Morindae Officinalis Radix (MOR) and Alpiniae Oxyphyllae Fructus (AOF) have been widely used as dietary supplements and traditional herbal medicines for centuries. Fungal and mycotoxin contamination in MOR and AOF has been reported recently. In this study, fungi in MOR and AOF are first investigated using DNA metabarcoding, and the differences in fungal microbiome between moldy and non−moldy samples are analyzed. The results show that Ascomycota is the most prevailing fungus at the phylum level in MOR and AOF with relative abundances of 49.53–94.32% and 14.81–81.85%, respectively. Penicillium (1.86–76.14%), Cladosporium (1.82–56.65%), and Trichoderma (0.12–19.71%) are the dominant genera in MOR. Penicillium (0.27–56.06%), Papiliotrema (0.04–51.71%), and Cladosporium (3.08–44.41%) are the dominant genera in AOF. Two potential toxigenic fungi were detected, namely, Trichoderma atroviride and Fusarium equiseti. Moreover, the differences in fungal communities between moldy and non−moldy samples were monitored. In conclusion, DNA metabarcoding can be used to assess the fungal microbiome in edible medicinal herbs, thereby providing a basis for ensuring food safety and drug efficacy.

Lonicerae Japonicae Flos (LJF) has been globally applied as an herbal medicine and tea. A number of reports recently revealed fungal and mycotoxin contamination in medicinal herbs. It is essential to analyze the fungal community in LJF to provide an early warning for supervision. In this study, the fungal community in LJF samples was identified through DNA metabarcoding. A total of 18 LJF samples were collected and divided based on the collection areas and processing methods. The results indicated that Ascomycota was the dominant phylum. At the genus level, Rhizopus was the most abundant, followed by Erysiphe and Fusarium. Ten pathogenic fungi were detected among the 41 identified species. Moreover, Rhizopus, Fusarium, and Aspergillus had lower relative abundances in LJF samples under oven drying than under other processing methods. This work is expected to provide comprehensive knowledge of the fungal community in LJF and a theoretical reference for enhanced processing methods in practical manufacturing.