DNA metabarcoding uncovers fungal communities in Zingiberis Rhizoma

Zingiberis Rhizoma (ZR, Ganjiang in Chinese), also known as dried ginger, is a popular spice and medicinal herb that has been used for several thousand years. However, ZR is easily contaminated by fungi and mycotoxin under suitable conditions, and might be hazardous to the health and safety of consumers, thus concerns about the herb's safety have been raised. The aim of this study was to investigate the fungal community and the effects of collection areas and processing methods on the fungal community in ZR.

A total of 18 ZR samples were collected from four provinces of China, and the samples were divided into four groups based on collecting sites. Meanwhile, the samples collected in Sichuan Province, China were divided into three groups based on the processing methods. We employed the Illumina MiSeq PE300 platform and targeted the internal transcribed spacer 2 (ITS2) sequences to investigate fungal contamination in ZR samples, and the difference in fungal community among the groups of different collection sites and processing methods.

All 18 samples were contaminated with fungi. Ascomycota was the dominant phyla, accounting for 34.46%-100% of the fungal reads. At the genus level, Candida, Diutina, and Aspergillus were the most dominant genera, with relative abundances of 0-98.37%, 0-99.82%, and 0-79.08%, respectively. Meanwhile, four potential toxigenic fungi and seven human pathogens were found. Furthermore, differences in the community composition of ZR samples from four collecting sites and three processing methods were observed.

DNA metabarcoding provides a novel insight into fungal community diversity in ZR samples, providing references to ensure the sustainable utilization and quality research of ZR.