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Plant–microbe interactions—whether pathogenic or symbiotic—exert major influences on plant physiology and productivity. Analysis of such interactions represents a particular challenge to metabolomic approaches due to the intimate association between the interacting partners coupled with a general commonality of metabolites. We here describe an approach based on co-cultivation of
Arabidopsis
cell cultures and bacterial plant pathogens to assess the metabolomes of both interacting partners, which we refer to as dual metabolomics.