BA, bile acid; BSH, bile salt hydrolase; Bile acids; CA, cholic acid; CAR; CAR, constitutive androstane receptor; CDCA, chenodeoxycholic acid; CITCO, 6-(4-chlorophenyl)imidazo[2,1-b][1,3]thiazole-5-carbaldehyde O-(3,4-dichlorobenzyl)oxime; CV, conventional; CYP, cytochrome P450; DCA, deoxycholic acid; EGF, epidermal growth factor; Feces; GF, germ free; GLP-1, glucagon-like peptide-1; GM-CSF, granulocyte-macrophage colony-stimulating factor; Gut microbiome; HDCA, hyodeoxycholic acid; IBD, inflammatory bowel disease; IFNγ, interferon-gamma; IL, interleukin; IS, internal standards; Inflammation; LCA, lithocholic acid; LC­MS/MS, liquid chromatography­tandem mass spectrometry; MCA, muricholic acid; MCP-1, monocyte chemoattractant protein-1; Mice; NF-κB, nuclear factor kappa-light-chain-enhancer of activated B cells; NSAID, non-steroidal anti-inflammatory drug; Nuclear receptor; OH, hydroxylated; OTUs, operational taxonomy units; PA, indole-3 propionic acid; PBDEs, polybrominated diphenyl ethers; PCBs, polychlorinated biphenyls; PCoA, Principle Coordinate Analysis; PXR; PXR, pregnane X receptor; PiCRUSt, Phylogenetic Investigation of Communities by Reconstruction of Observed States; QIIME, Quantitative Insights Into Microbial Ecology; SCFAs, short-chain fatty acids; SNP, single-nucleotide polymorphism; SPF, specific-pathogen-free; T, wild type; T-, taurine conjugated; TCPOBOP, 1,4-bis-[2-(3,5-dichloropyridyloxy)]benzene, 3,3',5,5'-Tetrachloro-1,4-bis(pyridyloxy)benzene; TGR-5, Takeda G-protein-coupled receptor 5; TLR4, toll-like receptor 4; TNF, tumor necrosis factor; UDCA, ursodeoxycholic acid; YAP, yes-associated protein; hPXR-TG, humanized PXR transgenic