Fermentation reactor systems are a key platform in studying intestinal microflora, specifically with respect to questions surrounding the effects of diet. In this study, we develop computational representations of colon fermentation reactor systems as a way to assess the influence of three design elements (number of reactors, emptying mechanism, and inclusion of microbial immobilization) on three performance measures (total biomass density, biomass composition, and fibre digestion efficiency) using a fractional-factorial experimental design. It was determined that the choice of emptying mechanism showed no effect on any of the performance measures. Additionally, it was determined that none of the design criteria had any measurable effect on reactor performance with respect to biomass composition. It is recommended that model fermentation systems used in the experimenting of dietary effects on intestinal biomass composition be streamlined to only include necessary system design complexities, as the measured performance is not benefited by the addition of microbial immobilization mechanisms or semi-continuous emptying scheme. Additionally, the added complexities significantly increase computational time during simulation experiments. It was also noted that the same factorial experiment could be directly adapted using in vitro colon fermentation systems. (c) 2013, The Society for Biotechnology, japan. All rights reserved.