Overriding bioprocess perturbations with a cell–machine interface for reliable microbial stress-response control

Controlling cell population dynamics and phenotypic diversification is a key objective in systems and synthetic biology, particularly for ensuring uniform responses from engineered gene circuits. While cell-machine interfaces have been employed to modulate host–gene circuit interactions, environmental perturbations typical of industrial bioreactor conditions remain underexplored. In this study, we investigate the impact of such perturbations on the general stress response in Escherichia coli and Saccharomyces cerevisiae . Using scale-down bioreactor experiments, we evaluate the performance of the Segregostat, a real-time control system that leverages automated flow cytometry to induce dynamic nutrient shifts. The Segregostat achieves robust stress response control, even under severe perturbations such as extended residence times in a two-compartment reactor. We hypothesize that this robustness arises from the system’s ability to amplify host-compatible fluctuations beyond bioreactor-induced perturbations. Our findings highlight the importance of integrating environmental factors into control strategies for reliable gene circuit behavior in industrial bioprocessing environments.