The gut virome includes eukaryotic viruses and bacteriophages that can shape the gut bacterial community and elicit host responses. The virome may be implicated in diseases such as irritable bowel syndrome (IBS), where gut bacteria play an important role in pathogenesis. Herein we provide a comprehensive and longitudinal characterization of the virome including DNA and RNA viruses and paired multi-omics data in a cohort of healthy subjects and patients with IBS.