The intestinal epithelial cells constitute the first line of defense against gut microbes, which includes secretion of various antimicrobial substances. Reactive oxygen species (ROS) are well characterized as part of the innate phagocytic immunity; however, a role in controlling microorganisms in the gut lumen is less clear. Here, we show a role for nitric oxide synthase (iNOS)- and NOX1-produced ROS in maintaining homeostasis of the gut microbiota. In vivo imaging revealed distinctly high levels of ROS in the ileum of normal healthy mice, regulated in accordance with the amount of gut bacteria. The ROS level was dependent on the nitric oxide and superoxide producers iNOS and NOX1, respectively, suggesting peroxynitrite as the effector molecule. In the ileum of iNOS- and NOX1-deficient mice, the bacterial load is increased and the composition is more cecum like. Our data suggest a unique role of ileum in maintaining homeostasis of gut microbes through production of ROS with potential importance for preventing reflux from the large intestine, bacterial overgrowth, and translocation.

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