Alternation of the gut microbiota in irritable bowel syndrome: an integrated analysis based on multicenter amplicon sequencing data

From BugSigDB
Needs review
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Chen H, Ou R, Tang N, Su W, Yang R, Yu X, Zhang G, Jiao J, Zhou X
Journal
Journal of translational medicine
Year
2023
Keywords:
Amplicon sequencing analysis, GMrepo database, Gut microbiota, Irritable bowel syndrome, Propensity score matching
BACKGROUND: Gut dysbacteriosis has been reported as one of the etiologies for irritable bowel syndrome (IBS). However, the association between gut microbiota and IBS is still inconclusive. METHOD: A paired-sample study was designed by retrieving original multicenter 16 s-rRNA data of IBS patients and healthy controls from the GMrepo database. The propensity score matching (PSM) algorithm was applied to reduce confounding bias. The differential analysis of microbiota composition was performed at different taxonomic levels. The co-occurrence network was established. Subgroup analysis was performed to identify specific microbial compositions in different IBS subtypes. RESULTS: A total of 1522 amplicon samples were initially enrolled. After PSM, 708 individuals (354 IBS and 354 healthy controls) were eligible for further analysis. A total of 1,160 genera were identified. We identified significantly changed taxa in IBS groups (IBS-enriched: the families Enterobacteriaceae, Moraxellaceae and Sphingobacteriaceae; the genera Streptococcus, Bacillus, Enterocloster, Sphingobacterium, Holdemania and Acinetobacter. IBS-depleted: the phyla Firmicutes, Euryarchaeota, Cyanobacteria, Acidobacteria and Lentisphaerae; the families Bifidobacteriaceae, Ruminococcaceae, Methanobacteriaceae and the other 25 families; the genera Faecalibacterium, Bifidobacterium and other 68 genera). The co-occurrence network identified three hub genera and six hub species (including Faecalibacterium prausnitzii) that may be involved in IBS pathophysiology. Strong positive interactions were identified among the Bifidobacterium longum, Bifidobacterium breve and Bifidobacterium adolescentis in the Bifidobacterium community. CONCLUSION: This study provides quantitative analysis and visualization of the interaction between the gut microbiota and IBS. The identification of key species should be further validated to evaluate their causal relationships with the pathogenesis of IBS.

Experiment 1


Needs review

Curated date: 2025/05/01

Curator: Joiejoie

Revision editor(s): Joiejoie

Subjects

Location of subjects
Australia
Canada
Switzerland
United Kingdom
United States of America
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
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,Irritable bowel syndrome
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
IBS Patients (Irritable Bowel Syndrome)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
This group represents individuals diagnosed with irritable bowel syndrome (IBS), as identified from multicenter 16S rRNA sequencing data curated in the GMrepo database.
Group 0 sample size Number of subjects in the control (unexposed) group
354
Group 1 sample size Number of subjects in the case (exposed) group
354

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
Not specified

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, body mass index, region, sex
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
age, body mass index, region, sex

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged
Richness Number of species
unchanged

Signature 1

Needs review

Curated date: 2025/05/03

Curator: Joiejoie

Revision editor(s): Joiejoie

Source: Fig. 2b, c, d, S4, S5 & S6

Description: The relative abundance of the taxa between the IBS and healthy controls.

Abundance in Group 1: increased abundance in IBS Patients (Irritable Bowel Syndrome)

NCBI Quality ControlLinks
Acinetobacter
Bacillota
Bacillus
Enterobacteriaceae
Enterocloster
Holdemania
Moraxellaceae
Sphingobacteriaceae
Sphingobacterium
Streptococcus

Revision editor(s): Joiejoie

Signature 2

Needs review

Curated date: 2025/05/03

Curator: Joiejoie

Revision editor(s): Joiejoie

Source: Fig. 2b, c, d, S4, S5 & S6

Description: The relative abundance of the taxa between the IBS and healthy controls.

