Spatially resolved metabolomics integrated with multi-omics analysis suggests a coordinated metabolic framework for lipid transformation and methyl ketone formation in Monascus-fermented cheese.

Methyl ketones play a crucial role in shaping the characteristic aroma of Monascus-fermented cheese (MC). However, their formation pathways within complex solid-state fermentation systems are not yet fully understood. Spatial metabolomics was integrated with lipidomics, sensomics, metagenomics, and metaproteomics to investigate lipid transformation and methyl ketone formation during MC ripening. Glycerophospholipids showed distinct spatial distribution patterns during mid-ripening, supporting spatially heterogeneous lipid transformation. Temporal analysis revealed sequential dynamics, with early accumulation of medium-chain fatty acids followed by increased methyl ketone production. Multi-omics data further suggested stage-specific associations between microbial succession and metabolic functions, with Lactococcus-associated lipid hydrolysis in the early stage and Monascus-associated downstream β-oxidation-related processes during later ripening. A spatially coordinated metabolic framework involving lipid hydrolysis, fatty acid transformation, and decarboxylation is proposed, providing insights into flavor formation and its regulation in complex fermented systems.