Time-dependent shifts in microbiota and metabolites of Yuba under ambient storage

Yuba (tofu skin) is a high-protein, high-lipid plant-based food that is prone to spoilage at ambient temperatures. Understanding the underlying mechanisms of this deterioration is critical for laboratory research into food preservation and metabolic stability in plant-derived products.

Researchers employed 16S rRNA gene sequencing and untargeted LC-MS/MS metabolomics to analyze Yuba samples stored at room temperature (25 ± 2 °C) for four durations: 7 days, 50 days, 105 days, and 460 days. Microbial DNA extraction, library construction, and bioinformatics analysis were performed alongside metabolite extraction and statistical pathway analysis.

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.

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. These findings offer a framework for laboratory-based investigation into food spoilage pathways, though clinical or commercial applications remain outside the scope of this research.