Fig. 1

Overview of the SHIME (top) and adapted SHIME (bottom) apparatus. The adapted SHIME used one reactor in a sequential setup to simulate the stomach under fasted conditions (red rectangle). The SHIME apparatus (top right) represents the gastrointestinal tract of adult humans and incorporates peristaltic pumps (for automated administration of secretions, acid or base), pH controllers (to register online pH), heating elements (to maintain temperature at 37 °C), and magnetic stirrers (to homogenize contents). The first two reactors use the ‘fill-and-draw’ principle to simulate different steps in food uptake and digestion, with peristaltic pumps adding a defined amount of SHIME feed and gastric secretions (pepsin and HCl) to the stomach compartment and pancreatic/bile liquid to the small intestinal compartment. Peristaltic pumps also ensure emptying of the respective reactors after specified intervals. The last three compartments—continuously stirred reactors with constant volume and pH control—simulate the ascending, transverse, and descending colon. Retention time and pH of the different vessels are chosen to resemble in vivo conditions in the different parts of the gastrointestinal tract. The TWINSHIME setup (top left) consists of two SHIME systems in parallel. SHIME, Simulator of the Human Intestinal Microbial Ecosystem (ProDigest, Belgium). Image provided courtesy of ProDigest