Single-bacterium metabolome revealing heterogeneous cellular states in bacterial populations

Bacterial metabolism is a complex system of interwoven pathways coordinated by an intricate, multilayered regulatory network. Dissecting the metabolism at single bacterial level is highly challenging. Herein, we greatly increase the sensitivity of the bacterial measurement with our home-made single-bacterium metabolome (SinBactM) mass spectrometry platform, which combines micro-extraction with induced nanoelectrospray ionization mass spectrometry, for mapping metabolites of the primary bacterium. The universal applicability of the SinBactM platform is demonstrated by successfully discriminating distinct metabolic profiles across different bacterial species. By measuring the bacterial uptake of antibiotics and observing the dynamic metabolic changes in response to external stimuli, the accuracy and reliability of SinBactM platform are further validated. We apply SinBactM to characterize clinical heteroresistant K. pneumoniae strains metabolic alteration under antibiotic perturbation. Several different subpopulations resulting from antibiotic perturbation are classified based on their metabolome, while pseudotemporal ordering reveals a trajectory of metabolic change across subpopulations. Thus, SinBactM platform paves the way for profiling metabolomics of individual bacterial cells, which might provide an exciting dimension to a thorough understanding of antibiotic-resistant evolution for in-depth interrogation of resistant mechanisms. Here the authors present a single-bacterium metabolomics platform that enables sensitive metabolic profiling of individual bacteria, revealing metabolic heterogeneity in heteroresistant K. pneumoniae strains and providing insights into bacterial survival and resistance.