There are over 5,000 metabolic reactions shared between microbes and people, and finding the underlying metabolic features that contribute to disease is a serious analytical challenge. To address this, we built the Calgary Metabolomics Research Facility (CMRF), a $4 million facility designed specifically for investigating the metabolism of infectious diseases. This facility includes an integrated microbiology laboratory, engineering suite and mass spectrometry instrumentation. Using this unique resource, we are unraveling the complex interactions pathogens have with people and finding the molecular underpinnings of disease. We are harnessing these unique insights to develop a new generation of rapid diagnostic tools, pioneer new strategies for treating infections and to elucidate the role metabolism has played in the evolution of pathogens.