Comparison of DNA purification methods during wine fermentation for high throughput sequencing of fungal communities

High throughput sequencing approaches, targeting a specific, taxonomically discriminant locus, allows great insights into the composition of microbial communities. Traditionally, microorganisms are studied by cultivation on artificial culture media; a method known for its pitfalls as only a minor part of microorganisms can be grown in vitro. It is particularly true during the winemaking process, where successions of molds, yeasts and bacteria are observed. Understanding the impact of this dynamic growth on the wine quality is one of the future challenges in enology. As of now, although several articles studied fungal communities using high throughput sequencing, no comparative study on DNA extraction performance in enological matrix is available. This work compares for the first time, five selected DNA extraction methods. These methods were tested on must, must under fermentation and wine. Methods were evaluated according to their extraction yields, purity of extracted DNA, and the robustness of downstream molecular analyses, including PCR and high throughput sequencing of fungal communities. Overall, only 2 out of 5 tested DNA extractions methods appeared suitable for robustly studying microbial communities in wine samples. Thus, this work provides data that aims to facilitate further studies focused on microbial communities during winemaking, using high throughput sequencing.