Widely Targeted Metabolomics Revealed the Metabolic Basis of Physiological Function and Flavor of Natto

<b>Background:</b> Natto is a fermented product derived from soybeans through the action of Bacillus subtilis natto, possessing various pharmacological and health-promoting properties. However, due to the absence of large-scale and systematic investigations into its metabolite profile, the mechanisms governing the biological functions and flavor characteristics of natto remain incompletely elucidated. <b>Methods:</b> In this study, a comprehensive, widely targeted metabolome analysis was conducted using UHPLC-MS/MS to compare soybeans and natto. <b>Results:</b> A total of 569 metabolites were identified, of which 160 exhibited differential expression between natto and soybeans, including 28 amino acids and their derivatives, 19 flavonoids, 18 alkaloids, and 10 nucleotides and their derivatives. Pathway enrichment analysis further demonstrated significant differences in the metabolic pathways between natto and soybeans, with these 160 differentially expressed metabolites primarily distributed across 40 metabolic pathways. KEGG pathway enrichment analysis of natto metabolites revealed that the majority of these mapped to three key metabolic pathways. Variations in the content of flavonoids and alkaloids, as well as changes in amino acid and saccharide composition and abundance, were found to collectively contribute to the distinctive flavor and biological functionality of natto. <b>Conclusions:</b> This study lays the foundation for future efforts to enhance the quality of natto.