Profiling of fungal communities in functional food Cistanches herba using high–throughput sequencing

Cistanches Herba (CH), known as Roucongrong, is a widely used health food supplement and medicinal herb. In recent years, fungal and mycotoxin contamination has affected the quality and safety of CH, posing a potential threat to consumer health. In this study, the Illumina MiSeq PE300 platform and targeted the internal transcribed spacer 2 sequences were used to investigate fungal communities in CH. The differences in the fungal communities of samples from different collection areas and processing methods were analyzed. As a result, 606 ASVs were obtained and were further classified into six phyla, 27 classes, 56 orders, 110 families, and 167 genera. Basidiomycota and Rhizopodaceae were the dominant phylum and family, respectively. Rhizopus (0%–43.72%), Aspergillus (0%–19.55%), and Fusarium (0%–20.27%) were the most dominant genera among the identified genera. Meanwhile, 13 species were identified, including two potential toxigenic fungi Aspergillus terreus and and Mucor circinelloides. In addition, variations in the composition of the fungal communities, the diversity of fungi, their trophic modes, and the functional guilds in CH samples from four different collection regions and two processing methods were observed. This work provides useful information for controlling fungal contamination in herbs and foods to ensure food safety and human health.