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Understanding how these molecules may contribute to, exacerbate, or even improve specific health conditions is a key mechanistic challenge in microbiome research. Using the germ\u2010free mouse model, we used a spatial biology approach to map the location of small molecules in intestinal and systemic tissues in addition to phenotyping cells in their vicinity. Significant differences were noted in molecular species across all tissues tested, including the ileum, colon, spleen, lung, liver, and kidney, with the greatest number of changes in the liver. Molecules putatively identified as phenol sulfate and 5\u2010amino valeric acid betaine were noted to have significantly changed in abundance in the germ\u2010free mouse intestine as well as systemically. 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