Next-Generation dynamic genome-scale model of Saccharomyces cerevisiae that leverages multi-omics time-series data to optimize Wine fermentation

Objetivo

Europe, as the global leader in wine production, faces major challenges: climate change affects grape ripening and wine composition, consumers demand more aromatic, lower-alcohol wines, and wineries need sustainable practices. Addressing these requires innovative, data-driven strategies, particularly in fermentation science, where microbial performance dictates product quality. Genome-scale metabolic models (GSMs) can simulate microbial fermentation but often assume steady-state conditions, use fixed biomass equations, and omit dynamic changes in biomass composition and multi-omics constraints, limiting predictive accuracy. Current models also cover only a subset of yeast-derived aroma compounds, excluding sulfur volatiles, phenolics, and carbonyls critical for wine aroma. The NextG-Wine project aims to develop a next-generation dynamic GSM of Saccharomyces cerevisiae, integrating time-resolved transcriptomics, proteomics, and exometabolomics, a dynamic biomass equation, and expanded aroma coverage to optimize fermentation and aroma profiles. The fellowship will be hosted by the BiSBi group at the Centre of Biological Engineering (CEB, Portugal) under the supervision of Dr Miguel Rocha, with a secondment at the Bio2Eng group (IIM-CSIC, Spain) led by Dr Eva Balsa Canto. State-of-the-art Python tools (Merlin, MEWpy, Troppo) will support omics integration, while Matlab-based AMIGO2 will be used for dynamic modelling and bioprocess optimization. Structured training in genome-scale modelling, bioprocess optimization, proteomics, and coding will complement this interdisciplinary project. By combining cutting-edge modelling, omics data, and expert mentorship, this fellowship will strengthen my network, foster collaborations, and equip me to lead research at the interface of microbial biotechnology and data science, supporting sustainable wine production in Europe and providing transferable tools for the bioeconomy.