FLYCOP: metabolic modeling-based analysis and engineering microbial communities.

摘要: Motivation Synthetic microbial communities begin to be considered as promising multicellular biocatalysts having a large potential replace engineered single strains in biotechnology applications, pharmaceutical, chemical and living architecture sectors. In contrast strain engineering, the effective high-throughput analysis engineering of consortia face lack knowledge, tools well-defined workflows. This manuscript contributes fill this important gap with framework, called FLYCOP (FLexible sYnthetic Consortium OPtimization), which modeling while improving knowledge about how these work. selects best consortium configuration optimize given goal, among multiple diverse configurations, flexible way, taking temporal changes metabolite concentrations into account. Results previous systems optimizing consortia, has novel characteristics up new problems, represent additional features analyze events influencing behavior. manuscript, optimizes Synechococcus elongatus-Pseudomonas putida produce maximum amount bio-plastic (PHA, polyhydroxyalkanoate), highlights influence metabolites exchange dynamics four auxotrophic Escherichia coli parallel growth. can also provide an explanation biological evolution driving evolutionary endeavors by describing why heterogeneous populations emerge from monoclonal ones. Availability implementation Code reproducing study cases described are available on-line: https://github.com/beatrizgj/FLYCOP. Supplementary information data at Bioinformatics online.