Adapting OptCouple to identify strategies with increased product yields in community cohorts of E. coli

Twycross, Jamie; Pearcy, Nicole

Abstract

Microbes as chemical factories provide an alternative sustainable approach for producing platform chemicals. Until recently, most efforts have involved engineering heterologous pathways into a single microbial chassis to maximise its production of a target chemical. More recently, cohorts of microbes have been used to engineer microbial communities to achieve higher yields than acheived in single chassis. In this paper, we present a computational approach to identify sets of metabolic modifications that create stable co-dependent communities of micro-organisms and improve the chemical yield of these communities. We demostrate our approach by designing communities which produce industrially relevant platform chemicals. We show that our approach is able to uncover metabolic engineering strategies for coupling these target chemicals to the growth of stable community cohorts.

Citation

Twycross, J., & Pearcy, N. (2025). Adapting OptCouple to identify strategies with increased product yields in community cohorts of E. coli. Metabolites, 15(5: Comprehensive Insights into Metabolic Pathways: Genome-Scale Modeling Techniques), Article 309. https://doi.org/10.3390/metabo15050309

• Journal Article Type: Article
• Acceptance Date: Apr 29, 2025
• Online Publication Date: May 6, 2025
• Publication Date: May 6, 2025
• Deposit Date: Apr 29, 2025
• Publicly Available Date: Apr 30, 2025
• Journal: Metabolites
• Electronic ISSN: 2218-1989
• Publisher: MDPI
• Peer Reviewed: Peer Reviewed
• Volume: 15
• Issue: 5: Comprehensive Insights into Metabolic Pathways: Genome-Scale Modeling Techniques
• Article Number: 309
• DOI: https://doi.org/10.3390/metabo15050309
• Keywords: OptCouple; community microbial designs; multi-directional dependent models; guaranteed product yields
• Public URL: https://nottingham-repository.worktribe.com/output/48354924
• Publisher URL: https://www.mdpi.com/2218-1989/15/5/309