Our team specialises in using advanced colon model systems to explore the human gut microbiome and its crucial role in health and disease.

The human gut microbiota is a remarkably diverse ecosystem, home to more than 1,000 microbial species including bacteria, viruses, fungi, and parasites. Together, these microorganisms form a community of around 100 trillion cells, with a collective genome 150 times larger than our own. The majority reside in the colon, making colon models a powerful tool for replicating this environment and uncovering new scientific insights.

We enable researchers to:

• Study how microbial communities differ between individuals
• Investigate how gut microbiota metabolise foods and bioactive compounds
• Advance knowledge that supports nutritional science and human health research

Types of model

Our facility is equipped with a range of cutting-edge in vitro gut models, each suited to different research needs.

Micro-matrix bioreactor

The Micro-Matrix offers 24 independent bioreactors in a microtiter plate format, each with separate controls. We use it to study interactions between the colonic microbiota and diets, foods, prebiotics, and probiotics. A typical run takes two to three days, making it ideal for high-throughput, short-term experiments.

Batch colon model

The batch model is the simplest, fastest, and most cost-effective way to mimic gut fermentation in vitro. It is primarily used to study microbiota interactions with dietary compounds under anaerobic conditions over short-term periods.

Continuous colon model

This system establishes a stable microbial ecosystem under physiologically relevant colon conditions, making it suitable for longer-term studies (three to five weeks).

It allows evaluation of both the spatial and temporal adaptation of the microbiota to dietary compounds, including microbial metabolism of ingredients. The model can also be run in a three-stage setup, with vessels replicating the ascending, transverse, and descending colon at pH values of 5.5, 6.2, and 6.8, respectively. Continuous replenishment of feed and removal of waste are required throughout the experiment.

SHIME (Simulator of the Human Intestinal Microbial Ecosystem)

SHIME is the most advanced colon model available at the facility. It consists of five vessels representing the stomach, small intestine, ascending colon, transverse colon, and descending colon. Nutrient feed passes sequentially through the system, closely mimicking physiological digestion.

SHIME is designed for long-term experiments lasting over seven weeks, with around two weeks needed each for stabilisation and control phases. This model enables highly detailed investigation of digestion, microbial adaptation, and metabolism across the entire gastrointestinal tract.

Training

We provide hands-on training for scientists interested in using these models and collaborate across diverse research projects within the Quadram Institute and with external partners.

Whether your goal is to understand the microbiome, test the effects of new dietary strategies, or explore microbiota–health interactions, the Colon Model Facility is here to support your research.