Quality in Relation to Other Models with the Same Applicability

The SHIME® model is the sole in vitro model that integrates the entire gastrointestinal transit into one system. This is interesting to study for example digestibility of prebiotic substrates and its subsequent fermentability in the colon or the survival of pathogens or probiotics in the upper digestive tract before they reach the colon environment. Yet, one must consider that the conventional SHIME system operates without an absorption unit: this means that the nutritional medium for the SHIME must already be deprived of easily digestible carbohydrates or proteins that would normally be absorbed in the intestine.

The SHIME is the last of a generation of multi-compartment models that operate according to a semi-continuous stirred tank reactors setup. In comparison with the Reading model (Macfarlane et al. 1989) the SHIME connects the different compartments through peristaltic pumps. In terms of studying the gut microbiome over a long timeframe, both models would however be applicable.

In general, it must be stressed that the SHIME model has a strong emphasis on the ecological aspects of the colon microbiome. This entails that incubation experiments with the SHIME reactor are seldomly short and commonly take several weeks. This is put in place to look at the gradual adaptation of the microbiome to incoming substrates of interest (e.g. prebiotics or pharmaceuticals) or to evaluate the resilience of the microbial community against colonization by a (opportunistic) pathogen. Such research, which often necessitates an experimental period of more than a week to several weeks, strongly differs from the TIM-2 model, which monitors the microbiome on a shorter timeframe. One could conclude that short term experiments are highly suitable for evaluating the immediate metabolic potency of a carbohydrate or colonization ability of a microorganism of interest, while longterm experiments are primarily suitable to look at the adaptation of the microbial ecosystem to changing environmental conditions or inputs.

A last strong asset of the SHIME is its extension to M-SHIME—incorporating the mucosal microbiota (Van den Abbeele et al. 2013). While previous attempts primarily focused on the immediate and aspecific adhesion potency of gut microorganisms to mucin-covered glass slides, the integration of mucin-covered microcosms that can be replaced, to mimic desquamation, has been a breakthrough in the simulation of the mucosal microbiome and in the understanding of its dynamics.

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