Fermentation vessels shape the koumiss lipidome and flavor via microbial regulation

Koumiss is a traditional fermented dairy product whose quality attributes are closely linked to fermentation practices. In this study, two traditional fermentation methods, jar fermentation and leather bag fermentation, were compared to elucidate their effects on microbial composition, lipid profiles, and flavor-related metabolites. Microbial communities and functional potential were characterized using metagenomic sequencing, while lipidomic and metabolomic analyses were employed to assess changes in lipid classes and flavor-active compounds. Jar-fermented samples were characterized by higher levels of phosphatidylglycerol, phosphatidylserine, and phosphatidylcholine, together with an enrichment of metabolites previously associated with sweet and creamy sensory attributes. In contrast, leather bag fermentation was associated with increased abundances of phosphatidylethanolamine, short-chain fatty acids, and metabolites linked to sour and umami characteristics. Metagenomic profiling revealed distinct microbial assemblages between the two fermentation methods, with Lactobacillus and Acetobacter predominating in jar fermentation, whereas Bifidobacterium was more abundant in leather bag fermentation. These microbial shifts coincided with differences in genes involved in glycerophospholipid metabolism (PGS1, CHO1, PISD). The study indicate that fermentation method is a key factor shaping the microbial ecology and metabolic landscape of koumiss, thereby contributing to differences in lipid composition and flavor-related characteristics. • Jar fermentation enriched PG, PS, and PC with sweet and creamy flavor compounds. • Leather bag fermentation increases PE and short-chain fatty acids, possibly related to umami–sour flavors. • Lactobacillus abundance correlated with elevated PGS1 and PG(220_181) synthesis. • Acetobacter activity associates with CHO1 and PISD, may influence PS and PE levels. • Glycerophospholipid metabolism was the most enriched lipid pathway in both methods.