New insights in metabolism modelling to decipher plant–microbe interactions

Summary Plant disease outbreaks, exacerbated by climate change, threaten food security and environmental sustainability world‐wide. Plants interact with a wide range of microorganisms. The quest for resilient agriculture requires a deep insight into the molecular and ecological interplays between plants and their associated microbial communities. Omics methods, by profiling entire molecular sets, have shed light on these complex interactions. Nonetheless, deciphering the relationships among thousands of molecular components remains a formidable challenge, and studies that integrate these components into cohesive biological networks involving plants and associated microbes are still limited. Systems biology has the potential to predict the effects of biotic and abiotic perturbations on these networks. It is therefore a promising framework for addressing the full complexity of plant–microbiome interactions.