Evolutionary engineering of functional resilience in synthetic microbial communities

Synthetic microbial communities (SynComs) are composed of intentionally assembled groups of microorganisms for specific appliucations. They offer exciting opportunities for controlled functional outputs in medicine, agriculture and industrial bioprocesses. Currently, the functional outputs of SynComs are tested mostly under unperturbed conditions. However, SynComs often experience perturbations such as nutrient shifts, temperature fluctuations, and microbial invasion in their environment. Achieving long-term compositional and functional resilience under these conditions remains a major challenge. There is an urgent need to uncover the ecological factors and genomic features that govern long-term resilience in the face of biotic and abiotic perturbations. Our hypothesis is that distinct perturbation regimes drive unique evolutionary trajectories and shape varying levels of resilience among SynComs. To test this, we will employ long-term experimental evolution under defined perturbation regimes to steer a yeast – lactic acid bacteria (LAB) SynCom toward stable functionality. Based on the experimental findings, we will develop a general framework that integrates ecological theory with engineering principles to aid the design of functionally stable SynComs. Overall, our work will provide fundamental insights into evolutionary engineering of SynCom resilience to enable more predictable and efficient bioprocessing across diverse industrial applications.