Background and Purpose We attempted to clarify a role of prostaglandin (PG) I2 and its specific receptor, IP in the pathogenesis of irritable bowel syndrome (IBS). Experimetal Approach Using a maternal separation (MS)-induced rat IBS model, the effect of IP agonist on the development of IBS phenotype such as visceral hypersentivity and depressive state. To further investigate the mechanisms of IP signaling on IBS phenotypes, serum hormone, metabolites and fecal microbiota were examined. Key Results Administration of beraprost (BPS), a specific IP agonist, improved visceral hypersensitivity and depressive state with decreased serum corticotropin-releasing factor (CRF) level in the IBS rats. In serum metabolome analysis, 1-methylnicotinamide (1-MNA) was identified as a possible candidate for a clue metabolite of pathogenesis of. The serum 1-MNA levels revealed inverse correlation to the level of visceral sensitivity, and positive correlation to a depression marker, immobilizing time. Administration of 1-MNA induced visceral hypersensitivity and depression with increased levels of serum CRF. Fecal microbiota by T-RFLP analysis revealed the proportion of clostridium cluster XI, XⅣa and XVⅢ was significantly changed in MS-induced IBS rats treated with BPS. Fecal microbiota transplant of BPS-treated rats improved visceral hypersensitivity and depression in MS-induced IBS rats. Conclusion and Implication PGI2-IP signaling plays an important role in IBS phenotypes such as visceral hypersensitivity and depressive state. BPS modified microbiota, thereby inhibition of 1-MNA-CRF pathway, followed by improvement of MS-induced IBS phenotype. These results suggest that the PGI2-IP signaling could be considered to be a therapeutic option for IBS.