Wine must metagenomic study

Microbial community profiling is a fundamental tool in modern viticulture and oenology, but high-quality DNA extraction from polyphenol-rich samples, such as wine must, is a critical barrier for shotgun metagenomics. In this study, we used two must samples to compare four DNA extraction protocols: an established standard commercial kit (DNeasy PowerFood Microbial Kit), an intermediate CTAB-PVP protocol, manual CTAB, and the PVP-EDTA-TE polyphenol removal approach. The PVP-EDTA-TE protocol, which employs sequential washes before kit-based lysis, achieved substantially higher DNA yields than all alternatives, consistently meeting input requirements for sequencing library preparation. We show that the shotgun sequencing of samples processed with this protocol produces high-quality data with low host DNA contamination, reliable taxonomic profiles, and metagenome assembled-genomes (MAGs), matching prior wine must studies. We provide full protocol and buffer preparation instructions. We advise that the PVP-EDTA-TE protocol ensures inhibitor removal and high yields: it is therefore the protocol of choice for metagenomic analysis of wine must fermentations.