Advantages, Disadvantages and Limitations of the System

The advantages, disadvantages and limitations of the system are summarized in Table 27.1.

Table 27.1 Advantages and disadvantages to the SHIME® system


• Integrates the entire gastrointestinal tract

• Microbiome inoculation from different target groups: adult vs. infant, healthy vs. diseased (e.g. ulcerative colitis patients: Vermeiren et al. 2012) and animals (pig, dog)

• Colon-region specific research (Possemiers et al. 2006)

• Maintains microbiome stability over a long timeframe: possibility to monitor microbiome adaptation

• Mechanistic research by multi-parametric control

• Differentiation between mucosal and luminal microbiome in M-SHIME setup (Van den Abbeele et al. 2013)

• Parallel control and treatment in TWIN-SHIME setups

• Interindividual variability can be studied in a SHIME setup as unique features of an individual's microbiome are preserved. Limiting microbiome simulation to one colon region, eight different subjects can be simultaneously assessed


• Conventional SHIME setup lacks dialysis. Incorporation of dialysis modules is possible after small intestine digestion (Ceuppens et al. 2012) and colon digestion

• Lack of peristalsis, mixing is conducted by means of stirrers as normally performed in a standard dissolution apparatus

• Absence of host cells in conventional SHIME. Solved by coupling to HMI module with epithelial or immune cells (Possemiers et al. 2013; Marzorati et al. 2014)


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Possemiers S, Bolca S, Grootaert C, Heyerick A, Decroos K, Dhooge W et al (2006) The prenylflavonoid isoxanthohumol from hops (Humulus lupulus L.) is activated into the potent phytoestrogen 8-prenylnaringenin in vitro and in the human intestine. J Nutr 136:1862–1867

Possemiers S, Pinheiro I, Verhelst A, Van den Abbeele P, Maignien L, Laukens D et al (2013) A dried yeast fermentate selectively modulates both the luminal and mucosal gut microbiota and protects against inflammation, as studied in an integrated in vitro approach. J Agric Food Chem 61:9380–9392

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Vermeiren J, Van den Abbeele P, Laukens D, Visgnaes LK, De Vos M et al (2012) Decreased colonization of fecal Clostridium coccoides/Eubacterium rectale species from ulcerative colitis patients in an in vitro dynamic gut model with mucin environment. FEMS Microbiol Ecol 79:685–696

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Wittebolle L, Marzorati M, Clement L, Balloi A, Daffonchio D, Heylen K et al (2009) Initial community evenness favours functionality under selective stress. Nature 458:623–626

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