Metabolomics is emerging as a powerful tool for studying metabolic processes, identifying crucial biomarkers responsible for metabolic characteristics and revealing metabolic mechanisms, which construct the content of discovery metabolomics. The crucial biomarkers can be used to reprogram a metabolome, leading to an aimed metabolic strategy to cope with alteration of internal and external environments, naming reprogramming metabolomics here. The striking feature on the similarity of the basic metabolic pathways and components among vastly different species makes the reprogramming metabolomics possible when the engineered metabolites play biological roles in cellular activity as a substrate of enzymes and a regulator to other molecules including proteins. The reprogramming metabolomics approach can be used to clarify metabolic mechanisms of responding to changed internal and external environmental factors and to establish a framework to develop targeted tools for dealing with the changes such as controlling and/or preventing infection with pathogens and enhancing host immunity against pathogens. This review introduces the current state and trends of discovery metabolomics and reprogramming metabolomics and highlights the importance of reprogramming metabolomics.

Significance: Exogenous metabolites have been documented to potentiate antibiotics to kill multidrug-resistant pathogens, but the mechanisms are largely unknown. The work presented here shows that intermetabolites from the TCA cycle and the phosphoenolpyruvate (PEP)-pyruvate-AcCoA pathway have the potential to improve targeting of these resistant microorganisms. The enzymes that connect the PEP-pyruvate-AcCoA pathway to the TCA cycle are essential for this potentiation, indicating both pathway and cycle can be merged to be considered a pyruvate cycle (P cycle). The P cycle operates routinely as a general mechanism for energy production and regulating the TCA cycle in Escherichia coli and Edwardsiella tarda . The results reported here provide insights into metabolite-facilitated targeting by antibiotics as well as bacterial energy metabolism and homeostasis.

Multidrug-resistant Escherichia coli metabolomes are reprogrammed by glutamine to be sensitive to ampicillin in vitro and in vivo.

Serum resistance is a poorly understood but common trait of some difficult-to-treat pathogenic strains of bacteria. Here, we report that glycine, serine and threonine catabolic pathway is down-regulated in serum-resistantEscherichia coli, whereas exogenous glycine reverts the serum resistance and effectively potentiates serum to eliminate clinically-relevant bacterial pathogens in vitro and in vivo. We find that exogenous glycine increases the formation of membrane attack complex on bacterial membrane through two previously unrecognized regulations: 1) glycine negatively and positively regulates metabolic flux to purine biosynthesis and Krebs cycle, respectively. 2) α-Ketoglutarate inhibits adenosine triphosphate synthase, which in together promote the formation of cAMP/CRP regulon to increase the expression of complement-binding proteins HtrE, NfrA, and YhcD. The results could lead to effective strategies for managing the infection with serum-resistant bacteria, an especially valuable approach for treating individuals with weak acquired immunity but a normal complement system.