A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist?
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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
Forbes JD, Chen CY, Knox NC, Marrie RA, El-Gabalawy H, de Kievit T, Alfa M, Bernstein CN, Van Domselaar G
Journal
Microbiome
Year
2018
Keywords:
16S rRNA gene amplicon sequencing, Bacteria, Gut microbiota, Immune-mediated inflammatory disease, Inflammatory bowel disease, Machine learning classifiers, Multiple sclerosis, Rheumatoid arthritis, Taxonomic biomarkers
BACKGROUND: Immune-mediated inflammatory disease (IMID) represents a substantial health concern. It is widely recognized that IMID patients are at a higher risk for developing secondary inflammation-related conditions. While an ambiguous etiology is common to all IMIDs, in recent years, considerable knowledge has emerged regarding the plausible role of the gut microbiome in IMIDs. This study used 16S rRNA gene amplicon sequencing to compare the gut microbiota of patients with Crohn's disease (CD; N = 20), ulcerative colitis (UC; N = 19), multiple sclerosis (MS; N = 19), and rheumatoid arthritis (RA; N = 21) versus healthy controls (HC; N = 23). Biological replicates were collected from participants within a 2-month interval. This study aimed to identify common (or unique) taxonomic biomarkers of IMIDs using both differential abundance testing and a machine learning approach. RESULTS: Significant microbial community differences between cohorts were observed (pseudo F = 4.56; p = 0.01). Richness and diversity were significantly different between cohorts (pFDR < 0.001) and were lowest in CD while highest in HC. Abundances of Actinomyces, Eggerthella, Clostridium III, Faecalicoccus, and Streptococcus (pFDR < 0.001) were significantly higher in all disease cohorts relative to HC, whereas significantly lower abundances were observed for Gemmiger, Lachnospira, and Sporobacter (pFDR < 0.001). Several taxa were found to be differentially abundant in IMIDs versus HC including significantly higher abundances of Intestinibacter in CD, Bifidobacterium in UC, and unclassified Erysipelotrichaceae in MS and significantly lower abundances of Coprococcus in CD, Dialister in MS, and Roseburia in RA. A machine learning approach to classify disease versus HC was highest for CD (AUC = 0.93 and AUC = 0.95 for OTU and genus features, respectively) followed by MS, RA, and UC. Gemmiger and Faecalicoccus were identified as important features for classification of subjects to CD and HC. In general, features identified by differential abundance testing were consistent with machine learning feature importance. CONCLUSIONS: This study identified several gut microbial taxa with differential abundance patterns common to IMIDs. We also found differentially abundant taxa between IMIDs. These taxa may serve as biomarkers for the detection and diagnosis of IMIDs and suggest there may be a common component to IMID etiology.
Experiment 1
Reviewed Marked as Reviewed by Fatima on 2022/05/17
Subjects
- Location of subjects
- Canada
- 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
- Crohn's disease Colitis, Granulomatous,CROHN DIS,Crohn Disease,Crohn disease,Crohn's associated gastritis,Crohn's disease,Crohn's disease of colon,Crohn's disease of large bowel,CROHNS DIS,Crohns Disease,Enteritis, Granulomatous,Enteritis, Regional,Gastritis Associated with Crohn Disease,Gastritis Associated with Crohn's Disease,granulomatous colitis,Ileitis, Regional,Ileitis, Terminal,Ileocolitis,pediatric Crohn's disease,regional enteritis,crohn disease,crohn's disease
- 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
- crohn's disease
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients with immune-mediated inflammatory disease (IMID)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 23
- 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)
- 8 weeks
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
- 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
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Reviewed Marked as Reviewed by Fatima on 2022/05/17
Curated date: 2021/01/10
Curator: Fatima Zohra
Revision editor(s): WikiWorks, Fatima, Merit, ChiomaBlessing
Source: Table 2
Description: Abundant taxa in Crohn's disease patients microbiota relative to healthy controls (HC)
Abundance in Group 1: increased abundance in crohn's disease
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Bacillota | ||
| Blautia | ||
| Carnobacteriaceae | ||
| Eggerthella | ||
| Faecalicoccus | ||
| Gemella | ||
| Intestinibacter | ||
| Rothia | ||
| Streptococcaceae | ||
| Streptococcus | ||
| unclassified Lachnospiraceae |
Revision editor(s): WikiWorks, Fatima, Merit, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by Fatima on 2022/05/17
Curated date: 2021/01/10
Curator: Fatima Zohra
Revision editor(s): Fatima, WikiWorks, ChiomaBlessing
Source: Table 2
Description: Abundant taxa in Crohn's disease patients microbiota relative to healthy controls (HC)
Abundance in Group 1: decreased abundance in crohn's disease
