(A) Human gut bacterial enzymes transform conjugated primary BAs into unconjugated secondary BAs. While hydrophilic unconjugated BAs damage epithelial integrity, the roles of unconjugated BAs and bacterial BSHs in intestinal membrane integrity are unclear. (B) Schematic of rat intestinal permeability time-course experiment. A choline-deficient, L-amino acid defined (CDAHFD) was fed to rats to induce intestinal permeability and liver damage. HFD-fed rats served as controls. Rats were euthanized at 48-hour, 1-week, 6-week, or 12-week time points. Tissues and blood were collected for metabolite quantification and evaluation of intestinal and liver injury markers. (C) Portal venous levels of LPS were significantly increased in CDAHFD-fed rats compared to control rats after 48 hours, 1 week, 6 weeks, and 12 weeks on diet (n = 4 per group, two-tailed Welch’s t test). (D) CDAHFD-fed rats developed increased intestinal permeability after 48 hours of diet. Measurement of fluorescein isothiocyanate (FITC)–dextran levels in systemic circulation after gavage in control and CDAHFD-fed rats (n = 8 per group, two-tailed Welch’s t test). (E and F) CDAHFD induced increased expression and apical membrane localization of ZO-1 at early time points. ZO-1 immunofluorescence staining of ileum from control and CDAHFD-fed rats at 48-hour (E) and 1-week (F) time points (n = 10 intestinal cells quantified per group; see Materials and Methods for statistical analyses). (G and H) Conjugated BA abundance was reduced at early time points (48 hours and 1 week) in the cecum (G) and portal vein (H) of CDAHFD-fed rats as determined by ultra-performance liquid chromatography–mass spectrometry (UPLC-MS) BA analysis from control and CDAHFD-fed animals (n = 8 per group, two-tailed Welch’s t test; see the Supplementary Materials for concentrations of total and individual BAs in cecal contents and portal vein at 48 hours and 1 week). See Materials and Methods for statistical analyses. *P < 0.05, **P < 0.005, ***P < 0.001, and ****P < 0.0001. Bars represent means ± SEM. ns, not significant; DAPI, 4′,6-diamidino-2-phenylindole; a.u., arbitrary units.