Whole-colon imaging in mice has revealed a continuous colonic mucus system, which forms a protective barrier between potentially harmful gut microbiota and host tissue by encapsulating fecal pellets as they form and as they are eliminated from the colon. While it remains unclear whether an analogous colonic mucus system exists in humans, understanding the role of the colonic tissue as a driver in mucus barrier formation may help in efforts to develop targeted therapeutic interventions for intestinal disease, like colitis. In mammals, the intestine is home to a dense and diverse commensal microbiota. The trillions of highly active microorganisms that reside there play an important role in both health and disease. The relationship between host and microbe is not always mutualistic - many types of common gut flora will have a pathogenic effect on host tissues if exposed, resulting in infection and inflammation. Separating the intestinal epithelium from the numerous hazards of the colonic environment is a thin layer of colon mucus, which is thought to regulate host-microbiota interaction. However, how this mucus system forms and functions across the entire length of the colon has been difficult to ascertain. Kirk Bergstrom and colleagues developed a whole-colon imaging method to analyze the origins and composition of colonic mucus in mice and evaluate its role in shielding host tissues from potentially harmful intestinal microorganisms during fecal elimination. Bergstom et al. found that the colonic mucus system consists of two different types of O-glycan rich mucus that form in different colonic regions. As fecal pellets form, proximal colon-derived mucus encapsulates the material, creating a primary barrier between the associated microbiota and host. As the pellets pass through the colon, mucus produced in the distal colonic regions form a secondary layer, which helps strengthen the mucus barrier and facilitates elimination. "Further investigation of how the mucus system works throughout the colon in humans is critical to provide targeted aid to the increasing number of people with intestinal disorders," write George Birchenough and Malin Johansson in a related Perspective.