A metabolomic workflow was developed for studying the microbiome-gut-brain axis involving addictive behavior in mice. A cohort of adult C57BL/6J mice treated with an antibiotic cocktail were found to consume more alcohol versus the control group over a six week period. Colon, duodenum, jejunum and liver tissues underwent metabolite extraction and untargeted metabolomic analysis using reverse phase liquid chromatography and high resolution mass spectrometry. Over 400 dysregulated features were identified as unique to the antibiotic treated group. After metabolic pathway analysis, the most significantly dysregulated pathways involved bile acid and ubiquinol biosynthesis. The most commonly dysregulated metabolites across these systems were taurocholic acid, glycocholic acid, and cholesterol. This method should be implemented in follow up studies to determine differing levels of metabolites in multiple locations of the intestinal tracts. A reversed-phase liquid chromatography (RPLC) method was developed to qualitatively study sticky bile acids, increase instrument productivity, and reduce costs. Over 400 significantly dysregulated metabolites were found across the four sample groups. The most significantly dysregulated metabolic pathways were the bile acid biosynthesis, and the ubiquinol-6 and ubiquinol-8 pathways.