Abundance in Group 1: decreased abundance in IBS Patients (Irritable Bowel Syndrome)

NCBI Quality ControlLinks
Acidobacteriota
Bifidobacteriaceae
Bifidobacterium
Corynebacteriaceae
Faecalibacterium
Lentisphaerota
Methanobacteriota
Mycoplasmatota
Oscillospiraceae
Planctomycetota
Prevotellaceae
Ruminococcus
Synergistota
Verrucomicrobiota
Victivallis
Pseudoclostridium
Methanosphaera

Revision editor(s): Joiejoie

Experiment 2


Needs review

Curated date: 2025/05/01

Curator: Joiejoie

Revision editor(s): Joiejoie

Differences from previous experiment shown

Subjects

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
IBS-C ( Irritable bowel syndrome with predominant constipation )
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
This group refers to patients diagnosed with irritable bowel syndrome complicated with predominant constipation.
Group 1 sample size Number of subjects in the case (exposed) group
79

Lab analysis

Statistical Analysis

Statistical test
Kruskall-Wallis
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
No

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged

Signature 1

Needs review

Curated date: 2025/05/04

Curator: Joiejoie

Revision editor(s): Joiejoie

Source: Fig. 4C

Description: Relative abundance of significantly enriched genera.

Abundance in Group 1: increased abundance in IBS-C ( Irritable bowel syndrome with predominant constipation )

NCBI Quality ControlLinks
Anaerofilum
Bacillus
Enterocloster
Holdemania
Sphingobacterium
Streptococcus

Revision editor(s): Joiejoie

Signature 2

Needs review

Curated date: 2025/05/04

Curator: Joiejoie

Revision editor(s): Joiejoie

Source: Fig. 4C

Description: Relative abundance of significantly depleted genera.

Abundance in Group 1: decreased abundance in IBS-C ( Irritable bowel syndrome with predominant constipation )

NCBI Quality ControlLinks
Acetivibrio
Acidaminococcus
Barnesiella
Bilophila
Coprococcus
Corynebacterium
Faecalibacterium
Haemophilus
Lachnospira
Oscillibacter
Oscillospiraceae incertae sedis
Peptoniphilus
Phocaeicola
Prevotella
Roseburia
Ruminococcus
Sarcina
Sporobacter

Revision editor(s): Joiejoie

Experiment 3


Needs review

Curated date: 2025/05/01

Curator: Joiejoie

Revision editor(s): Joiejoie

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
IBS-D (Irritable bowel syndrome with predominant diarrhea )
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
This group refers to patients diagnosed with irritable bowel syndrome complicated with predominant diarrhea.
Group 1 sample size Number of subjects in the case (exposed) group
81

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged

Signature 1

Needs review

Curated date: 2025/05/04

Curator: Joiejoie

Revision editor(s): Joiejoie

Source: Fig. 4C

Description: Relative abundance of significantly enriched genera.

Abundance in Group 1: increased abundance in IBS-D (Irritable bowel syndrome with predominant diarrhea )

NCBI Quality ControlLinks
Haemophilus
Sphingobacterium
Holdemania
Streptococcus
Bacillus
Peptoniphilus
Roseburia
Enterocloster

Revision editor(s): Joiejoie

Signature 2

Needs review

Curated date: 2025/05/04

Curator: Joiejoie

Revision editor(s): Joiejoie

Source: Fig. 4C

Description: Relative abundance of significantly depleted genera.

Abundance in Group 1: decreased abundance in IBS-D (Irritable bowel syndrome with predominant diarrhea )

NCBI Quality ControlLinks
Bilophila
Corynebacterium
Barnesiella
Prevotella
Phocaeicola
Faecalibacterium
Anaerofilum
Oscillibacter
Sporobacter
Lachnospira
Ruminococcus
Acetivibrio
Coprococcus
Oscillospiraceae incertae sedis
Acidaminococcus
Sarcina

Revision editor(s): Joiejoie

Experiment 4


Needs review

Curated date: 2025/05/01

Curator: Joiejoie

Revision editor(s): Joiejoie

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
IBS-C (Irritable bowel syndrome with predominant constipation)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
This refers to patients diagnosed with irritable bowel syndrome complicated with predominant diarrhea.
Group 0 sample size Number of subjects in the control (unexposed) group
79

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged

Signature 1

Needs review

Curated date: 2025/05/04

Curator: Joiejoie

Revision editor(s): Joiejoie

Source: Fig. 4C

Description: Relative abundance of significantly enriched genera.