Revision editor(s): Fatima, WikiWorks, ChiomaBlessing
Experiment 2
Reviewed Marked as Reviewed by Fatima on 2022/05/17
Differences from previous experiment shown
Subjects
- 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 1 name Corresponds to the case (exposed) group for case-control studies
- ulcerative colitis
- Group 1 sample size Number of subjects in the case (exposed) group
- 19
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Reviewed Marked as Reviewed by Fatima on 2022/05/17
Curated date: 2021/01/10
Curator: Fatima Zohra
Revision editor(s): WikiWorks, Fatima, Merit, ChiomaBlessing
Source: Table 2
Description: Abundant taxa in Ulcerative colitis patients microbiota relative to healthy controls (HC)
Abundance in Group 1: increased abundance in ulcerative colitis
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Anaerofustis | ||
| Bifidobacterium | ||
| Eggerthella | ||
| Faecalicoccus | ||
| Gemella | ||
| Streptococcaceae | ||
| Streptococcus | ||
| unclassified Lachnospiraceae |
Revision editor(s): WikiWorks, Fatima, Merit, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by Fatima on 2022/05/17
Source: Table 2
Description: Abundant taxa in Ulcerative colitis patients microbiota relative to healthy controls (HC)
Abundance in Group 1: decreased abundance in ulcerative colitis
| NCBI | Quality Control | Links |
|---|---|---|
| Gemmiger | ||
| Gordonibacter | ||
| Lachnospira | ||
| Mogibacterium | ||
| Ruminococcus | ||
| Sporobacter |
Revision editor(s): WikiWorks, ChiomaBlessing
Experiment 3
Reviewed Marked as Reviewed by Fatima on 2022/05/17
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Multiple sclerosis Disseminated Sclerosis,generalized multiple sclerosis,insular sclerosis,MS,MS (Multiple Sclerosis),multiple sclerosis,MULTIPLE SCLEROSIS ACUTE FULMINATING,Multiple Sclerosis, Acute Fulminating,Sclerosis, Disseminated,Sclerosis, Multiple,Multiple sclerosis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- multiple sceloris
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Reviewed Marked as Reviewed by Fatima on 2022/05/17
Source: Table 2
Description: Abundant taxa in Multiple sclerosis patients microbiota relative to healthy controls (HC)
Abundance in Group 1: increased abundance in multiple sceloris
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Anaerofustis | ||
| Clostridia | ||
| Clostridiaceae | ||
| Clostridium | ||
| Eggerthella | ||
| Faecalicoccus | ||
| Streptococcus | ||
| Turicibacter |
Revision editor(s): WikiWorks, Merit, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by Fatima on 2022/05/17
Source: Table 2
Description: Abundant taxa in Multiple sclerosis patients microbiota relative to healthy controls (HC)
Abundance in Group 1: decreased abundance in multiple sceloris
| NCBI | Quality Control | Links |
|---|---|---|
| Butyricicoccus | ||
| Dialister | ||
| Faecalibacterium | ||
| Fusicatenibacter | ||
| Gemmiger | ||
| Lachnospira | ||
| Sporobacterium | ||
| Subdoligranulum |
Revision editor(s): WikiWorks, ChiomaBlessing
Experiment 4
Reviewed Marked as Reviewed by Fatima on 2022/05/17
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Rheumatoid arthritis Arthritis or polyarthritis, rheumatic,arthritis or polyarthritis, rheumatic,Arthritis, Rheumatoid,arthritis, rheumatoid,atrophic Arthritis,atrophic arthritis,autoimmune arthritis,Chronic rheumatic arthritis,Proliferative arthritis,RA,RA - Rheumatoid arthritis,RhA - Rheumatoid arthritis,Rheumatic gout,rheumatoid arthritis,Rheumatoid arthritis (disorder),Rheumatoid arthritis NOS,Rheumatoid arthritis NOS (disorder),rheumatoid arthritis, susceptibility to,Rheumatoid disease,Rheumatoid arthritis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- arthiritis
- Group 1 sample size Number of subjects in the case (exposed) group
- 21
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Reviewed Marked as Reviewed by Fatima on 2022/05/17
Curated date: 2021/01/10
Curator: Fatima Zohra
Revision editor(s): WikiWorks, Fatima, Merit, ChiomaBlessing
Source: Table 2
Description: Abundant taxa in Rheumatoid arthritis patients microbiota relative to healthy controls (HC)
Abundance in Group 1: increased abundance in arthiritis
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Bacillota | ||
| Eggerthella | ||
| Faecalicoccus | ||
| Gemella | ||
| Rothia | ||
| Streptococcaceae | ||
| Streptococcus | ||
| unclassified Lachnospiraceae |
Revision editor(s): WikiWorks, Fatima, Merit, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by Fatima on 2022/05/17
Source: Table 2
Description: Abundant taxa in Rheumatoid arthritis patients microbiota relative to healthy controls (HC)
Abundance in Group 1: decreased abundance in arthiritis
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerofustis | ||
| Butyricicoccus | ||
| Clostridium | ||
| Faecalibacterium | ||
| Fusicatenibacter | ||
| Gemmiger | ||
| Lachnospira | ||
| Romboutsia | ||
| Roseburia | ||
| Sporobacter | ||
| Subdoligranulum |
Revision editor(s): WikiWorks, ChiomaBlessing
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