Gut microbiota analyses of inflammatory bowel diseases from a representative Saudi population
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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
Alsulaiman RM, Al-Quorain AA, Al-Muhanna FA, Piotrowski S, Kurdi EA, Vatte C, Alquorain AA, Alfaraj NH, Alrezuk AM, Robinson F, Dowdell AK, Alamri TA, Hamilton L, Lad H, Gao H, Gandla D, Keating BJ, Meng R, Piening B, Al-Ali AK
Journal
BMC gastroenterology
Year
2023
Keywords:
Crohn’s disease, IBD, Inflammation, Microbiota, Saudi, Ulcerative colitis
BACKGROUND: Crohn's diseases and ulcerative colitis, both of which are chronic immune-mediated disorders of the gastrointestinal tract are major contributors to the overarching Inflammatory bowel diseases. It has become increasingly evident that the pathological processes of IBDs results from interactions between genetic and environmental factors, which can skew immune responses against normal intestinal flora. METHODS: The aim of this study is to assess and analyze the taxa diversity and relative abundances in CD and UC in the Saudi population. We utilized a sequencing strategy that targets all variable regions in the 16 S rRNA gene using the Swift Amplicon 16 S rRNA Panel on Illumina NovaSeq 6000. RESULTS: The composition of stool 16 S rRNA was analyzed from 219 patients with inflammatory bowel disease and from 124 healthy controls. We quantified the abundance of microbial communities to examine any significant differences between subpopulations of samples. At the genus level, two genera in particular, Veillonella and Lachnoclostridium showed significant association with CD versus controls. There were significant differences between subjects with CD versus UC, with the top differential genera spanning Akkermansia, Harryflintia, Maegamonas and Phascolarctobacterium. Furthermore, statistically significant taxa diversity in microbiome composition was observed within the UC and CD groups. CONCLUSIONS: In conclusion we have shown that there are significant differences in gut microbiota between UC, CD and controls in a Saudi Arabian inflammatory bowel disease cohort. This reinforces the need for further studies in large populations that are ethnically and geographically diverse. In addition, our results show the potential to develop classifiers that may have add additional richness of context to clinical diagnosis of UC and CD with larger inflammatory bowel disease cohorts.
Experiment 1
Reviewed Marked as Reviewed by Svetlana up on 2023-10-26
Subjects
- Location of subjects
- Saudi Arabia
- 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
- 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 diagnosed with inflammatory bowel disease (IBD) through colonoscopy examinations, for ulcerative colitis (UC)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 124
- Group 1 sample size Number of subjects in the case (exposed) group
- 84
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 2 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V9
- 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).
- raw counts
- 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)?
- No
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2023-10-26
Source: Supplementary File 14: Table S2
Description: Differential microbial abundance between ulcerative colitis (UC) and healthy controls
Abundance in Group 1: decreased abundance in ulcerative colitis (UC)
Revision editor(s): ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2023-10-26
Source: Supplementary File 14: Table S2
Description: Differential microbial abundance between ulcerative colitis (UC) and healthy controls
Abundance in Group 1: increased abundance in ulcerative colitis (UC)
Revision editor(s): ChiomaBlessing
Experiment 2
Reviewed Marked as Reviewed by Svetlana up on 2023-10-26
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 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 diagnosed with inflammatory bowel disease (IBD) through endoscopy examinations, for Crohn's disease (CD)
- Group 1 sample size Number of subjects in the case (exposed) group
- 135
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2023-10-26
Source: Supplementary File 15: Table S3
Description: Differential microbial abundance between Crohn's disease (CD) and healthy controls
Abundance in Group 1: decreased abundance in Crohn's disease (CD)
Revision editor(s): ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2023-10-26
Source: Supplementary File 15: Table S3, Figure 4: left plot
Description: Differential microbial abundance between Crohn's disease (CD) and healthy controls
Abundance in Group 1: increased abundance in Crohn's disease (CD)
Revision editor(s): ChiomaBlessing
Experiment 3
Reviewed Marked as Reviewed by Svetlana up on 2023-10-26
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- ulcerative colitis (UC)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 84
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2023-10-26
Source: Figure 4: right plot
Description: Differential microbial abundance between ulcerative colitis (UC) and Crohn's disease (CD)
Abundance in Group 1: increased abundance in Crohn's disease (CD)
| NCBI | Quality Control | Links |
|---|---|---|
| Turicibacter |
Revision editor(s): ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2023-10-26
Source: Figure 4, Plot 2
Description: Differential microbial abundance between ulcerative colitis (UC) and Crohn's disease (CD)
Abundance in Group 1: decreased abundance in Crohn's disease (CD)
Revision editor(s): ChiomaBlessing, Peace Sandy
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