

Curator: Kwekuamoo

Revision editor(s): Kwekuamoo

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 ControlLinks
Blautia
Blautia coccoides
Veillonella
Bacteroides
Pseudomonas aeruginosa

Revision editor(s): Kwekuamoo

Signature 2

Needs review

Curated date: 2021/07/18

Curator: Kwekuamoo

Revision editor(s): Kwekuamoo

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 ControlLinks
Lactobacillus
Bifidobacterium catenulatum

Revision editor(s): Kwekuamoo

Experiment 4


Needs review

Curated date: 2021/07/18

Curator: Kwekuamoo

Revision editor(s): LGeistlinger, Kwekuamoo, WikiWorks

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 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

Needs review

Curated date: 2021/07/18

Curator: Kwekuamoo

Revision editor(s): Kwekuamoo

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 ControlLinks
Bifidobacterium catenulatum
Bacteroides
Pseudomonas aeruginosa

Revision editor(s): Kwekuamoo

Signature 2

Needs review

Curated date: 2021/07/18

Curator: Kwekuamoo

Revision editor(s): Kwekuamoo

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 ControlLinks
Lactobacillus
Blautia
Blautia coccoides
Veillonella

Revision editor(s): Kwekuamoo