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ABSTRACT Understanding how the human microbiome affects human health has consequences for treating disease and minimizing unwanted side effects in clinical research. Here, we present MetaMed (http://metamed.rwebox.com/index), a novel and integrative system-wide correlation mapping system to link bacterial functions and medicine therapeutics, providing novel hypotheses for deep investigation of microbe therapeutic effects on human health. Furthermore, comprehensive relationships between microbes living in the environment and drugs were discovered, providing a rich source for discovering microbiota metabolites with great potential for pharmaceutical applications.