Human Gut MicrobiotaNCT02653001
The QIB Colon Model
A study testing Stool sample collection in people with Human Gut Microbiota, run by Quadram Institute Bioscience at 1 site in United Kingdom.
Trial summary
The aim of this project is to establish a list of volunteers willing and able to donate stool samples for use in the model colon so as to facilitate research directed toward understanding the basic science underlying the interactions between the gut microbiome, potential external modifiers, and health. Read more about this study
- Who is it for?
- Ages 18 years and olderHealthy volunteers can take part
- Conditions the study is for
- Human Gut Microbiota
- What is being tested?
- Stool sample collection
- Could I receive a placebo?
- No, everyone receives an active treatment
- How many people
- 20 participants
- Where
- 1 siteUnited Kingdom
- Study dates
- 18 Dec 2015to May 2030
- Phase
- Interventional
- Are there results?
- Not yet: the study is under way
Key requirements
Who can take part, as listed by the sponsor. Only the study team can confirm whether you are eligible, so take this list to your doctor.
- Ages 18 years and older
- All sexes
- Healthy volunteers accepted
- Adult, Older adult
Who may be able to join
- Live or work within 10 miles of the Norwich Research Park.
- Having a normal bowel habit; assessed as regular defecation between 3 times a day and 3 times a week, with a form similar to 3-5 on the Bristol Stool Chart.
- Do not have any diagnosed chronic gastrointestinal health problem, such as irritable bowel syndrome, inflammatory bowel disease, or coeliac disease.
Who cannot join
- This will depend on individual experiments but in most cases samples will not be collected from individuals:
- who have used antibiotics or probiotics in the last 2 months.
- who are pregnant or breast feeding.
- who have recently used other medications or food supplements (considered on a study-specific basis).
- who have recently had an operation requiring general anaesthetic.
- who have had a gastrointestinal upset, such as vomiting or diarrhoea within the last 72hrs.
Trial locations and contacts
1 site in 1 country. Contact the study team or a site near you to ask about taking part.
United Kingdom1 site
Quadram Institute Bioscience
Norwich, Norfolk, NR4 7UA
About this study
Official title: Stool Sample Collection for Research Using the In-vitro QIB Colon Model
The aim of this project is to establish a list of volunteers willing and able to donate stool samples for use in the model colon so as to facilitate research directed toward understanding the basic science underlying the interactions between the gut microbiome, potential external modifiers, and health.
Read the detailed description
Adult volunteers will be recruited to donate stool samples for laboratory-based experiments. Once the sample has arrived at QIB 50-100g will be added to the colon model and, depending on the system used, either cultured for 24h or for up to 40 days. During this time, factors under investigation will be added to the model.
Samples added mimic food chyme arriving at the ileal-caecal valve in the intestinal tract. At this stage digested, but non-absorbed food components plus cells and mucous shed from the lining of the small intestine enter the large intestine. Samples of bacteria and media can be taken at any point during the incubation.
Four models are used:
- a simple batch culture in which bacteria, media and test compounds are added to a single compartment and analysed over 24h
- a three compartment model with continuous flow of media, test compounds and bacteria from the entrance port of the first chamber to the exit of the third chamber mimicking movement through the three main compartments of the colon. This model allows for a stable bacterial population to be established before addition of test compounds, and can remain viable for up to 40 days. In the case of these longer incubations, multiple time points can allow for quite complex experiments looking at interactions between bacteria, food and pharmaceutical products where different factors are added at different time points.
- a 24-well cassette-based fermenter system (Micro-Matrix Bioreactor) 4. a dynamic model SHIME (Simulator of the Human Intestinal Microbial Ecosystem) (Figure 4).
The SHIME model which is currently the most representative in vitro combined simulation of the gastrointestinal tract in including the three parts of the colon. It's used to study the gut microbiota, and how it interacts with food, drugs, and pathogens.
Samples collected during the incubation will be analysed by centrifuging the sample to create a pellet containing bacteria and a supernatant containing a wide range of metabolites. The bacteria will be analysed by extracting their DNA for genomic analysis or using RNA based approaches. On occasion, conventional microbiological techniques might be used. The supernatant will be filter sterilised prior to analysis of its chemical composition by techniques such as mass spectrometry, gel electrophoresis, or chromatography. Alternatively the supernatant may be added to cell lines to model the interaction between the bacterial ecosystem and the cells lining the colon.
