Variations in fungal microbiota and aflatoxin contamination during the processing of Yuanzhi, a traditional Chinese medicine

Abstract A traditional Chinese medicine (TCM) root extract known as Yuanzhi has recently garnered extensive attention because of its ability to improve cognitive function and memory. We attempted to advance understanding of the complex biological processes that accompany the harvest and post-harvest processing of this chemically and anatomically unique material. Here, we report changes in the fungal microbiota during the processing of Polygala tenuifolia roots, as determined by high-throughput sequencing. Our results showed that compacting the roots in airtight polyethylene bags prior to the heart removal process, which is undertaken to facilitate the heart-removal process, did not alter the fungal operational taxonomic unit (OTU) abundance or composition significantly. Once the heart of the P. tenuifolia roots was discarded, the OTU counts decreased for many fungal taxa, such as endophytes, while the Penicillium increased markedly. These results can help inform provide practical guidelines for improving the storage and processing protocols used by both P. tenuifolia producers and by the TCM apothecaries who prepare and prescribe Yuanzhi.