Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease
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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.
Authors
Nishino K, Nishida A, Inoue R, Kawada Y, Ohno M, Sakai S, Inatomi O, Bamba S, Sugimoto M, Kawahara M, Naito Y, Andoh A
Journal
Journal of gastroenterology
Year
2018
Keywords:
16S rRNA, IBD, Mucosa-associated microbiome
BACKGROUND: The mucosa-associated gut microbiota directly modulates epithelial and mucosal function. In this study, we investigated the mucosa-associated microbial community in patients with inflammatory bowel disease (IBD), using endoscopic brush samples. METHODS: A total of 174 mucus samples from 43 patients with ulcerative colitis (UC), 26 with Crohn's disease (CD) and 14 non-IBD controls were obtained by gentle brushing of mucosal surfaces using endoscopic cytology brushes. The gut microbiome was analyzed using 16S rRNA gene sequencing. RESULTS: There were no significant differences in microbial structure among different anatomical sites (the ileum, cecum and sigmoid colon) within individuals. There was, however, a significant difference in microbial structure between CD, UC and non-IBD controls. The difference between CD and non-IBD controls was more marked than that between UC patients and non-IBD controls. α-Diversity was significantly lower in UC and CD patients than non-IBD controls. When comparing CD patients with non-IBD controls, the phylum Proteobacteria was significantly increased and the phyla Firmicutes and Bacteroidetes were significantly reduced. These included a significant increase in the genera Escherichia, Ruminococcus (R. gnavus), Cetobacterium, Actinobacillus and Enterococcus, and a significant decrease in the genera Faecalibacterium, Coprococcus, Prevotella and Roseburia. Comparisons between CD and UC patients revealed a greater abundance of the genera Escherichia, Ruminococcus (R. gnavus), Clostridium, Cetobacterium, Peptostreptococcus in CD patients, and the genera Faecalibacterium, Blautia, Bifidobacterium, Roseburia and Citrobacter in UC patients. CONCLUSIONS: Mucosa-associated dysbiosis was identified in IBD patients. CD and UC may be distinguishable from the mucosa-associated microbial community structure.
Experiment 1
Reviewed Marked as Reviewed by Atrayees on 2023-6-27
Subjects
- Location of subjects
- Japan
- 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
- Non-IBD
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- CD
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Crohn's disease activity index <150
- Group 0 sample size Number of subjects in the control (unexposed) group
- 14
- Group 1 sample size Number of subjects in the case (exposed) group
- 26
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Current
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-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
- T-Test
- 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
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-6-27
Source: Figure 5(a)
Description: Comparative analyses of the taxonomic composition of the microbial community at the genus level. Representative genera with significant differences between groups are presented.
Abundance in Group 1: increased abundance in CD
| NCBI | Quality Control | Links |
|---|---|---|
| Actinobacillus | ||
| Cetobacterium | ||
| Clostridium | ||
| Enterococcus | ||
| Escherichia | ||
| Lachnoanaerobaculum | ||
| Mediterraneibacter gnavus | ||
| unclassified Bacteroidota |
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-6-27
Source: Figure 5(a)
Description: Comparative analyses of the taxonomic composition of the microbial community at the genus level. Representative genera with significant differences between groups are presented.
Abundance in Group 1: decreased abundance in CD
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes | ||
| Coprococcus | ||
| Faecalibacterium | ||
| Gemmiger | ||
| Lachnospiraceae | ||
| Oscillospiraceae | ||
| Prevotella | ||
| Roseburia | ||
| Ruminococcus bromii | ||
| Pseudomonas |
Revision editor(s): Aiyshaaaa
Experiment 2
Reviewed Marked as Reviewed by Atrayees on 2023-6-27
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-IBD controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- UC
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The patient who is diagnosed from ulcerative colitis(UC).
- Group 1 sample size Number of subjects in the case (exposed) group
- 43
Lab analysis
Statistical Analysis
- Statistical test
- Welch's T-Test
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-6-27
Source: Figure 5(b)
Description: Comparative analyses of the taxonomic composition of the microbial community at the genus level. Representative genera with significant differences between groups are presented
Abundance in Group 1: increased abundance in UC
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium | ||
| Blautia | ||
| Citrobacter | ||
| Lactobacillus | ||
| Veillonella | ||
| unclassified Bacillota |
Revision editor(s): Aiyshaaaa
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-6-27
Source: Figure 5(b)
Description: Comparative analyses of the taxonomic composition of the microbial community at the genus level. Representative genera with significant differences between groups are presented.
Abundance in Group 1: decreased abundance in UC
| NCBI | Quality Control | Links |
|---|---|---|
| Brachyspira | ||
| Helicobacter | ||
| Odoribacter | ||
| Alistipes | ||
| Gemmiger | ||
| Pseudomonas | ||
| Coprococcus | ||
| Prevotella |
Revision editor(s): Aiyshaaaa
Experiment 3
Reviewed Marked as Reviewed by Atrayees on 2023-6-27
Differences from previous experiment shown
Subjects
- 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
- UC
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- CD
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The patient who is diagnosed from Crohn's disease(CD).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 43
- 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
- unchanged
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-6-27
Source: Figure 5(c)
Description: Comparative analyses of the taxonomic composition of the microbial community at the genus level. Representative genera with significant differences between groups are presented
Abundance in Group 1: increased abundance in CD
| NCBI | Quality Control | Links |
|---|---|---|
| Cetobacterium | ||
| Clostridium | ||
| Escherichia | ||
| Morganella | ||
| Peptostreptococcus | ||
| Mediterraneibacter gnavus |
Revision editor(s): Aiyshaaaa
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-6-27
Source: Figure 5(c)
Description: Comparative analyses of the taxonomic composition of the microbial community at the genus level. Representative genera with significant differences between groups are presented.
Abundance in Group 1: decreased abundance in CD
| NCBI | Quality Control | Links |
|---|---|---|
| Eggerthella | ||
| Butyricicoccus | ||
| Lachnospira | ||
| Gemmiger | ||
| Citrobacter | ||
| Roseburia | ||
| Bifidobacterium | ||
| Blautia | ||
| Faecalibacterium |
Revision editor(s): Aiyshaaaa
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