Burden-aware feedback control of microbial consortia

Abstract

Abstract Engineered microbial consortia are emerging as programmable systems capable of sensing and responding to their environment. However, maintaining defined community composition over time remains challenging, particularly in bioprocesses where growth conditions and metabolic burdens continuously shift. Here, we develop a burden-aware multicellular RNA-based feedback control system that stabilises coculture composition by coupling gene expression burden to growth regulation. The system integrates three modules: quorum sensing-based communication, an RNA-based comparator computing deviations from a target ratio, and tuneable growth regulation via heterologous expression burden or CRISPRi-mediated knockdowns. In a two-strain E. coli coculture, this architecture maintains stable coculture ratios over 24-hour batch cultures, recovers growth rates by up to 90% following burden-induced growth reduction, and increases protein production yields by up to 81% in the slower-growing strain. We achieve tuneability by adjusting RNA binding strength and quorum-sensing signal production. This work demonstrates that burden-driven growth control can be used to stabilise and tune synthetic microbial consortia.