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The gut governs digestion and nutrient absorption, is a promising target for drug delivery, and teems with active micro-organisms that can have remarkably strong effects on host health. Many of the materials that transit through it regularly are complex fluids composed of ingested/secreted polymers and active microbes. Despite their importance, however, little is known about the interactions between the gut and the complex fluids within it. By combining animal experiments, biophysical processing and characterization, and microscopy, we show how polymers abundant in the gut can alter the structure of the gut and its contents. These alterations could impact how microbes transit through the gut, potentially take up residence within it, and potentially infect it. Our results provide physical principles by which we can better understand the hydrodynamics of the gut. More broadly, this research stimulates new findings and questions at the interface of engineering, physics, and biology.