Multi-omics insights into co-fermentation by Saccharomycopsis fibuligera and Bacillus velezensis enhancing the nutritional, metabolic, and aromatic quality of Pueraria thomsonii
Pueraria thomsonii is rich in isoflavonoids; however, its glycoside-dominated forms exhibit limited intestinal absorption and metabolism, and the material possesses undesirable sensory traits. This study employs a defined co-culture of Saccharomycopsis fibuligera and Bacillus velezensis to achieve coordinated starch hydrolysis, cell-wall degradation, and β -glucosidase-mediated deglycosylation. We investigate the resulting nutritional, metabolic, and volatile profiles through integrated multi-omics, establishing this consortium as a bioprocessing method for value-added P. thomsonii . Solid-state fermentation (SSF) was conducted at 30 °C for 72 h under microaerophilic conditions across five treatments: raw P. thomsonii (Y), natural fermentation (K), single-strain fermentation with S. fibuligera YPD01 (S) or B. velezensis NA03 (B), and co-fermentation with both strains at a 1:1 ratio (M). Nutritional components, total flavonoids, and total phenolics were quantified. Activities of α -amylase, β -glucosidase, and cellulase were assayed. The microbial community structure and functional genes were characterized through metagenomic sequencing. Untargeted metabolomics was performed using UPLC–MS, and volatile compounds were analyzed by GC–MS. Co-fermentation achieved the highest nutritional quality, yielding reducing sugars (15.45 ± 0.26 mg/g), total flavonoids (9.30 ± 0.17 mg RUT/g), total phenolics (13.19 ± 0.25 mg GAE/g), total amino acids (52.11 ± 0.53 g/kg), and crude protein (12.56 ± 0.26%), all significantly surpassing other treatments. Both inoculated strains effectively colonized the substrate. Co-fermentation exhibited the highest activities of β -glucosidase (90.67 ± 2.66 U/g) and cellulase (343.77 ± 10.75 U/g). Metagenomic analysis generated approximately 659 million reads, identifying 7,737 KEGG entries, with enriched CAZy families in co-fermentation. Untargeted metabolomics identified 1,693 metabolites, with co-fermentation uniquely enriching isoflavone aglycones, peptides, and esterase-related compounds. GC–MS analysis revealed that co-fermentation produced the highest levels of fruity esters, including ethyl linoleate (1009.73 ± 32.51 μg/g) and ethyl palmitate (335.85 ± 9.76 μg/g), while hexanal was eliminated in all fermented groups. The S. fibuligera – B. velezensis consortium enhanced the nutritional, metabolic, and aromatic quality of P. thomsonii through enzymatic biotransformation and metabolic complementarity. Co-fermentation outperformed both natural and single-strain fermentations in the release of phenolic compounds and isoflavone aglycones, amino acid enrichment, and flavor development. These findings provide a theoretical basis and technical guidance for developing high-value fermented foods and offer a reference framework for the precision microbial transformation of medicinal and edible homologous materials.