The QIB Colon Model

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.

Study Overview

• Status: Enrolling by invitation
• Conditions: Human Gut Microbiota
• Intervention / Treatment: Other: Stool sample collection

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:

1. a simple batch culture in which bacteria, media and test compounds are added to a single compartment and analysed over 24h
2. 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.

3. 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 Type: Interventional
• Enrollment (Estimated): 20
• Phase: Not Applicable

Contacts and Locations

Study Locations

• United Kingdom
  • Norfolk
    • Norwich, Norfolk, United Kingdom, NR4 7UA
      • Quadram Institute Bioscience

Participation Criteria

Eligibility Criteria

• Ages Eligible for Study: 18 years and older (Adult, Older Adult)
• Accepts Healthy Volunteers: Yes

Description

Inclusion Criteria:

• 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.

Exclusion Criteria:

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.

Study Plan

How is the study designed?

Design Details

• Primary Purpose: Basic Science
• Allocation: N/A
• Interventional Model: Single Group Assignment
• Masking: None (Open Label)

Number of Arms

1

Arms and Interventions

Participant Group / Arm	Intervention / Treatment
Experimental: Experimental arm; 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	Other: Stool sample collection; Collection of complete stool sample

What is the study measuring?

Primary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Measurement of 16S rDNA gene (%)	Measurement of 16S rDNA gene in human stool samples will reflect the bacterial population of the colon.	Across an initial period of ten years

Secondary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Methane concentration (mmol/L)	Measurement of methane concentration in gaseous production of human stool samples in colon model.	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.	Across an initial period of ten years
Glucosinolate concentration (mM)	Concentration of glucosinolates in the colon model milieu.	Across an initial period of ten years
Fiber concentration (mM)	Concentration of fiber in the colon model milieu.	Across an initial period of ten years

Collaborators and Investigators

• Sponsor: Quadram Institute Bioscience
• Investigators: Principal Investigator: Emad Shehata, Ph.D, Quadram Institute Bioscience

Publications and helpful links

General Publications

• Day-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.

Study record dates

Study Major Dates

• Study Start (Actual): December 18, 2015
• Primary Completion (Estimated): May 1, 2030
• Study Completion (Estimated): May 1, 2030

Study Registration Dates

• First Submitted: January 5, 2016
• First Submitted That Met QC Criteria: January 11, 2016
• First Posted (Estimated): January 12, 2016

Study Record Updates

• Last Update Posted (Actual): April 27, 2026
• Last Update Submitted That Met QC Criteria: April 22, 2026
• Last Verified: January 1, 2026

More Information

Terms related to this study

• Keywords: in vitro gut model, colon model, stool sample, faecal sample, gut microbiome
• Other Study ID Numbers: IFR01/2015

Plan for Individual participant data (IPD)

• Plan to Share Individual Participant Data (IPD)?: NO

Drug and device information, study documents

• product manufactured in and exported from the U.S.: No