Comprehensive characterization of traditional Korean fermented foods via integrated physicochemical, metagenomic, and metabolomic approaches

Fermented foods are highly valued for their nutritional properties and health benefits, including probiotic, antioxidant, and anti-inflammatory effects. This study investigated the physicochemical properties, amplicon-based metagenomic profiles, and metabolomic signatures of ten traditional Korean fermented foods, including six kimchi varieties, two types of salted fish, one soybean paste, and one rice punch. Results showed that pH ranged from 4.22 to 5.09 in kimchi samples, 5.60 to 6.21 in salted fish, 5.24 in soybean paste, and 6.19 in rice punch. Salinity was the highest in soybean paste (4.16 %), followed by salted fish (2.01 %–2.80 %), and kimchi samples (1.11 %–1.85 %). Microbiome analysis demonstrated a predominance of Firmicutes and Proteobacteria. Key genera included Leuconostoc, Latilactobacillus, Weissella, Bacillus, Psychrobacter, and Tetragenococcus. Notably, dried radish kimchi exhibited the highest alpha diversity. Salinity and pH were identified as key factors shaping microbial community composition, which was dominated by lactic acid bacteria (LAB) such as Leuconostoc, Latilactobacillus, Weissella, and halotolerant genera like Bacillus and Tetragenococcus. Metabolomic profiling using ultra-high-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UHPLC-QTOF-MS) revealed distinct metabolite patterns and enriched metabolic pathways, including amino acid biosynthesis, pyrimidine, pyruvate, glycerolipid, and sugar metabolism. Correlation analysis highlighted strong associations between key microbial genera (LAB species, Bacillus, and Tetragenococcus) and metabolites such as sugars, organic acids, phenolic compounds, and amino acids, emphasizing their roles in fermentation and flavor development. This integrated approach deepens our understanding of the dynamic interplay between microbial communities, physicochemical characteristics, and metabolic fingerprints in Korean fermented foods, paving the way for innovative functional food development and application.