Abundance in Group 1: increased abundance in IBS-D (Irritable bowel syndrome with predominant diarrhea )

NCBI Quality ControlLinks
Haemophilus
Corynebacterium
Prevotella
Faecalibacterium
Lachnospira
Streptococcus
Coprococcus
Peptoniphilus
Roseburia
Enterocloster

Revision editor(s): Joiejoie

Signature 2

Needs review

Curated date: 2025/05/04

Curator: Joiejoie

Revision editor(s): Joiejoie

Source: Fig. 4C

Description: Relative abundance of significantly depleted genera

Abundance in Group 1: decreased abundance in IBS-D (Irritable bowel syndrome with predominant diarrhea )

NCBI Quality ControlLinks
Bilophila
Barnesiella
Phocaeicola
Anaerofilum
Holdemania
Sarcina
Acidaminococcus
Oscillospiraceae incertae sedis
Bacillus
Oscillibacter
Sporobacter
Ruminococcus
Acetivibrio

Revision editor(s): Joiejoie

Experiment 5


Needs review

Curated date: 2025/05/01

Curator: Joiejoie

Revision editor(s): Joiejoie

Differences from previous experiment shown

Subjects

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
IBS-NPD ( Irritable Bowel Syndrome without psychiatric disorders )
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
This group refers to patients with irritable bowel syndrome without psychiatric disorders (IBS-NPD)
Group 0 sample size Number of subjects in the control (unexposed) group
354
Group 1 sample size Number of subjects in the case (exposed) group
214

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged

Signature 1

Needs review

Curated date: 2025/05/04

Curator: Joiejoie

Revision editor(s): Joiejoie

Source: Fig. 5C

Description: The relative abundance of significantly enriched genera.

Abundance in Group 1: increased abundance in IBS-NPD ( Irritable Bowel Syndrome without psychiatric disorders )

NCBI Quality ControlLinks
Sphingobacterium
Holdemania
Enterocloster
Niallia

Revision editor(s): Joiejoie

Signature 2

Needs review

Curated date: 2025/05/04

Curator: Joiejoie

Revision editor(s): Joiejoie

Source: Fig. 5C

Description: The relative abundance of significantly depleted genera.

Abundance in Group 1: decreased abundance in IBS-NPD ( Irritable Bowel Syndrome without psychiatric disorders )

NCBI Quality ControlLinks
Acetivibrio
Acidaminococcus
Bifidobacterium
Bilophila
Butyrivibrio
Coprococcus
Corynebacterium
Faecalibacterium
Phocaeicola
Prevotella
Pseudoclostridium
Ruminiclostridium
Ruminococcus
Sarcina
Sporobacter

Revision editor(s): Joiejoie

Experiment 6


Needs review

Curated date: 2025/05/01

Curator: Joiejoie

Revision editor(s): Joiejoie

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
IBS-PD ( Irritable Bowel Syndrome with psychiatric disorders )
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
This group refers to patients with irritable bowel syndrome with psychiatric disorders (IBS-PD)
Group 1 sample size Number of subjects in the case (exposed) group
140

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged

Signature 1

Needs review

Curated date: 2025/05/04

Curator: Joiejoie

Revision editor(s): Joiejoie

Source: Fig. 5C

Description: The relative abundance of significantly enriched genera.

