Microbial community succession and toxic alkaloids change during fermentation of Huafeng Dan Yaomu

Fermentation is a traditional processing method that can impact the abundance of relevant components in Chinese herbal medicines. Huafeng Dan Yaomu was processed by fermentation. In this study, we investigated changes in toxic alkaloids using high-performance liquid chromatography and analysed the changes in microbial communities during fermentation of Huafeng Dan Yaomu by Illumina MiSeq platform. The results indicated that highly toxic alkaloid compounds including aconitine, mesaconitine and hypaconitine were decreased, whereas benzoylmesaconine and benzoylhypaconitine were increased during fermentation. The dominant bacterial genera in the raw material (day 0) were Bacillus (58·38%), Enterobacter (16·05%), Enterococcus (4·10%) and others (11·48%). After 7 days of fermentation, Pediococcus predominated, increasing from 98·26 to 99·97%. The dominant fungal genera in the raw material (day 0) were IncertaeSedisᵢncertaeₛedis (45·36%), Eurotialesᵤnclassified (20·63%), Millerozyma (15·58%) and Saccharomycopsis (10·64%). After 7 days of fermentation, Saccharomycopsis was increased to 90·84%. After 14 days of fermentation, Pichia became the main fungal genera in the fermentation process. There were 16 bacterial genera and seven fungal genera that displayed significant correlation with toxic alkaloids. The dynamics of the microbiota and chemical compounds during fermentation of Huafeng Dan Yaomu were revealed, providing a foundation for further investigation of the effects of microbes on chemical compounds and insights into the manufacturing of Huafeng Dan Yaomu. SIGNIFICANCE AND IMPACT OF THE STUDY: Huafeng Dan Yaomu is a unique fermentation-based micro-organism product. This study reveals that the change in toxic alkaloids during fermentation was related to micro-organisms. The results of this study can be used to improve the Chinese herb medicine fermentation process, such as the selection of beneficial strains and their composition for modern fermentation. The results of this study may also provide new ideas for the processing of Traditional Chinese Medicine.