The cause of Inflammatory Bowel Disease (IBD) is unknown, but intestinal bacteria—involved in the production of molecules that impact health—are widely accepted to play a key role. A significant proportion of IBD patients with pouches (surgically created rectums after the diseased colon is removed) continue to have inflammation similar to their previous disease, whereas non-IBD patients with pouches rarely have inflammation. Our results show key differences in the composition of an important class of bacteria-modified molecules known as secondary bile acids (SBAs) between these groups and that these SBAs reduce inflammation. We have also found that these SBA differences may be explained by reduced composition of specific gut bacteria. The research proposed will improve our understanding of the role of SBAs in controlling gut inflammation. Restoring the microbiome by correcting these compositional differences or administration of SBAs hold potential as new therapeutic targets for IBD.