Dynamical model-guided SynCom design for sustainable agriculture

Synthetic microbial communities (SynComs) are emerging as promising alternatives to single-strain inoculants in agriculture, offering greater functional robustness and environmental adaptability. However, transforming conceptual studies into engineerable and scalable agricultural practices remains challenging. In this opinion article, we synthesize current research on plant SynComs through a framework that moves from strain-centered assembly toward system-level design, linking the identification of truly stable coexisting communities in natural microbiomes to the elucidation of plant-microbe-soil interaction mechanisms, the development of dynamical models, and the integration of these models into platform-based design and production pipelines. We focus on recent advances that integrate generalized Lotka-Volterra and consumer-resource models with multi-omics data and other system-level constraints, with the aim of introducing model-driven concepts of SynCom design and promoting their large-scale application in agriculture.