The QIB Colon Model

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.

• 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]