Use of High-Throughput Sequencing to Identify Fungal Communities on the Surface of Citri Reticulatae Pericarpium During the 3-Year Aging Process

Citri Reticulatae Pericarpium (CRP) is a natural product that is used widely in food and is an ingredient in traditional Chinese medicine. CRP improves gradually with aging; this process typically takes 3 years or more. During the aging process, CRP can be colonized with fungi and mildew. Molds and mildew may result in an increased flavonoid content; however, this has been observed only in response to fungi of the genera Penicillium and Aspergillus . As fungal colonization may alter the quality and properties of CRP, it is critical to have an understanding of the fungal communities detected on the surface of CRP during the aging process. We used a high-throughput sequencing (HiSeq) platform to sequence internal transcribed spacers (ITS) region to identify the contaminants associated with CRP during the 3-year aging process. We also evaluated the distribution of the dominant fungi of the genera Aspergillus and Penicillium over time. At the phylum level, we identified Ascomycota (36.26%) and Basidiomycota (18.98%), along with smaller populations of Mucoromycota , Glomeromycota , and Mortierellomycota . At the genus level, the fungi detected include Wallemia (12.40%), Cystofilobasidium (4.62%), Zasmidium (4.52%), Cladosporium (3.72%), Hanseniaspora (3.55%), Fusarium (3.49%), Kurtzmaniella (2.03%), Candida (1.74%), Passalora (1.47%), Ceramothyrium (1.33%), Mucor (1.07%), and Aspergillus (1.03%). Fungi of the genus Penicillium were detected primarily during the first year of storage. By contrast, fungi of the genus Aspergillus were not detected during the early stages (fresh peel–8 months), but appeared gradually at later stages of the aging process. Taken together, our results indicate that HiSeq is an effective method to study the changes in fungal communities that develop on the CRP surface over time. These findings provide a basis for further research into the correlation between dominant fungi and the mechanisms underlying the successful aging of CRP.