Multi-omics insights into co-fermentation by Saccharomycopsis fibuligera and Bacillus velezensis enhancing the nutritional, metabolic, and aromatic quality of Pueraria thomsonii

Abstract

Background 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. Methods 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. Results 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. Conclusion 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.