Microscopically, the inflammation of ulcerative colitis is confined primarily to the mucosa. Here, the mucosa is eroded by an inflammatory process with ulceration that undermines surrounding mucosa. The resulting ulceration often has a flask shape (Erlenmeyer flask...triggering flashbacks to organic chemistry).

Zinc is a key micronutrient for both microbial pathogens and human host cells, particularly immune cells. Zinc can be concentrated by phagocytic cells, particularly neutrophils containing a cytoplasmic protein call calprotectin. These phagocytes can then signal T lymphocytes for an adaptive immune response, and they can concentrate free zinc toxic to microbes. Measurement of calprotectin can provide a means for assessing the magnitude of an inflammatory reaction, such as stool calprotectin measurement to gauge inflammatory bowel disease.