Trial Outcomes & Findings for Advanced Metagenomic Analysis of Human Colonic Microbiota in Patients With Chronic GI Disorders (NCT NCT01099111)

Last Updated: 2014-05-22

Results Overview

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.

Recruitment status

COMPLETED

Target enrollment

225 participants

Primary outcome timeframe

1 - 2 weeks

Results posted on

2014-05-22

Participant Flow

Recruitment was conducted at KFMC (tertiary care medical center), starting 1/7/2010 and completed 29/9/2012. Demographic and clinical data were collected for all, together with performance of colonoscopy at entry and collection of samples as specified.

We were able to recruit the desired number for normal, IBS and UC groups. However, in view of strict inclusion and exclusion criteria, only 46 were recruited for CD and only 29 were recruited for CRC. Moreover, DNA extraction was not sufficient for some subjects at all groups that indicate replacing them with other patients.

Participant milestones

Participant milestones
Measure	Irritable Bowel Syndrome 50 subjects that exactly meet our inclusion \& exclusion criteria were recruited. Demographic and clinical data were entered for each during the introduction to the study and verifying acceptance to participate. Then after unified bowel preparation protocol, a full Colonoscopy was performed after signing the consent, during which mucosal washing samples were collected from the unified 4 colonic segment sites, as specified in methodology. Recruitment were completed on 08/05/2011, however, in view of insufficient DNA extraction of 5 subjects they have been replaced (on 28/07/2012) with other 5 subjects following exactly the same protocol. Now, all are identified as sufficient DNA extraction and had been enrolled into a comprehensive analysis of the gastrointestinal tract microbiota and its contribution on gut homeostasis by using state of the art metagenomics technology.	Ulcerative Colitis 50 subjects that exactly meet our inclusion \& exclusion criteria were recruited. Demographic and clinical data were entered for each during the introduction to the study and verifying acceptance to participate. Then after unified bowel preparation protocol, a full Colonoscopy was performed after signing the consent, during which mucosal washing samples were collected from the unified 4 colonic segment sites, as specified in methodology. Recruitment were completed on 05/06/2012, however, in view of insufficient DNA extraction of 3 subjects they have been replaced on 16/09/2012 with other 3 subjects following exactly the same protocol. Now, all are identified as sufficient DNA extraction and had been enrolled into a comprehensive analysis of the gastrointestinal tract microbiota and its contribution on gut homeostasis by using state of the art metagenomics technology.	Crohn's Disease 46 subjects that exactly meet our inclusion \& exclusion criteria were recruited. Demographic and clinical data were entered for each during the introduction to the study and verifying acceptance to participate. Then after unified bowel preparation protocol, a full Colonoscopy was performed after signing the consent, during which mucosal washing samples were collected from the unified 4 colonic segment sites, as specified in methodology. Recruitment were completed on 27/05/2012, however, in view of insufficient DNA extraction of 2 subjects they have been replaced on 05/09/2012 with other 2 subjects following exactly the same protocol. Now, all are identified as sufficient DNA extraction and had been enrolled into a comprehensive analysis of the gastrointestinal tract microbiota and its contribution on gut homeostasis by using state of the art metagenomics technology.	Colo Rectal Cancer 29 subjects that exactly meet our inclusion \& exclusion criteria were recruited. Demographic and clinical data were entered for each during the introduction to the study and verifying acceptance to participate. Then after unified bowel preparation protocol, a full Colonoscopy was performed after signing the consent, during which mucosal washing samples were collected from the unified 4 colonic segment sites, as specified in methodology. Recruitment were completed on 28/05/2012, and all have been identified as sufficient DNA extraction. Now, all are identified as sufficient DNA extraction and had been enrolled into a comprehensive analysis of the gastrointestinal tract microbiota and its contribution on gut homeostasis by using state of the art metagenomics technology.	Control: Normal Subjects 50 subjects that exactly meet our inclusion \& exclusion criteria were recruited. Demographic and clinical data were entered for each during the introduction to the study and verifying acceptance to participate. Then after unified bowel preparation protocol, a full Colonoscopy was performed after signing the consent, during which mucosal washing samples were collected from the unified 4 colonic segment sites, as specified in methodology. Recruitment were completed on 22/12/2010, however, in view of insufficient DNA extraction of 6 subjects they have been replaced on 19/09/2012 with other 6 subjects following exactly the same protocol. Now, all are identified as sufficient DNA extraction and had been enrolled into a comprehensive analysis of the gastrointestinal tract microbiota and its contribution on gut homeostasis by using state of the art metagenomics technology.
Overall Study STARTED	50	50	46	29	50
Overall Study COMPLETED	50	50	46	29	50
Overall Study NOT COMPLETED	0	0	0	0	0

