*4.2. DNA Metabarcoding Is a Powerful Tool for the Analysis of Fungal Diversity in CHMs*

Mycotoxins, the toxic secondary metabolites, can lead to numerous health problems and even death in just small intakes, and they are mainly produced by *Penicillium*, *Aspergillus*, and *Fusarium* [40]. Mycotoxins cannot degrade during storage and are difficult to remove from CHMs because of their thermostability [41,42]. Moreover, considerable transfer rates of AFs and OTA have been observed from herbal medicines to decoctions and pose a threat to consumer health [43,44]. Comprehensive and efficient fungi identification in CHMs is an important basis for preventing fungal and mycotoxin contamination. Current assessment methods for fungal contamination in CHMs are based on fungal isolation and culture, which may affect the real extent of fungal diversities because of the difficulty to cultivate and isolate certain microorganisms. The application of DNA metabarcoding could overcome this limitation and better reveal the fungal diversity. For example, Xia et al. found that 55 genera in Chinese Cordyceps that were not observed by culture-dependent methods were identified through Illumina Miseq sequencing [45]. Similarly, another study indicated that the number of fungi in Coix Seed detected by HTS was considerably greater than that by potato dextrose agar medium [46]. In addition, DNA metabarcoding also overcomes some of the limitations of a culture-dependent approach (e.g., time-consuming and complicated procedure). It could be used as an effective tool for the simultaneous characterization of numerous microbial species. In previous studies, DNA metabarcoding has been successfully applied in the investigation of fungal contamination in Platycladi Semen [33], Myristicae Semen [34], and Cassiae Semen [35]. In the present study, DNA metabarcoding efficiently analyzed the fungal microbiomes in MOR and AOF. Thus, it can serve as a powerful tool for identifying fungi in CHMs.
