13C-Flux Spectral Analysis of Host-Pathogen Metabolism Reveals a Mixed Diet for Intracellular Mycobacterium tuberculosis

Whereas intracellular carbon metabolism has emerged as an attractive drug target, the carbon sources of intracellularly replicating pathogens, such as the tuberculosis bacillus Mycobacterium tuberculosis, which causes long-term infections in one-third of the world’s population, remain mostly unknown. We used a systems-based approach—13C-flux spectral analysis (FSA) complemented with manual analysis—to measure the metabolic interaction between M. tuberculosis and its macrophage host cell. 13C-FSA analysis of experimental data showed that M. tuberculosis obtains a mixture of amino acids, C1 and C2 substrates from its host cell. We experimentally confirmed that the C1 substrate was derived from CO2. 13C labeling experiments performed on a phosphoenolpyruvate carboxykinase mutant revealed that intracellular M. tuberculosis has access to glycolytic C3 substrates. These findings provide constraints for developing novel chemotherapeutics. •The intracellular metabolism of Mycobacterium tuberculosis was directly measured•A tool for analyzing metabolic interactions between host and pathogen was developed•Amino acids C1, C2, and C3 are intracellular substrates for M. tuberculosis•CO2 was identified as an intracellular carbon source for M. tuberculosis Despite being a potential drug target, intracellular metabolism of Mycobacterium tuberculosis (Mtb) is one of the least understood aspects of host pathogen biology. Beste et al. probe the metabolism of the pathogen directly growing inside the macrophage and see that Mtb has access to a diverse diet and nutrients.