Irritable bowel syndrome (IBS) is a common and painful gastrointestinal disorder that is difficult to treat. IBS pathogenesis likely involves the gut microbiome, but no consistent changes have yet been identified. However, most research to date has focused on the community composition of the microbiome. So, a new study instead used a multi-omics approach to identify functional shifts in the microbiome. The researchers found key changes in the bacterial community, microbial gene expression, and fecal metabolite profile. The overall multi-omics profile was characterized by an increased ability to utilize fermentable carbohydrates, a result consistent with the previously observed clinical benefit of reducing dietary fermentable carbohydrates. The researchers also developed a multi-omics classifier for IBS that outperformed single-dataset-based classifiers. The subtypes of IBS, diarrhea- and constipation-predominant, could also be distinguished by a classifier based on metabolites and microbial transcripts, which implies that microbial metabolic activity may play a key role in dictating IBS bowel habit alterations. Taken together, the results indicate that an integrative assessment of microbial function is needed to investigate the role of the microbiome in IBS and that multi-omics approaches like this could lead to novel microbiome-related therapeutic targets.