Inflammasomes have emerged as central regulators of intestinal infection, immunity, and inflammation. Inflammasome activity mediates intestinal epithelial integrity, antimicrobial responses, and initiates inflammation through generation of the cytokines interleukin (IL-)1 and IL-18. Recent studies have identified an additional layer of inflammasome function in the intestine, namely, the control of intestinal microflora composition. Inflammasome-deficient mice show an aberrant microbial community which is dominantly transmissible to healthy mice. This dysbiosis in inflammasome-deficient mice has a profound impact on their physiology and pathophysiology, both locally in the intestine and systemically. Therefore, it is essential to consider the influence of the composition of microbial communities on experiments performed with inflammasome-deficient and other innate molecule-deficient mice, and to conduct experiments to control for potential dominant effects of the microflora on host responses. In this chapter, we provide experimental procedures to monitor inflammasome-mediated modifications of the intestinal microflora composition in mice and to test the resultant functional consequences of these changes in microbial communities and their transmission to cohoused mice.