- Conditions
- Human Gut Microbiota
- Being tested
- Stool sample collection
- Keywords
- in vitro gut model, colon model, stool sample, faecal sample, gut microbiome
What participants receive
What participants receive. In a randomised study each person is assigned to one group by chance.
Stool sample collectionOther
Collection of complete stool sample
| Study group | Role | What they receive |
|---|---|---|
| Experimental arm | Experimental | Stool sample collection: Stool samples collected from study participants will be introduced into the colon model to enhance our understanding of the colonic bacterial ecosystem in response to various food components, drugs or biological therapies, and/or to allow investigation the impact of the bacterial ecosystem itself on these added components Receives: Other: Stool sample collection |
What is being measured
The primary outcome is the main question the study is designed to answer.
Measurement of 16S rDNA gene (%)
Measurement of 16S rDNA gene in human stool samples will reflect the bacterial population of the colon.
Measured: Across an initial period of ten years
Secondary outcomes (4)
Methane concentration (mmol/L)
Measurement of methane concentration in gaseous production of human stool samples in colon model.
Measured: Across an initial period of ten years
Concentration of short chain fatty acids (mM)
Concentration of short chain fatty acids in the colon model milieu.
Measured: Across an initial period of ten years
Glucosinolate concentration (mM)
Concentration of glucosinolates in the colon model milieu.
Measured: Across an initial period of ten years
Fiber concentration (mM)
Concentration of fiber in the colon model milieu.
Measured: Across an initial period of ten years
Timeline
From the start of the study to its completion; the mark is today. Estimated dates are the sponsor’s plan.
- First posted12 Jan 2016 (estimated)
- Study start18 Dec 2015
- Primary completionMay 2030 (estimated)
- Study completionMay 2030 (estimated)
Resources
- Official record on ClinicalTrials.govThe registry entry this page is built from, with its full change history.
- Publications (2)Papers the sponsor has linked to this study.
- Other trials for Human Gut MicrobiotaStudies of the same condition, open and under way.
- What the trial phases meanHow a treatment moves from first tests in people to approval.
More details
For doctors and researchers: how the study is designed, who runs it, and its registry IDs.
Study design
- Study type
- Interventional
- Phase
- Phase N/A
- Primary purpose
- Basic science
- Allocation
- Not applicable
- Intervention model
- Single group
- Masking
- None (open label)
- Enrolment
- 20 participants (estimated)
Sponsor and investigators
- Lead sponsor
- Quadram Institute Bioscience
- Sponsor type
- University, hospital or other
- Responsible party
- Sponsor
- Investigators
- Emad Shehata, Ph.D, Principal investigator, Quadram Institute Bioscience
IDs, dates and publications
- ClinicalTrials.gov ID
- NCT02653001
- Sponsor's protocol ID
- IFR01/2015
- Status last verified
- Jan 2026
- First submitted
- 5 Jan 2016
- Last updated
- 27 Apr 2026
- Results posted
- No
- Data monitoring committee
- No
- Individual data sharing
- No
Publications
Haarhuis JE, Day-Walsh P, Shehata E, Savva GM, Peck B, Philo M, Kroon PA. A Pomegranate Polyphenol Extract Suppresses the Microbial Production of Proatherogenic Trimethylamine (TMA) in an In Vitro Human Colon Model. Mol Nutr Food Res. 2025 Oct;69(20):e70166. doi: 10.1002/mnfr.70166. Epub 2025 Jun 29.
PubMed 40583322Day-Walsh P, Shehata E, Saha S, Savva GM, Nemeckova B, Speranza J, Kellingray L, Narbad A, Kroon PA. The use of an in-vitro batch fermentation (human colon) model for investigating mechanisms of TMA production from choline, L-carnitine and related precursors by the human gut microbiota. Eur J Nutr. 2021 Oct;60(7):3987-3999. doi: 10.1007/s00394-021-02572-6. Epub 2021 May 2.
PubMed 33934200
Study at a glance
From the registry record, last updated by the sponsor on 27 Apr 2026. Recruitment status is as the sponsor reported it: confirm with the study team.
