Multi-omics reveals metabolic division of labor in mixed-starter soymilk fermentation

Fermentation by multiple microorganisms significantly improves the sensory quality and nutritional value of soymilk, yet the molecular mechanisms underlying the synergistic interactions, particularly regarding substrate utilization and nutrient exchange were not clear. Here, metatranscriptomics and non-targeted metabolomics were integrated to characterize the microbial succession and metabolic reprogramming of a mixed starter culture (Streptococcus salivarius subsp. thermophilus, Lactobacillus delbrueckii subsp. bulgaricus, and Lactiplantibacillus plantarum) during soymilk fermentation. Taxonomic analysis revealed a cooperative succession pattern, where S. thermophilus dominated the mid-stage fermentation, facilitating the subsequent dominance of L. plantarum in the late-stage. Controlled soymilk fermentation with systematic exclusion of single strains, omics results elucidated a sophisticated metabolic division of labor. Specifically, S. thermophilus acts as the primary oligosaccharide metabolizer, as its absence induced compensatory galactose utilization pathways in the remaining strains. Furthermore, the removal of L. bulgaricus led to the significant derepression of vitamin and amino acid biosynthetic gene clusters, providing transcriptional evidence that L. bulgaricus functions as a key cross-feeding bacterium to support the auxotrophic community via cross-feeding. These findings unravel the essential gene-metabolite linkages driving synergistic fermentation and offer a theoretical basis to robustly reproduce fine fermented soymilk characteristics.