Microbiome Survey of the Inflamed and Noninflamed Gut at Different Compartments Within the Gastrointestinal Tract of Inflammatory Bowel Disease Patients
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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, Van Domselaar G, Bernstein CN
Journal
Inflammatory bowel diseases
Year
2016
BACKGROUND: We aimed to contrast the mucosal microbiota in Crohn's disease (CD) and ulcerative colitis (UC). METHODS: We assessed the concept of localized dysbiosis by comparing the bacterial communities of inflamed and noninflamed mucosa of patients with inflammatory bowel disease (IBD) and by analysis of the microbiota composition at distinct gut compartments (ileum, cecum, mid-colon, and rectum). We performed 16S rDNA sequencing to analyze population structures. Quality control and operational taxonomic unit classification of reads were performed using mothur with statistical analyses executed in the R package, phyloseq. RESULTS: There was no variation in any phyla or genera comparing inflamed to noninflamed mucosa within CD (or UC) or when comparing different gut compartments within CD (or UC). There were differences between the inflamed and noninflamed mucosa between CD and UC: analysis of the inflamed IBD gut at the phylum level indicated that Bacteroidetes (P = 0.002) and Fusobacteria (P < 0.05) were detected more frequently in inflamed CD mucosa than in inflamed UC mucosa. Conversely, Proteobacteria and Firmicutes (P < 0.05) were more frequently observed in the inflamed UC mucosa. At the genus level, the abundance of Faecalibacterium (P ≤ 0.05), Bacteroides (P = 0.003), and Pseudomonas (P < 0.001) were significantly different between the inflamed CD and UC and the abundance of 13 genera were significantly different within the noninflamed mucosa. The noninflamed UC mucosa was the most different from non-IBD mucosa. CONCLUSIONS: Dramatic shifts of microbial communities were not observed between the noninflamed and inflamed mucosa within CD (or UC) although both the inflamed (and noninflamed) mucosa was different between CD and UC.
Experiment 1
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-15
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
- Cecum mucosa , Colonic mucosa , Mucosa of rectum , Ileal mucosa Caecum mucosa,Caecum mucosa of organ,Caecum mucous membrane,Caecum organ mucosa,Cecal mucosa,Cecum mucosa of organ,Cecum mucous membrane,Cecum organ mucosa,Intestinum crassum caecum mucosa,Intestinum crassum caecum mucosa of organ,Intestinum crassum caecum mucous membrane,Intestinum crassum caecum organ mucosa,Mucosa of caecum,Mucosa of cecum,Mucosa of intestinum crassum caecum,Mucosa of organ of caecum,Mucosa of organ of cecum,Mucosa of organ of intestinum crassum caecum,Mucous membrane of caecum,Mucous membrane of cecum,Mucous membrane of intestinum crassum caecum,Organ mucosa of caecum,Organ mucosa of cecum,Organ mucosa of intestinum crassum caecum,Cecum mucosa,cecum mucosa,Colon mucosa,Colon mucous membrane,Colonic mucosa,Colonic mucous membrane,Large bowel mucosa,Mucosa of colon,Mucosa of large bowel,colonic mucosa,Mucosa of organ of rectum,Mucous membrane of rectum,Organ mucosa of rectum,Rectal mucosa,Rectal mucous membrane,Rectum mucosa,Rectum mucosa of organ,Rectum mucous membrane,Rectum organ mucosa,Mucosa of rectum,mucosa of rectum,Ileal mucous membrane,Ileum mucosa,Ileum mucosa of organ,Ileum mucous membrane,Ileum organ mucosa,Mucosa of ileum,Mucosa of organ of ileum,Mucous membrane of ileum,Organ mucosa of ileum,Ileal mucosa,ileal mucosa
- 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
- non-inflammatory bowel disease who were undergoing colonoscopy either for screening or for other gastrointestinal complaints unrelated to IBD
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- non-inflamed crohn's disease
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- biopsies collected from patients with crohn's disease at colonoscopy that were deemed as non-inflamed as per the clinical pathologist.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 7
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- N/A
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V6
- 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
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-15
Source: Table 2
Description: Microbial Distribution of Taxa (Phylum and Genus) Found to Be Differentially Abundant According to Disease and Inflammatory State of Biopsy. ^aP = <0.05, ^bP = <0.01, ^cP = <0.001. Up and down arrows are comparisons to non-IBD.
Abundance in Group 1: decreased abundance in non-inflamed crohn's disease
| NCBI | Quality Control | Links |
|---|---|---|
| Coprococcus | ||
| Oscillibacter |
Revision editor(s): Yjung24
Experiment 2
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-15
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 0 name Corresponds to the control (unexposed) group for case-control studies
- non-inflammatory bowel disease patients who were undergoing colonoscopy either for screening or for other gastrointestinal complaints unrelated to IBD
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- non-inflamed ulcerative colitis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- biopsies collected from patients with ulcerative colitis at colonoscopy that were deemed as non-inflamed as per the clinical pathologist.
- 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
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-15
Source: Table 2
Description: Microbial Distribution of Taxa (Phylum and Genus) Found to Be Differentially Abundant According to Disease and Inflammatory State of Biopsy. ^aP = <0.05, ^bP = <0.01, ^cP = <0.001. Up and down arrows are comparisons to non-IBD.
Abundance in Group 1: increased abundance in non-inflamed ulcerative colitis
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Bacillota | ||
| Marinobacter | ||
| Pseudomonadota | ||
| Pseudomonas |
Revision editor(s): Yjung24
Signature 2
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-15
Source: Table 2
Description: Microbial Distribution of Taxa (Phylum and Genus) Found to Be Differentially Abundant According to Disease and Inflammatory State of Biopsy. ^aP = <0.05, ^bP = <0.01, ^cP = <0.001. Up and down arrows are comparisons to non-IBD.
Abundance in Group 1: decreased abundance in non-inflamed ulcerative colitis
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes | ||
| Bacteroides | ||
| Bacteroidota | ||
| Dorea | ||
| Oscillibacter | ||
| Parabacteroides | ||
| Phascolarctobacterium | ||
| Prevotella |
Revision editor(s): Yjung24
Experiment 3
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-15
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- inflamed ulcerative colitis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- biopsies collected from patients with ulcerative colitis at colonoscopy that were deemed as inflamed as per the clinical pathologist.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 27
- Group 1 sample size Number of subjects in the case (exposed) group
- 26
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- increased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-15
Source: Table 2
Description: Microbial Distribution of Taxa (Phylum and Genus) Found to Be Differentially Abundant According to Disease and Inflammatory State of Biopsy. ^aP = <0.05, ^bP = <0.01, ^cP = <0.001. Up and down arrows are comparisons to non-IBD.
Abundance in Group 1: increased abundance in inflamed ulcerative colitis
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonadota | ||
| Pseudomonas |
Revision editor(s): Yjung24
Signature 2
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-15
Source: Table 2
Description: Microbial Distribution of Taxa (Phylum and Genus) Found to Be Differentially Abundant According to Disease and Inflammatory State of Biopsy. ^aP = <0.05, ^bP = <0.01, ^cP = <0.001. Up and down arrows are comparisons to non-IBD.
Abundance in Group 1: decreased abundance in inflamed ulcerative colitis
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota | ||
| Alistipes | ||
| Parabacteroides |
Revision editor(s): Yjung24
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