Defined YNB-free mineral medium improves reproducibility and enables high-titer production in Yarrowia lipolytica

Yarrowia lipolytica is an emerging host for producing acetyl-CoA– and malonyl-CoA–derived chemicals. However, most processes rely on yeast nitrogen base (YNB), a historical formulation with poorly controlled trace metal content. This variability impairs metabolic performance, limits reproducibility, and complicates process transfer. Commercial YNB batches differed markedly, causing 1.5–2-fold variation in growth and docosahexaenoic acid (DHA) production. We developed a malonyl-CoA–responsive flaviolin reporter strain and combined it with a structured Design of Experiments (DoE) workflow to systematically re-engineer YNB mineral composition. Dissection of all 20 YNB components revealed that vitamins are dispensable under the tested conditions, whereas a small subset of salts and trace elements - particularly ZnSO4, FeCl3, KH2PO4, MgSO4, CaCl2, and CuSO4 - dominantly shape precursor availability and product formation. One-factor-at-a-time (OFAT), factorial, steepest ascent, and central composite designs converged in an optimized synthetic mineral medium assembled entirely from individual salts and trace metals. This formulation increased flaviolin titers to 1.41 ± 0.08 g L-1, a more-than threefold improvement over commercial YNB, while ensuring high reproducibility. Key mineral interventions also translated to complex pathways: omission of ZnSO4 increased PUFA titers by 7.6-fold (docosapentaenoic acid, DPA) and 58-fold (eicosapentaenoic acid, EPA) and enhanced DHA formation in independent production strains. The defined formulation substantially reduces cost and eliminates batch-to-batch variability inherent to commercial YNB powders. Our results establish mineral balancing as a major yet underused lever for improving acetyl-CoA– and malonyl-CoA–derived production in Y. lipolytica and demonstrate a generalizable, model-guided workflow for creating simplified, reproducible, and cost-efficient synthetic media for non-conventional yeast cell factories.