Anaerobic microbial metabolism drives critical functions within global ecosystems, host-microbiota interactions, and industrial applications, yet remains ill-defined. We resolved dynamic metabolism in living cells of the anaerobic pathogen Clostridioides difficile using High-Resolution Magic Angle Spinning (HRMAS) Nuclear Magnetic Resonance (NMR) spectroscopy to inform genome-scale predictions of cellular metabolism. Analyses leveraged the sensitivity of 13C NMR spectroscopy to simultaneously track cellular carbon and nitrogen flow from fermentable 13C and 15N-labeled substrates. We illustrate a versatile approach to elaborate complex anaerobic metabolism for clinical, scientific, and industrial applications.
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