*Article* **Analysis of Fungal Microbiomes in Edible Medicinal Morindae Officinalis Radix and Alpiniae Oxyphyllae Fructus Using DNA Metabarcoding**

**Wenjun Jiang 1,†, Xuyu Chen 2,†, Mengyue Guo 1, Jingsheng Yu 1, Meihua Yang <sup>1</sup> and Xiaohui Pang 1,\***


**Abstract:** 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.

**Keywords:** Morindae Officinalis Radix; Alpiniae Oxyphyllae Fructus; DNA metabarcoding; fungal microbiome; toxigenic fungi
