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Stability and Reproducibility of the System

As the SHIME® reactor is inoculated with a fecal microbiome, the latter needs an appropriate amount of time to adapt to the prevailing environmental conditions in the respective colon compartments. This adaptation process was studied more in detail by Possemiers et al. (2004) who monitored the increasing colonization of microbial groups of interest upon inoculation, as well as their metabolic activity. Highlyabundant groups such as Bacteroides obtained stable concentrations more easily, at 10 days, compared to less-abundant groups such as lactobacilli which needed 15 days of stabilization. To obtain a stable functionality in terms of short chain fatty acid production, an adaptation period of at least 15 days, even approaching 20 days, was needed. The length of stabilization obviously relates to the residence time that is imposed in the SHIME, but may also depend on the microbiome composition as such.

As the SHIME is a highly standardized system, and many digestive parameters are under control of the operator, it also leads to highly reproducible results. This is especially required when different products such as novel prebiotics, candidate drug components or new plant extracts, need to be compared with one another.

When it is not always possible to run different SHIMEs in parallel, for example because of the multitude of test compounds, SHIME experiments may need to be repeated. The scientist in charge needs to be cautious to conduct this experiment in exactly the same way and with the same inoculum to enable an adequate comparison between different compounds. Such reproducibility was previously tested for the conventional SHIME (without mucin-coated microcosms) and proven very effective in obtaining a reproducible microbial colonization process and accompanied metabolic activity (Van den Abbeele et al. 2010). Noteworthy, the authors found a small preferential colonization of Bacteroidetes and Clostridium cluster IX in the colon compartments in comparison with the stool sample. While the overall colonization profile was still representative of the in vivo colonization process, this slight bias has been a common observation for several dynamic models that work with luminal content only. Van den Abbeele et al. (2013) succeeded in removing this colonization selectivity by incorporating mucin-covered microcosms in the SHIME, thereby creating the M-SHIME or mucosal SHIME. Butyrate producing Clostridium clusters IV and XIVa were found to specifically colonize the mucosal environment thereby compensating for their lower abundance in the lumen.

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