Intestinal ROS triggers stress-induced dysbiosis by dismantling the hypoxic barrier

Stress consistently disrupts the vertebrate gut microbiome, leading to negative health outcomes. However, how systemic stress translates into reproducible microbial dysbiosis remains poorly understood. While current research primarily focuses on late-stage compositional shifts, the early biochemical signals and microenvironmental alterations that precede and initiate this structural breakdown represent a critical knowledge gap. Here we show that stress destabilizes the gut microbiome through a cascade initiated by intestinal reactive oxygen species (ROS). In zebrafish, stress rapidly elicits intestinal ROS accumulation in the distal intestine, emerging within hours and preceding any detectable changes in microbial composition. This early oxidative response does not immediately restructure the community but instead induces a functional collapse: anaerobic fermentation is selectively suppressed and short-chain fatty acids (SCFAs) production sharply declines while community structure remains largely intact. The resulting SCFAs deficit weakens PPARγ-dependent epithelial metabolic programs, diminishes epithelial oxygen consumption, and erodes the physiological hypoxic barrier. Loss of this barrier re-engineers the luminal niche, enabling the relative enrichment of facultative pathobionts. Restoring epithelial bioenergetics or neutralizing intestinal ROS in zebrafish preserves hypoxia and prevents dysbiosis despite continued stress, identifying intestinal ROS as an early initiating signal of stress-induced dysbiosis. In restraint-stressed mice, the same ordered sequence—early ROS elevation, SCFAs decline, hypoxia loss, and the relative enrichment of facultative taxa—is likewise observed, supporting phenotypic and temporal conservation of this cascade. Our findings reveal that stress-induced dysbiosis is not a stochastic microbial drift, but a highly reproducible ecological cascade that is triggered by an early intestinal ROS burst in zebrafish and phenotypically conserved in mice. By shifting the paradigm from late-stage structural dysbiosis to the initial functional and microenvironmental collapse, we identify the maintenance of the intestinal hypoxic barrier as a critical therapeutic target for stress-related microbiome disorders. Video Abstract