- Official title
- Stool Sample Collection for Research Using the In-vitro QIB Colon Model
- ClinicalTrials.gov ID
- NCT02653001
- Acronym / sponsor ID
- IFR01/2015
- Conditions
- Human Gut Microbiota
- Keywords
- in vitro gut model, colon model, stool sample, faecal sample, gut microbiome
- Study type
- Interventional
- Recruitment status
- Enrolling by invitation
- Enrolment
- 20 participants (estimated)
- Lead sponsor
- Quadram Institute BioscienceUniversity, hospital or other
- Study start
- 18 Dec 2015 (actual)
- Primary completion
- May 2030 (estimated)
- Study completion
- May 2030 (estimated)
- First posted
- 12 Jan 2016 (estimated)
- Results
- Not posted in the source record
Clinical summary
The research question as the sponsor registered it. This describes what the study plans to test, not what it found.
The aim of this project is to establish a list of volunteers willing and able to donate stool samples for use in the model colon so as to facilitate research directed toward understanding the basic science underlying the interactions between the gut microbiome, potential external modifiers, and health.
Detailed description
Adult volunteers will be recruited to donate stool samples for laboratory-based experiments. Once the sample has arrived at QIB 50-100g will be added to the colon model and, depending on the system used, either cultured for 24h or for up to 40 days. During this time, factors under investigation will be added to the model.
Samples added mimic food chyme arriving at the ileal-caecal valve in the intestinal tract. At this stage digested, but non-absorbed food components plus cells and mucous shed from the lining of the small intestine enter the large intestine. Samples of bacteria and media can be taken at any point during the incubation.
Four models are used:
- a simple batch culture in which bacteria, media and test compounds are added to a single compartment and analysed over 24h
- a three compartment model with continuous flow of media, test compounds and bacteria from the entrance port of the first chamber to the exit of the third chamber mimicking movement through the three main compartments of the colon. This model allows for a stable bacterial population to be established before addition of test compounds, and can remain viable for up to 40 days. In the case of these longer incubations, multiple time points can allow for quite complex experiments looking at interactions between bacteria, food and pharmaceutical products where different factors are added at different time points.
- a 24-well cassette-based fermenter system (Micro-Matrix Bioreactor) 4. a dynamic model SHIME (Simulator of the Human Intestinal Microbial Ecosystem) (Figure 4).
The SHIME model which is currently the most representative in vitro combined simulation of the gastrointestinal tract in including the three parts of the colon. It's used to study the gut microbiota, and how it interacts with food, drugs, and pathogens.
Samples collected during the incubation will be analysed by centrifuging the sample to create a pellet containing bacteria and a supernatant containing a wide range of metabolites. The bacteria will be analysed by extracting their DNA for genomic analysis or using RNA based approaches. On occasion, conventional microbiological techniques might be used. The supernatant will be filter sterilised prior to analysis of its chemical composition by techniques such as mass spectrometry, gel electrophoresis, or chromatography. Alternatively the supernatant may be added to cell lines to model the interaction between the bacterial ecosystem and the cells lining the colon.
Study design
- Primary purpose
- Basic science
- Allocation
- Not applicable
- Intervention model
- Single group
- Masking
- None (open label)
- Number of arms
- 1
| Arm | Type | Receives |
|---|---|---|
| Experimental arm | Experimental | Other: Stool sample collectionStool sample collection: Stool samples collected from study participants will be introduced into the colon model to enhance our understanding of the colonic bacterial ecosystem in response to various food components, drugs or biological therapies, and/or to allow investigation the impact of the bacterial ecosystem itself on these added components |
Who may qualify
- Ages
- 18 years and older
- Sex
- All
- Healthy volunteers
- Accepted
- Age groups
- Adult, Older adult
Key inclusion criteria (3 listed)
- Live or work within 10 miles of the Norwich Research Park.
- Having a normal bowel habit; assessed as regular defecation between 3 times a day and 3 times a week, with a form similar to 3-5 on the Bristol Stool Chart.
- Do not have any diagnosed chronic gastrointestinal health problem, such as irritable bowel syndrome, inflammatory bowel disease, or coeliac disease.
