Microbe-driven flavonoid biotransformation revealed by multi-omics analysis during Hua Feng Dan Yao Mu fermentation

Microbes play an important role in the transformation of bioactive components in traditional Chinese medicine (TCM) fermentation. It is not understood how the microbial succession relates to the changes in active components of Hua Feng Dan Yao Mu (HFDYM) fermentation. This study systematically characterized the chemical and microbial dynamics during HFDYM fermentation, using multi-omics analyses, with a focus on flavonoid transformation. Single-strain fermentation identified specific microorganisms involved in flavonoid metabolism. During fermentation, there were significant abundance changes in 60 flavonoids. Metabolic pathway analysis revealed a distinct remodeling of flavonoid metabolism, marked by increased levels of (+)-catechin and naringin alongside decreases in many other flavonoids. The analysis of the microbial community showed that the dominant bacterial genera were Tetragenococcus , Levilactobacillus , and Bacillus while the dominant fungi were Wickerhamomyces and Aspergillus . Further correlation studies related the Bacillus and Aspergillus to 10 flavonoids. A follow-up fermentation using Bacillus amyloliquefaciens and Aspergillus niger enhanced the total flavonoid content significantly, which effectively promotes the accumulation of (+)-catechin, luteolin and kaempferol. Moreover, it accelerated the degradation of vitexin and eriodictyol. The findings elucidate the mechanism of microbial-mediated flavonoid changes occurred in HFDYM fermentation. This would provide a scientific basis for its process standardization and optimization to improve TCM quality.