Multi-omics profiling of palmitoleic acid-associated changes in Zygosaccharomyces rouxii

High‑salt fermentation creates a unique ecological niche where salt‑tolerant yeasts must sustain cellular activity under severe osmotic pressure. Here, we focused on Zygosaccharomyces rouxii, a representative yeast in soy sauce fermentation, and investigated the molecular effects of exogenous palmitoleic acid (C16:1) supplementation under 120 g/L NaCl stress. Using integrated transcriptomic, DIA‑based proteomic, and untargeted metabolomic datasets, we obtained a pathway‑level view of C16:1‑associated responses. The treatment (1.0 mM C16:1 in ethanol, 24 h, with equal ethanol added to the control) was performed with three biological replicates per group. Applying stringent criteria (|log₂FC| ≥ 1.5, adjusted *p* < 0.05), we identified 142 up‑ and 87 down‑regulated genes, 65 up‑ and 43 down‑regulated proteins, and 38 up‑ and 29 down‑regulated metabolites in the treatment versus control (NaCl only). Joint pathway enrichment (KEGG and Reactome, hypergeometric test) revealed that C16:1 supplementation consistently upregulated branched‑chain amino acid degradation while downregulating several fatty acid β‑oxidation enzymes, alongside altered levels of redox‑related metabolites (e.g., decreased oxidized glutathione). These changes suggest that C16:1 may alleviate oxidative burden and modulate membrane fluidity‑related gene expression, which are relevant to yeast performance in high‑salt environments. Importantly, because fermentation performance (e.g., growth rate or ethanol tolerance) was not directly measured, these interpretations remain hypotheses that require functional validation through targeted gene deletions and actual soy sauce moromi trials. This study thus provides a comprehensive multi‑omics resource for understanding how a defined nutritional factor influences molecular adjustments in Z. rouxii under severe salt stress, and offers a foundation for future mechanistic and applied studies on salt‑tolerant yeasts in fermented food production.