Key exclusion criteria (6 listed)
- This will depend on individual experiments but in most cases samples will not be collected from individuals:
- who have used antibiotics or probiotics in the last 2 months.
- who are pregnant or breast feeding.
- who have recently used other medications or food supplements (considered on a study-specific basis).
- who have recently had an operation requiring general anaesthetic.
Eligibility is decided by the study team after screening; this overview does not establish that a patient qualifies. Full inclusion and exclusion criteria.
Interventions
| Intervention | Type | Arms |
|---|---|---|
| Stool sample collectionCollection of complete stool sample | Other | Experimental arm |
Primary outcome
Measurement of 16S rDNA gene (%)
Time frame: Across an initial period of ten years
Measurement of 16S rDNA gene in human stool samples will reflect the bacterial population of the colon.
4 secondary outcomes
Methane concentration (mmol/L)
Time frame: Across an initial period of ten years
Concentration of short chain fatty acids (mM)
Time frame: Across an initial period of ten years
Glucosinolate concentration (mM)
Time frame: Across an initial period of ten years
Fiber concentration (mM)
Time frame: Across an initial period of ten years
Results and safety
This study is still under way. Results are not available in the source record yet.
Research links
- Official record on ClinicalTrials.govLast updated by the sponsor 27 Apr 2026.
- Derived from this study: PubMed 40583322Haarhuis JE, Day-Walsh P, Shehata E, Savva GM, Peck B, Philo M, Kroon PA. A Pomegranate Polyphenol Extract Suppresses the Microbial Production of Proatherogenic Trimethylamine (TMA) in an In Vitro Human Colon Model. Mol Nutr Food Res. 2025 Oct;69(20):e70166. doi: 10.1002/mnfr.70166. Epub 2025 Jun 29.
- Derived from this study: PubMed 33934200Day-Walsh P, Shehata E, Saha S, Savva GM, Nemeckova B, Speranza J, Kellingray L, Narbad A, Kroon PA. The use of an in-vitro batch fermentation (human colon) model for investigating mechanisms of TMA production from choline, L-carnitine and related precursors by the human gut microbiota. Eur J Nutr. 2021 Oct;60(7):3987-3999. doi: 10.1007/s00394-021-02572-6. Epub 2021 May 2.
- Individual participant dataSharing planned: No
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Referral and contact
AzTrials does not enrol participants or take referrals. Contact the study team or a site listed below; they decide who can take part.
Emad Shehata, Ph.D principal investigator
Quadram Institute Bioscience
1 site in 1 country: see every site and its status.
Questions about this trial
What is this clinical trial studying?
A study testing Stool sample collection in people with Human Gut Microbiota, run by Quadram Institute Bioscience at 1 site in United Kingdom.
The full registered description is in the About this study section and the official record.
Who may be eligible to take part?
The sponsor lists 3 inclusion and 6 exclusion criteria. Eligibility is decided by the study team after screening, so read the full criteria and contact a listed site.
Is this clinical trial currently recruiting?
The record says: enrolling by invitation, as of the sponsor's last update on 27 Apr 2026. Status can change between updates, so confirm with the study contact before making plans.
Where is the study taking place?
The record lists 1 site in United Kingdom. Whether a site is taking part right now should be confirmed with that site. See every site.
What are the possible benefits and risks?
They depend on the study and the treatment, and no study can promise a benefit. The study team explains the known risks during informed consent, before anyone joins; the record itself does not list them.
Are results available for this study?
This study is still under way. Results are not available in the source record yet.
How can a doctor refer a patient or contact the research team?
The record lists no contact. The official record names the sponsor, who can be asked directly. AzTrials does not enrol participants or take referrals.
What does the primary outcome measure?
Measurement of 16S rDNA gene (%) (time frame: Across an initial period of ten years). It is what the study was designed to measure, not a finding.
Where can I read the original study information?
On the ClinicalTrials.gov record for NCT02653001, which also lists 2 linked publications.
Does a listing mean the treatment is approved or proven to work?
No. A listing means the study is registered. It does not show that the treatment is safe, works, or is approved by a regulator.
How often is this information updated?
AzTrials copies changed records from ClinicalTrials.gov every night and reloads the whole registry every week. The sponsor last updated this record on 27 Apr 2026.