Time-dependent shifts in microbiota and metabolites of Yuba under ambient storage: implication for quality deterioration and spoilage

Abstract

Introduction Yuba (tofu skin), a high-protein and high-lipid plant-based food, is prone to spoilage at ambient temperatures, but the underlying mechanisms are not fully understood. This study aimed to elucidate the dynamic changes in the microbial community and metabolites of Yuba during ambient storage to investigate quality deterioration and identify potential biomarkers for quality control. Methods 16S rRNA gene sequencing and untargeted LC-MS/MS metabolomics were employed to analyze Yuba samples stored at room temperature (25 ± 2 °C) for four durations: 7 days (FZ), 50 days (C), 105 days (B), and 460 days (A). Microbial DNA extraction, library construction, sequencing, and bioinformatics analysis were performed. Metabolite extraction and LC-MS/MS analysis were conducted, followed by data preprocessing, identification, and statistical and pathway analysis. Correlation analysis was performed between differentially abundant metabolites and microbial genera. Results Storage duration significantly influenced the Yuba metabolome, as evidenced by clear separation in Principal Component Analysis (PCA) and Partial Least Squares-Discriminant Analysis (PLS-DA) scores. Glycerophospholipid and fatty acyl metabolism were significantly altered, with increases in LysoPEs, LysoPA, PCs, and fatty acyls observed during prolonged storage. At the microbial level, Firmicutes dominated throughout storage, with a shift towards increasing abundance of Firmicutes and decreasing abundance of Proteobacteria as storage time increased. Lysinibacillus emerged as the predominant genus after long-term storage (460 days), showing a significant increase in relative abundance from 0.27% to 52.33%. Specific bacterial genera, notably Lysinibacillus and Macrococcus, demonstrated significant correlations with metabolite levels, suggesting their crucial roles in shaping the Yuba metabolome. Microbial functional predictions were associated with lipid, amino acid, and nucleotide metabolism. Eleven common pathways were identified between significantly altered microbes and metabolites, including glycerophospholipid metabolism and amino acid biosynthesis. Discussion This study provides a systematic perspective on Yuba deterioration during ambient storage, identifying microbial and metabolic signatures correlated with quality changes. The dynamic remodeling of the metabolome, particularly the increase in lipids and amino acid-related metabolites, coupled with the dominance of Lysinibacillus, highlights their potential roles in spoilage. The identified microbial and metabolic signatures serve as promising candidates for future validation as biomarkers to extend shelf life and maintain product quality. Further research involving pure culture studies and metatranscriptomics is warranted to confirm causal relationships and elucidate specific mechanisms.