Multi-Omics Reveals Carvacrol Inhibits Gas Production in Pichia manshurica by Disrupting Membrane Integrity and Energy Metabolism

Pichia manshurica (P. manshurica), a gas-producing spoilage yeast prevalent in fermented foods, causes package swelling, off-flavor formation, and quality deterioration, thereby shortening shelf life and reducing commercial value. Carvacrol, a natural phenolic compound from plant essential oils, has broad-spectrum antimicrobial activity, but its mechanism for inhibiting P. manshurica’s gas production is unclear. In this study, in vitro and in situ experiments confirmed that carvacrol significantly inhibits gas production by P. manshurica in a concentration-dependent manner. Transcriptomic analysis identified 374 differentially expressed genes (DEGs), which were mainly enriched in biological processes such as nitrogen compound metabolism, lipid metabolism, and organic substance biosynthesis, as well as cellular components including the cell membrane, mitochondrion, and endoplasmic reticulum. Metabolomic analysis screened a total of 440 differentially accumulated metabolites (DAMs), primarily involving carboxylic acids, phospholipids, fatty acids, and amino acids. Integrated transcriptome–metabolome analysis revealed that carvacrol disrupts cell membrane integrity, blocks the tricarboxylic acid cycle and oxidative phosphorylation, and interferes with energy, lipid, and amino acid metabolism in P. manshurica, thereby suppressing its gas production. This study elucidates the molecular mechanism by which carvacrol inhibits gas production by P. manshurica, providing a theoretical basis for the development and application of carvacrol as a natural preservative in fermented foods.