Chronic stress constitutes one of the strongest risk factors for depression and can disrupt various aspects of homeostasis, including gut microbiota composition. We found that stress-induced changes in gut microbiota promote depression and decrease adult hippocampal neurogenesis upon transfer to antibiotic-treated recipient mice. Subdiaphragmatic vagotomy abrogated the microbiota-induced effects on behavior and neurogenesis, suggesting that gut microbiota can influence brain plasticity and behavior through vagal afferents.