Dysbiosis in the Gut Microbiota in Patients with Inflammatory Bowel Disease during Remission
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
Authors
Pisani A, Rausch P, Bang C, Ellul S, Tabone T, Marantidis Cordina C, Zahra G, Franke A, Ellul P
Journal
Microbiology spectrum
Year
2022
Keywords:
Enterobacteriaceae, dysbiosis, flavonoid-degrading bacteria, inflammatory bowel disease, microbiota, remission
Inflammatory bowel disease (IBD) is a chronic, relapsing, inflammatory disorder which comprises two main conditions: Crohn's disease (CD) and ulcerative colitis (UC). Although the etiology of IBD has not been fully elucidated, the gut microbiota is hypothesized to play a vital role in its development. The aim of this cross-sectional study was to characterize the fecal microbiota in CD or UC patients in a state of remission to reveal potential factors sustaining residual levels of inflammation and triggering disease relapses. Ninety-eight IBD patients in a state of clinical remission (66 UC, 32 CD) and 97 controls were recruited, and stool samples, as well as detailed patient data, were collected. After DNA extraction, the variable regions V1 and V2 of the 16S rRNA gene were amplified and sequenced. Patients with IBD had a decrease in alpha diversity compared to that of healthy controls, and the beta diversity indices showed dissimilarity between the cohorts. Healthy controls were associated with the beneficial organisms unclassified Akkermansia species (Akkermansia uncl.), Oscillibacter uncl., and Coprococcus uncl., while flavonoid-degrading bacteria were associated with IBD. Network analysis identified highly central and influential disease markers and a strongly correlated network module of Enterobacteriaceae which was associated with IBD and could act as drivers for residual inflammatory processes sustaining and triggering IBD, even in a state of low disease activity. The microbiota in IBD patients is significantly different from that of healthy controls, even in a state of remission, which implicates the microbiota as an important driver of chronicity in IBD. IMPORTANCE Dysbiosis in inflammatory bowel disease (IBD) has been implicated as a causal or contributory factor to the pathogenesis of the disease. This study, done on patients in remission while accounting for various confounding factors, shows significant community differences and altered community dynamics, even after acute inflammation has subsided. A cluster of Enterobacteriaceae was linked with Crohn's disease, suggesting that this cluster, which contains members known to disrupt colonization resistance and form biofilms, persists during quiescence and can lead to chronic inflammation. Flavonoid-degrading bacteria were also associated with IBD, raising the possibility that modification of dietary flavonoids might induce and maintain remission in IBD.
Experiment 1
Needs review
Subjects
- Location of subjects
- Malta
- 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
- Ulcerative colitis colitis ulcerative,Colitis, Ulcerative,Left-sided ulcerative (chronic) colitis,Left-sided ulcerative colitis,left-sided ulcerative colitis,Other ulcerative colitis,Other ulcerative colitis (disorder),UC - ulcerative colitis,ulcerative colitis,ulcerative colitis (disease),ulcerative colitis (disorder),Ulcerative colitis, unspecified,ULCERATVE COLITIS UNSPCF,Ulcerative colitis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls (HC)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Ulcerative colitis (UC)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Ulcerative colitis (UC) in a state of remission
- Group 0 sample size Number of subjects in the control (unexposed) group
- 97
- Group 1 sample size Number of subjects in the case (exposed) group
- 66
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V2
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- DESeq2
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index, sex
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- decreased
Signature 1
Needs review
Source: Appendix Table 5
Description: Analyses of differential abundances at lower taxonomic levels with respect to IBD status/health condition
Abundance in Group 1: increased abundance in Ulcerative colitis (UC)
Revision editor(s): Samreen-19
Signature 2
Needs review
Source: Appendix Table 5
Description: Analyses of differential abundances at lower taxonomic levels with respect to IBD status/health condition
Abundance in Group 1: decreased abundance in Ulcerative colitis (UC)
Revision editor(s): Samreen-19
Experiment 2
Needs review
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Crohn’s disease (CD)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Crohn’s disease (CD) in a state of remission
- Group 1 sample size Number of subjects in the case (exposed) group
- 32
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- decreased
Signature 1
