The complex microbial community that lives in the colon plays an important role in diverse biological pathways and is linked to many diseases including inflammatory bowel disease, obesity, and cancer. Defining how microbial interactions influence host cellular molecular pathways is crucial for exploring the potential therapeutic benefits of manipulating microbial communities to treat intestinal disorders. In 2009, pioneering work in the gastrointestinal field led to the development of intestinal organoid cultures, either derived from pluripotent embryonic or reprogrammed somatic stem cells,1 or from adult stem cells derived directly from intestinal tissue or biopsy specimens.