Abundance in Group 1: increased abundance in IBS-PD ( Irritable Bowel Syndrome with psychiatric disorders )

NCBI Quality ControlLinks
Sphingobacterium
Holdemania
Enterocloster
Pseudoflavonifractor

Revision editor(s): Joiejoie

Signature 2

Needs review

Curated date: 2025/05/04

Curator: Joiejoie

Revision editor(s): Joiejoie

Source: Fig. 5C

Description: The relative abundance of significantly depleted genera.

Abundance in Group 1: decreased abundance in IBS-PD ( Irritable Bowel Syndrome with psychiatric disorders )

NCBI Quality ControlLinks
Bilophila
Bifidobacterium
Corynebacterium
Paraprevotella
Phocaeicola
Prevotella
Faecalibacterium
Ruminococcus
Sarcina
Acetivibrio
Coprococcus
Sporobacter
Pseudoclostridium
Ruminiclostridium
Butyrivibrio
Niallia
Acidaminococcus

Revision editor(s): Joiejoie

Experiment 7


Needs review

Curated date: 2025/05/01

Curator: Joiejoie

Revision editor(s): Joiejoie

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
IBS-NPD (Irritable Bowel Syndrome without psychiatric disorders)
Group 1 name Corresponds to the case (exposed) group for case-control studies
IBS-PD (Irritable Bowel Syndrome with psychiatric disorders)
Group 0 sample size Number of subjects in the control (unexposed) group
214

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged

Signature 1

Needs review

Curated date: 2025/05/05

Curator: Joiejoie

Revision editor(s): Joiejoie

Source: Fig. 5C

Description: The relative abundance of significantly enriched genera.

Abundance in Group 1: increased abundance in IBS-PD (Irritable Bowel Syndrome with psychiatric disorders)

NCBI Quality ControlLinks
Bifidobacterium
Phocaeicola
Prevotella
Sphingobacterium
Faecalibacterium
Ruminococcus
Enterocloster
Pseudoflavonifractor
Butyrivibrio

Revision editor(s): Joiejoie

Signature 2

Needs review

Curated date: 2025/05/05

Curator: Joiejoie

Revision editor(s): Joiejoie

Source: Fig. 5C

Description: The relative abundance of significantly depleted genera.

Abundance in Group 1: decreased abundance in IBS-PD (Irritable Bowel Syndrome with psychiatric disorders)

NCBI Quality ControlLinks
Acidaminococcus
Niallia
Ruminiclostridium
Pseudoclostridium
Holdemania
Sarcina
Paraprevotella
Bilophila
Coprococcus
Sporobacter
Acetivibrio

Revision editor(s): Joiejoie

Experiment 8


Needs review

Curated date: 2025/05/01

Curator: Joiejoie

Revision editor(s): Joiejoie

Differences from previous experiment shown

Subjects

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
IBS Patients (Irritable Bowel Syndrome)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
This group represents individuals diagnosed with irritable bowel syndrome (IBS), as identified from multicenter 16S rRNA sequencing data curated in the GMrepo database.
Group 0 sample size Number of subjects in the control (unexposed) group
354
Group 1 sample size Number of subjects in the case (exposed) group
354

Lab analysis

Statistical Analysis

Statistical test
Mann-Whitney (Wilcoxon)

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged
Richness Number of species
unchanged

Signature 1

Needs review

Curated date: 2025/05/04

Curator: Joiejoie

Revision editor(s): Joiejoie

Source: Fig. 6E

Description: The relative abundance of significantly changed species belonging to the genera Bifidobacterium in IBS.

Abundance in Group 1: decreased abundance in IBS Patients (Irritable Bowel Syndrome)

NCBI Quality ControlLinks
Bifidobacterium breve
Bifidobacterium adolescentis
Bifidobacterium boum
Bifidobacterium coryneforme
Bifidobacterium callitrichos
Bifidobacterium gallicum
Bifidobacterium lemurum
Bifidobacterium saguini
Bifidobacterium pullorum
Bifidobacterium longum
Bifidobacterium tsurumiense
Bifidobacterium pseudocatenulatum

Revision editor(s): Joiejoie