Recent studies have suggested that alterations in the composition of the intestinal microbiota may play an important role in irritable bowel syndrome (IBS) symptoms. However, an association between the composition of the intestinal microbiota and IBS symptoms has not been clearly demonstrated. In the current issue of the Journal, Tana et al. suggest that altered intestinal microbiota contributes to the symptoms of IBS through increased levels of organic acids. In fecal samples, IBS patients had significantly higher numbers of Veillonella and Lactobacillus than healthy controls. They also showed significantly higher levels of acetic acid and propionic acid. Furthermore, IBS patients with high acetic acid or propionic acid levels presented more severe symptoms, impaired quality of life and negative emotions. These results are in accordance with the concept that the gut microbiota influences the sensory, motor and immune system of the gut and interacts with higher brain centers. Small intestinal bacterial overgrowth observed in a subset of IBS patients describes quantitative changes in the small intestinal microbiota. Data on qualitative changes in the gut microbiota in IBS patients are lacking. Different members of gut bacteria may have different influence on gut function. The concepts identified here may lead to the development of novel therapeutic strategies for IBS using manipulation of the intestinal microbiota.