The Simulator of the Human Intestinal Microbial Ecosystem (SHIME®)

This chapter provides a general explanation of the Simulator of the Human Intestinal Microbial Ecosystem (SHIME®). The SHIME is one of the few gut models that mimics the entire gastrointestinal tract incorporating stomach, small intestine and different colon regions. After a general description of the model’s development history and an overview of the specific features that distinguish SHIME from other gut models, we will give some insight in the general protocol of running SHIME experiments. However, with the SHIME being a highly flexible experimental setup, we also dedicate some part of this chapter discussing the modifications that can be performed, especially with respect to simulation of the mucosal (micro-)environment and interaction with host cells.