Irritable bowel syndrome (IBS) is characterized by recurrent abdominal pain and abnormal bowel habits. Even though the etiology and pathophysiology of IBS are largely unknown, alterations in the gut microenvironment have been proposed to be of relevance for symptom generation. In particular, alterations in gut microbiota and its metabolites have been proposed to be associated with IBS. There is growing evidence that an altered gut microbiota would in turn influence the host physiology. Elucidation of the molecular targets and causative factors in these host-microbiota interactions promises to reveal new possibilities to treat IBS. In this study, we have utilized metagenomic sequencing, RNA sequencing, mass-spectrometry-based metabolomics, and other approaches to identify possible treatment targets for IBS.