Background: The gut microbiota composition is closely linked to both the pathogenesis of inflammatory bowel disease (IBD) and the response to therapy. Intestinal dysbiosis can alter the host bile acid profile, which regulates immunity via the immunosuppressive bile acid receptor Takeda G protein-coupled receptor 5 (TGR5). This study investigates whether dysbiosis in IBD affects microbial conversion of bile acids and bile acid-induced bioactivity of TGR5. Metagenomic sequencing was performed on fecal samples from 33 patients with Crohn's Disease, 28 patients with ulcerative colitis, and 21 healthy controls. Microbial bile acid pathways were analyzed within the metabolic networks. Bile acid profiles in stool and plasma were measured by mass spectrometry, and TGR5 bioactivity was quantified. About this Repository: This repository contains the R-based workflow for the project's data analysis. Therefore, it includes R scripts for data analysis and visualization, input data, i.e., bile acid profiles in stool and blood, and metagenome-derived microbiome metrics, such as relative abundances of microorganisms. The repository also contains files for genome-scale metabolic models of representative human gut microbiome genomes. See README.md for more details.