AMPs, Antimicrobial peptides; BAs, Bile acids; BC, Bray Curtis; CD, Crohn's disease; CDI, Clostridioides difficile infection; DC, Diversion colitis; DCA, Deoxycholic acid; DSS, Dextran sulfate sodium; FAs, Fatty acid; FMT, Fecal microbiota transplantation; FODMAP, Fermentable oligosaccharide, disaccharide, monosaccharide, and polyol; GC­MS, Gas chromatography-mass spectrometry; Gut microbiota; HDAC, Histone deacetylase; IBD, Inflammatory bowel disease; Inflammatory bowel diseases; LC-MS, Liquid chromatography-mass spectrometry; LCA, Lithocholic acid; LCFAs, Long-chain fatty acids; MCFAs, Medium-chain fatty acids; MD, Mediterranean diet; MS, Mass spectrometry; Metabolite; Metabolomics; Metagenomics; Microbial therapeutics; NMR, Nuclear magnetic resonance; PBAs, Primary bile acids; SBAs, Secondary bile acids; SCD, Special carbohydrate diet; SCFAs, Short-chain fatty acids; TNBS, 2,4,6-trinitro-benzene sulfonic acid; UC, Ulcerative colitis; UDCA, Ursodeoxycholic acid; UPLC-MS, ultraperformance liquid chromatography coupled to mass spectrometry; UU, Unweighted UniFrac; WMS, Whole-metagenome shotgun