Needs review
Source: Appendix Table 5
Description: Analyses of differential abundances at lower taxonomic levels with respect to IBD status/health condition
Abundance in Group 1: increased abundance in Crohn’s disease (CD)
Revision editor(s): Samreen-19
Signature 2
Needs review
Source: Appendix Table 5
Description: Analyses of differential abundances at lower taxonomic levels with respect to IBD status/health condition
Abundance in Group 1: decreased abundance in Crohn’s disease (CD)
Revision editor(s): Samreen-19
Experiment 3
Needs review
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Gut microbiome measurement Gut microbiome measurement,gut microbiome measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Crohn's disease (CD)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Ulcerative colitis (UC)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Ulcerative colitis (UC) in a state of remission
- Group 0 sample size Number of subjects in the control (unexposed) group
- 32
- Group 1 sample size Number of subjects in the case (exposed) group
- 66
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- decreased
Signature 1
Needs review
Source: Appendix Table 5
Description: Analyses of differential abundances at lower taxonomic levels with respect to IBD status/health condition
Abundance in Group 1: increased abundance in Ulcerative colitis (UC)
| NCBI | Quality Control | Links |
|---|---|---|
| unclassified Parabacteroides | ||
| unclassified Faecalibacterium | ||
| unclassified Parasutterella |
Revision editor(s): Samreen-19
Signature 2
Needs review
Source: Appendix Table 5
Description: Analyses of differential abundances at lower taxonomic levels with respect to IBD status/health condition
Abundance in Group 1: decreased abundance in Ulcerative colitis (UC)
| NCBI | Quality Control | Links |
|---|---|---|
| unclassified Dorea | ||
| unclassified Subdoligranulum | ||
| unclassified Escherichia |
Revision editor(s): Samreen-19
Experiment 4
Needs review
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Smoking behavior smoking,Smoking behavior,smoking behavior
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Yes
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Inflammatory Bowel Disease (IBD) who are smokers
- Group 0 sample size Number of subjects in the control (unexposed) group
- 63
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- decreased
Signature 1
Needs review
Source: Appendix Table 9
Description: Differential abundance analysis for smoking behaviour
Abundance in Group 1: increased abundance in Yes
| NCBI | Quality Control | Links |
|---|---|---|
| unclassified Lachnospiraceae | ||
| unclassified Bacteroides | ||
| unclassified Faecalibacterium | ||
| unclassified Sutterella |
Revision editor(s): Samreen-19
Signature 2
Needs review
Source: Appendix Table 9
Description: Differential abundance analysis for smoking behaviour
Abundance in Group 1: decreased abundance in Yes
Revision editor(s): Samreen-19
Experiment 5
Needs review
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Ex
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Inflammatory Bowel Disease (IBD) who were ex-smokers (had stopped smoking for at least 6 months).
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- decreased
Signature 1
Needs review
Source: Appendix Table 9
Description: Differential abundance analysis for smoking behaviour
Abundance in Group 1: increased abundance in Ex
| NCBI | Quality Control | Links |
|---|---|---|
| Phocaeicola dorei | ||
| unclassified Lachnospiraceae | ||
| unclassified Bacteroides | ||
| unclassified Parasutterella | ||
| unclassified Faecalibacterium |
Revision editor(s): Samreen-19
Signature 2
Needs review
Source: Appendix Table 9
Description: Differential abundance analysis for smoking behaviour
Abundance in Group 1: decreased abundance in Ex
Revision editor(s): Samreen-19
Experiment 6
Needs review
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Ex
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Yes
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Inflammatory Bowel Disease (IBD) who are smokers
- 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
- 10
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- decreased
Signature 1
Needs review
Source: Appendix Table 9
Description: Differential abundance analysis for smoking behaviour
Abundance in Group 1: increased abundance in Yes
| NCBI | Quality Control | Links |
|---|---|---|
| unclassified Bilophila | ||
| unclassified Faecalibacterium | ||
| unclassified Bacteroides | ||
| unclassified Sutterella |
Revision editor(s): Samreen-19
Signature 2
Needs review
Source: Appendix Table 9
Description: Differential abundance analysis for smoking behavior
Abundance in Group 1: decreased abundance in Yes
Revision editor(s): Samreen-19
Retrieved from "https://bugsigdb.org/w/index.php?title=Study_1007&oldid=126467"
Hidden category:
