Crohn's disease is a common chronic inflammatory disease affecting the digestive tract. Although its exact causes are unknown, strong evidence points toward abnormal responses of the immune system to microbes living in the gut. Now, recent advancements in gene profiling technology have allowed scientists to take a closer look at this connection, revealing how specific bacteria interact with human cells to uncover the hidden patterns fueling inflammation. Researchers found more bacteria associated with intestinal tissue from patients with Crohn’s disease than in those without and that a greater number of bacteria-containing cells was linked to more severe disease. The team also identified 16 potentially beneficial bacterial species, including several newly discovered risk-modulating species, as well as 9 species considered to be pathogenic. Further analysis showed the presence of certain bacterial species triggered defense responses in specific human gut cells. These findings provide crucial new insight into the progression of Crohn’s disease at the cellular level and may pave the way toward the development of novel predictive biomarkers or even new microbe-based treatments for this debilitating condition.