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Advanced Metagenomic Analysis of Human Colonic Microbiota in Patients With Chronic GI Disorders

This study has been completed.
King AbdulAziz City for Science and Technology
Information provided by (Responsible Party):
Ahmed Al Omair, King Fahad Medical City Identifier:
First received: April 1, 2010
Last updated: April 24, 2014
Last verified: April 2014

This clinical trial hypothesize that Gut Microbiota (bacteria, viruses, fungi)play a major role in the occurrence and progression of many chronic gastrointestinal diseases like Irritable Bowel Syndrome, Inflammatory Bowel Diseases and Colo-Rectal Cancer.

Hence, aims to study the spectrum of such microbiota in these patients as compared to normal subjects, by utilizing metagenomic techniques rather than cultural methods.

Irritable Bowel Syndrome
Colitis, Ulcerative
Crohn Disease
Colonic Neoplasms

Study Type: Observational
Study Design: Observational Model: Case Control
Time Perspective: Cross-Sectional
Official Title: Advanced Metagenomic Analysis of Human Colonic Microbiota in Patients With Chronic Gastrointestinal Disorders (IBS, IBD, CRC)

Resource links provided by NLM:

Further study details as provided by King Fahad Medical City:

Primary Outcome Measures:
  • Colonic-Mucosa Associated Microbial Species Per Compiled Participants in 5 Different Arms [ Time Frame: 1 - 2 weeks ]

    The entire mucosal microbial community were profiled using high-throughput DNA sequencing and microarray technology. The microarray approach is based on 16S rRNA gene targeted oligonucleotide allowing the rapid detection of thousands of DNA sequences simultaneously and thus constitutes an ideal tool to generate a comprehensive and holistic view of the gut microbial community in all participants of all study arms.

    Then they will be analysed between different colonic segments in each participant, pooled results of participants in each of the 5 arms will be compared to the measurable outcomes of other arms in general.

Biospecimen Retention:   Samples With DNA

Colonic washing samples from 4 specific segments (cecum, transverse, proximal sigmoid and rectum) of every subject will be retained for 16S rRNA analysis for the study purpose, and more samples will be retained for further analysis later on.

Samples from the unified colonic segments (each collected as 15 cc in each of four 20 cc tubes and stored in -70 Freezer) were completely recruited from 50 normal subjects, 50 IBS, 50 UC, 46 CD and only 29 CRC.

One to two tubes from each segment sample of all subjects have been utilized for DNA extraction and accepted if identified sufficient according to lab. Hence submitted for 16S rRNA analysis. Currently we are waiting for intra-cohort comparison of samples, then inter-cohort comparisons among different study groups will be done.

Enrollment: 225
Study Start Date: July 2010
Study Completion Date: March 2012
Primary Completion Date: January 2012 (Final data collection date for primary outcome measure)
Irritable Bowel Syndrome
only one Colonoscopy with mucosal washing samples collection at the time of recruitment
Ulcerative Colitis
only one Colonoscopy with mucosal washing samples collection at the time of recruitment
Crohn's Disease
only one Colonoscopy with mucosal washing samples collection at the time of recruitment
Colo Rectal Cancer
only one Colonoscopy with mucosal washing samples collection at the time of recruitment
Control: Normal Subjects
only one Colonoscopy with mucosal washing samples collection at the time of recruitment

  Show Detailed Description


Ages Eligible for Study:   16 Years to 70 Years   (Child, Adult, Senior)
Sexes Eligible for Study:   All
Accepts Healthy Volunteers:   Yes
Sampling Method:   Non-Probability Sample
Study Population
We propose to recruit our cohort of patients from the King Fahad Medical City in Riyadh (largest tertiary care hospital of Saudi MOH with wide open referral system), over one year between July 2010 and July of 2011. Fifty participants with each of the focus conditions (IBS, UC, CD, CRC) will be compared to fifty participants with no GI complaints and have a normal colonic mucosa (by endoscopic and histological examination).

Inclusion Criteria:

IBS: 50 consecutive patients presenting to KFMC GI service after launching the project on July 2010, will be recruited if they meet the following conditions:

  1. Meet the diagnostic criteria as per ROME-II classification and as judged by experienced consultants for not less than 5 years.
  2. IBS with diarrhea or constipation or mixed predominance pattern will be included.
  3. Standard diagnostic tests have to be done to exclude any possible organic lesion to explain the abdominal pain, and all have to be negative.

IBD: from the KFMC GI service database, 50 Ulcerative Colitis (UC) and 50 Crohn's Disease (CD) will be selected according to following:

  1. Confirmed diagnosis as CD or UC based on clinical, endoscopic and histological criteria.
  2. Specifically did not use antibiotics for last 6 months before enrollment.
  3. Detailed information about current treatment regimen has to be provided, and current use of 5-ASA, Steroid or Azathioprine will not hold from enrolling the patients as we cannot have patients off any one or more of these medications. (Obviously, we cannot exclude effects of these medications on microbiota, but it is not the focus of the current study).
  4. None of the patients selected would be on anti-TNF medications.

CRC: 50 consecutive cases of confirmed CRC as per histological diagnosis made by 2 experienced pathologists will be included. Feasibility to do full colonoscopy before any surgical resection would be a condition to recruit any patient.

Normal Subjects: 50 normal control groups that are matched for age and sex to the other 3 disease groups will be selected from consecutive CRC screening colonoscopy subjects who get referred to KFMC GI service during the study period, and proved to have no GI disorders. 25 will be selected from Urban and 25 from Rural areas of KSA.

Exclusion Criteria:

  1. Treatment with antibiotics for the last 6 months before enrollment.
  2. Absence of recent infective colitis, bowel obstruction, or colonic/small intestinal resection surgery.
  3. Not on any medication that may affect gut microbiota, like: cholestyramine, ursodeoxycholic acid, gut prokinetic agents.
  4. Refusal to comply with the unified bowel preparation instructions for all cases.
  Contacts and Locations
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Please refer to this study by its identifier: NCT01099111

Saudi Arabia
Riyadh, Saudi Arabia, 11525
Sponsors and Collaborators
King Fahad Medical City
King AbdulAziz City for Science and Technology
Principal Investigator: Ahmed O AlOmair, MD KFMC
Study Chair: Ali Al Shanqeeti, MD KACST
  More Information

Responsible Party: Ahmed Al Omair, Head, GI section + GI Consultant, King Fahad Medical City Identifier: NCT01099111     History of Changes
Other Study ID Numbers: 09 -116
243 - 29 - AT ( Other Grant/Funding Number: KACST (Saudi Arabia) )
Study First Received: April 1, 2010
Results First Received: March 22, 2014
Last Updated: April 24, 2014

Keywords provided by King Fahad Medical City:

Additional relevant MeSH terms:
Crohn Disease
Irritable Bowel Syndrome
Colitis, Ulcerative
Colonic Neoplasms
Inflammatory Bowel Diseases
Gastrointestinal Diseases
Digestive System Diseases
Intestinal Diseases
Colonic Diseases, Functional
Colonic Diseases
Colorectal Neoplasms
Intestinal Neoplasms
Gastrointestinal Neoplasms
Digestive System Neoplasms
Neoplasms by Site
Neoplasms processed this record on May 25, 2017