The relationship between gut microbiota and health has been of keen interest for the past several years. The physical inaccessibility of the colon makes alternative research approaches a valuable addition to the clinical research done in this area. In this seminar, we discuss the compuGUT - a numerical simulation tool for studying anaerobic digestion and physiology in the colon. The underlying mathematical model is a system of partial differential equations with stiff, non-linear source terms. Our discussion will focus on the construction of the model, with additional discussion of the potential integration of metabolomics information to extend and validate simulation results.