COSMOS: COmmunity and Single Microbe Optimisation System

Bioprocessing harnesses the potential of microbial communities and monocultures to convert renewable resources like agricultural by-products and wastewater into valuable products. While monocultures offer simplicity and control, microbial communities provide metabolic diversity, enabling complex substrate breakdown and cooperative biosynthesis. However, balancing efficiency with stability requires a nuanced approach, as each system presents unique advantages and limitations, particularly under different environmental conditions. To systematically explore the potential of these systems, we developed the COmmunity and Single Microbe Optimisation System (COSMOS), a dynamic computational framework that compares microbial monocultures and communities across diverse fermentation conditions. COSMOS identifies optimal microbial systems tailored to specific carbon sources and environments. Our findings reveal that communities outperform monocultures under harsher environmental conditions, demonstrating the value of cooperative interactions. A key result is the identification of the Shewanella oneidensis – Klebsiella pneumoniae community as the most efficient producer of 1,3-propanediol under anaerobic conditions. Notably, this aligns with experimental findings, with COSMOS accurately predicting the optimal carbon source concentration and inoculum ratio used in the study. Additional findings highlight the value of communities for nutrient-limited processes and emphasise the importance of computational screening to balance productivity with ease of control. The insights gained from this study offer a roadmap toward optimising microbial systems for sustainable bioprocesses and circular bio-economies.