Integrative multi-omics elucidates distinct fermentation systems between traditional Korean and Chinese chili pepper pastes

Gochujang (GCJ) and Pixian-Douban (PXDB), the most representative traditional bean-based fermented chili pastes of Korea and China, respectively, exhibit distinct organoleptic properties due to their ingredients and fermentation techniques. To elucidate the microbial metabolic systems driving these differences, a multi-omics approach integrating metagenomic and metabolomic analyses was employed. A capillary electrophoresis–time-of-flight mass spectrometry (CE-TOF/MS) analysis identified 329 metabolites (Level 1 confidence); among these, 129 metabolites showed significant variation between the two bean-based chili pastes (VIP > 1.0). Fumaric acid and trehalose-6-phosphate were specific to GCJ, whereas PXDB contained high levels of amino acids and dipeptides ( p < 0.01). Metagenomics revealed that GCJ was dominated by Bacillus and Aspergillus , whereas PXDB was characterized by lactic acid bacteria ( Lactiplantibacillus, Leuconostoc , and Periweissella ) and osmotolerant yeasts ( Wickerhamiella, Pichia , and Zygosaccharomyces ). Functional genes, metabolic pathways, and binning analyses linked these microbial communities to their distinct metabolic potential, highlighting their roles in shaping the organoleptic properties of the chili pastes. This study provides a multidimensional elucidation of the fermentation system differences between GCJ and PXDB, establishing a theoretical basis for process optimization and marker-based product authentication. • Differences between GCJ and PXDB fermentation systems elucidated by multi-omics. • Fumaric acid and trehalose-6-phosphate are GCJ specific biomarkers. • PXDB exhibited higher levels of amino acid and dipeptides. • PXDB is dominated by lactic acid bacteria and osmotolerant yeast. • GCJ is dominated by Bacillus and Aspergillus.