Reasons for withdrawal

Withdrawal data not reported

Baseline Characteristics

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

Baseline characteristics by cohort

Baseline characteristics by cohort
Measure	Irritable Bowel Syndrome n=50 Participants 50 subjects that exactly meet our inclusion \& exclusion criteria were recruited. Demographic and clinical data were entered for each during the introduction to the study and verifying acceptance to participate. Then after unified bowel preparation protocol, a full Colonoscopy was performed after signing the consent, during which mucosal washing samples were collected from the unified 4 colonic segment sites, as specified in methodology. Recruitment were completed on 08/05/2011, however, in view of insufficient DNA extraction of 5 subjects they have been replaced (on 28/07/2012) with other 5 subjects following exactly the same protocol. Now, all are identified as sufficient DNA extraction and had been enrolled into a comprehensive analysis of the gastrointestinal tract microbiota and its contribution on gut homeostasis by using state of the art metagenomics technology.	Ulcerative Colitis n=50 Participants 50 subjects that exactly meet our inclusion \& exclusion criteria were recruited. Demographic and clinical data were entered for each during the introduction to the study and verifying acceptance to participate. Then after unified bowel preparation protocol, a full Colonoscopy was performed after signing the consent, during which mucosal washing samples were collected from the unified 4 colonic segment sites, as specified in methodology. Recruitment were completed on 05/06/2012, however, in view of insufficient DNA extraction of 3 subjects they have been replaced on 16/09/2012 with other 3 subjects following exactly the same protocol. Now, all are identified as sufficient DNA extraction and had been enrolled into a comprehensive analysis of the gastrointestinal tract microbiota and its contribution on gut homeostasis by using state of the art metagenomics technology.	Crohn's Disease n=46 Participants 46 subjects that exactly meet our inclusion \& exclusion criteria were recruited. Demographic and clinical data were entered for each during the introduction to the study and verifying acceptance to participate. Then after unified bowel preparation protocol, a full Colonoscopy was performed after signing the consent, during which mucosal washing samples were collected from the unified 4 colonic segment sites, as specified in methodology. Recruitment were completed on 27/05/2012, however, in view of insufficient DNA extraction of 2 subjects they have been replaced on 05/09/2012 with other 2 subjects following exactly the same protocol. Now, all are identified as sufficient DNA extraction and had been enrolled into a comprehensive analysis of the gastrointestinal tract microbiota and its contribution on gut homeostasis by using state of the art metagenomics technology.	Colo Rectal Cancer n=29 Participants 29 subjects that exactly meet our inclusion \& exclusion criteria were recruited. Demographic and clinical data were entered for each during the introduction to the study and verifying acceptance to participate. Then after unified bowel preparation protocol, a full Colonoscopy was performed after signing the consent, during which mucosal washing samples were collected from the unified 4 colonic segment sites, as specified in methodology. Recruitment were completed on 28/05/2012, and all have been identified as sufficient DNA extraction. Now, all are identified as sufficient DNA extraction and had been enrolled into a comprehensive analysis of the gastrointestinal tract microbiota and its contribution on gut homeostasis by using state of the art metagenomics technology.	Control: Normal Subjects n=50 Participants 50 subjects that exactly meet our inclusion \& exclusion criteria were recruited. Demographic and clinical data were entered for each during the introduction to the study and verifying acceptance to participate. Then after unified bowel preparation protocol, a full Colonoscopy was performed after signing the consent, during which mucosal washing samples were collected from the unified 4 colonic segment sites, as specified in methodology. Recruitment were completed on 22/12/2010, however, in view of insufficient DNA extraction of 6 subjects they have been replaced on 19/09/2012 with other 6 subjects following exactly the same protocol. Now, all are identified as sufficient DNA extraction and had been enrolled into a comprehensive analysis of the gastrointestinal tract microbiota and its contribution on gut homeostasis by using state of the art metagenomics technology.	Total n=225 Participants Total of all reporting groups
Age, Categorical <=18 years	0 Participants n=93 Participants	4 Participants n=4 Participants	11 Participants n=27 Participants	0 Participants n=483 Participants	0 Participants n=36 Participants	15 Participants n=10 Participants
Age, Categorical Between 18 and 65 years	45 Participants n=93 Participants	45 Participants n=4 Participants	34 Participants n=27 Participants	23 Participants n=483 Participants	41 Participants n=36 Participants	188 Participants n=10 Participants
Age, Categorical >=65 years	5 Participants n=93 Participants	1 Participants n=4 Participants	1 Participants n=27 Participants	6 Participants n=483 Participants	9 Participants n=36 Participants	22 Participants n=10 Participants
Age, Continuous	43.93 years STANDARD_DEVIATION 14.505 • n=93 Participants	34.42 years STANDARD_DEVIATION 12.586 • n=4 Participants	25.19 years STANDARD_DEVIATION 10.672 • n=27 Participants	55.03 years STANDARD_DEVIATION 10.137 • n=483 Participants	53.58 years STANDARD_DEVIATION 12.747 • n=36 Participants	42.43 years STANDARD_DEVIATION 12.71 • n=10 Participants
Sex: Female, Male Female	31 Participants n=93 Participants	34 Participants n=4 Participants	24 Participants n=27 Participants	14 Participants n=483 Participants	32 Participants n=36 Participants	135 Participants n=10 Participants
Sex: Female, Male Male	19 Participants n=93 Participants	16 Participants n=4 Participants	22 Participants n=27 Participants	15 Participants n=483 Participants	18 Participants n=36 Participants	90 Participants n=10 Participants
Region of Enrollment Saudi Arabia	50 participants n=93 Participants	50 participants n=4 Participants	46 participants n=27 Participants	29 participants n=483 Participants	50 participants n=36 Participants	225 participants n=10 Participants

PRIMARY outcome

Timeframe: 1 - 2 weeks

Population: Each participant colonic mucosal microbiota populations pattern were analysed, and then compared to control to look for specific enrichments. If the DNA extract was not enough for sequencing, then the participant sample was excluded, however analysis calculation was based on all enrolled participants. The number analyzed here represent all enrolled