Metabolic-inhibitor profiling links phenotype and transcriptome of Lachancea thermotolerans to wine fermentation chemistry.

We applied targeted metabolic inhibitors to 145 Lachancea thermotolerans strains to uncover fermentation traits with direct relevance to wine quality. Oxamate, a lactate dehydrogenase inhibitor, reduced lactic acid and total titratable acidity by 21% and 26%, respectively, while increasing succinic acid and pH without affecting ethanol levels, offering a promising strategy to fine-tune wine freshness and balance. Notably, industrial grape-associated strains (clusters C4-C6) maintained robust growth under oxamate stress, unlike wild strains, positioning oxamate resistance as a practical marker for selecting high-performing, acidifying yeasts for winemaking. Additional inhibitors such as metformin shifted redox metabolism, significantly enhancing glycerol (+25%) and acetic acid (+319%) production. Transcriptomic analyses showed that OXA alone, and even more so the DSF + OXA combination, repressed LDH2 and upregulated GPD1 and oxidative phosphorylation genes, whereas MET caused only moderate changes. This integrated phenomic-transcriptomic approach not only provides valuable tools for yeast screening but also defines a roadmap for optimizing wine composition through the precision selection of L. thermotolerans strains.