The SHIME is a dynamic in vitro model of the human intestinal tract, composed of five double‐jacketed vessels, respectively simulating the stomach, small intestine and the three colon regions. In this experiment, only the first colon compartment was used (Fig. 5). Two SHIME units were used in parallel ('Twin‐SHIME') in order to obtain identical environmental conditions and identical microbial composition and activities for both units (Van den Abbeele et al., 2010 (link)). Whereas the first unit consisted of the conventional set‐up that only harbours luminal microbes (= luminal SHIME or L‐SHIME), the second unit was modified by incorporating a mucosal environment (= mucosal SHIME or M‐SHIME). In order to achieve a representative mucosal surface in the M‐SHIME, 100 mucin‐covered microcosms were added per 500 ml luminal suspension. The microcosms (length = 7 mm, diameter = 9 mm, total surface area = 800 m2/m3, AnoxKaldnes K1 carrier, AnoxKaldnes AB, Lund, Sweden) were coated by submerging them in mucin agar. To simulate the renewal of the mucus layer, half of the mucin‐covered microcosms were replaced daily by sterile ones.
The ascending compartment (500 ml) from both SHIME units was inoculated with 40 ml of a 1:5 dilution of fresh stools provided by a healthy human volunteer (25 years) who had no history of antibiotic treatment 6 months before the study. Inoculum preparation was done as previously described by Possemiers and colleagues (2004 (link)). Three times per day, 140 ml SHIME feed and 60 ml pancreatic juice were added to the stomach and small intestine respectively.