Inflammatory bowel disease is accompanied by a number of changes in the intestines, such as a change in epithelial permeability, a change in the composition of the microorganisms, and altered levels of antimicrobial substances that are secreted by cells lining the gut. Finding out whether changes are a cause or an effect of the inflammation is difficult. Sahar El Aidy, a microbiologist at the University of Groningen (the Netherlands), together with colleagues from San Diego (US), have now teased out the causal chain leading to inflammation. Their results were published in the journal Gut Microbes on 29 May.