Exploring characteristics of value-added production of anthraquinones in rhubarb via fermentation: Compartmental modelling and molecular docking analysis

• Third cycle of acclimation for fermentation of R. palmatum L. effectively maximize the yields of value-added intermediates. • Lactococcus and Klebsiella were the dominant species before and after fermentation, respectively; microbial biodiversity was influenced by the substrate. • Anthraquinone glucosides have higher affinity to β-glucosidases of Klebsiella spp. compared to the Lactococcus spp. Rhubarb is an anthraquinone-rich herb with extensive pharmacological properties. The study adopted compartmental modeling, metagenomic analysis, and molecular docking analysis to predict optimal cycles of acclimation and maximal value-added production in fermentation of Rheum palmatum L. The work highlights the importance of fermentation and microbial consortia in value-added production. According to transient dynamics of four anthraquinones (i.e., aloe-emodin, rhein, emodin, and chrysophanol) in R. palmatum L. fermentation, compartmental modeling was applied to quantitatively reveal the optimal cycle of acclimation for value-added production. Metagenomic analysis and comparative molecular docking analysis were used to scrutinize the fermentation process for microbial community and metabolic pathway assessment. Compartmental modelling indicated that the third cycle had the lowest k 2 k 1 ratio and the highest bioconversion rates for aloe-emodin, emodin, and chrysophanol in acclimation using S. cerevisiae and microbial consortia. This coincides with the experimental findings, supporting the optimal performance of value-added production. The metabolic pathway of anthraquinone intermediates in R. palmatum L. using different cultures was established. As metagenomic analysis indicated, evolution of biodiversity in microbial community before and after fermentation suggested that Firmicutes and Proteobacteria tended to be the most dominant phyla. The β-glucosidase from Klebsiella spp . seemed to have more affinity than Lactococcus spp . that may explain Klebsiella's dominance after fermentation.