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. 2024 Dec 1;14(12):663.
doi: 10.3390/metabo14120663.

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

Xiaolong Yin  1 , Xiaona Wang  2 , Lili Xu  1 , Jianzhi Zhao  1 , Can Li  1 , Jianqiang Lin  3
Affiliations

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

Xiaolong Yin et al. Metabolites. .

Abstract

Background: 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. Methods: In this study, a comprehensive, widely targeted metabolome analysis was conducted using UHPLC-MS/MS to compare soybeans and natto. Results: 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. Conclusions: This study lays the foundation for future efforts to enhance the quality of natto.

Keywords: KEGG; UHPLC-MS/MS; metabolite profiling; natto.

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Conflict of interest statement

Author Xiaona Wang was employed by the company Shandong Freda Biotech Co., Ltd. This paper reflects the views of the scientists and not the company. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Morphology of soybeans (before fermentation), natto (fermentation completed), and freeze-dried natto (vacuum freezing after fermentation).
Figure 2
Figure 2
Difference in metabolite concentration in soybean and natto. (A) PCA of soybean and natto metabolites. Equal volumes of soybean and natto samples were mixed as a control. (B) Cluster analysis of soybean and natto metabolites. Colors indicate the level of accumulation of each metabolite (blue: lower concentrations; red: higher concentrations). Z-score represents a deviation from the mean in standard deviation units.
Figure 3
Figure 3
Differentially accumulated metabolites between soybean and natto. (A) Volcano plot of 569 metabolites identified. Differential metabolites were defined as metabolites with a fold change ≥ 2.0 or ≤0.5 in natto compared to soybeans. A threshold of VIP ≥ 1.0 was considered to separate differential metabolites from non-differential metabolites. (B) Biochemical categories of differential metabolites between natto and soybean.
Figure 4
Figure 4
KEGG classification of differentially accumulated metabolites. (A) KEGG category: metabolism. (B) Metabolome view maps of metabolic pathways in natto and soybean.
See this image and copyright information in PMC

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