The role of mycobiome in terroir and during Muscat grapes fermentation unveiled by multi-omic analysis

The wine microbiome is a key determinant in shaping wine terroir. To date, a comprehensive understanding of how microbial signatures influence wine metabolic profile remains poorly understood. To address this, in the present study an integrated shotgun metagenomics and untargeted metabolomic approach was employed to investigate the wine metabolome and connect the composition and functions of microbiomes involved in wine fermentation of Muscat grapes harvested in Italy and Greece. Beta diversity highlighted the dissimilarity between Italian and Greek fungal terroirs. A marked reduction in diversity during fermentation underscored the dominance of the inoculated Saccharomyces cerevisiae starter culture. The LEfSe analysis revealed an enrichment of Torulaspora delbrueckii in Greek samples, while Kluyveromyces marxianus and lactis were more abundant in Italian samples. Functional analysis revealed geographic differences in nucleotide, fatty acids and lysine metabolisms. Significant shifts were observed in energy, carbohydrate, and amino acid metabolisms, reflecting terroir-specific microbial activity. The metabolomics data highlighted regional differences in oligosaccharides, glycosylated phenolics, peptide and amino acid turnover, and central redox metabolites, suggesting divergent microbial responses and metabolic trajectories shaped by terroir and fermentation conditions. Obtained results highlight the effectiveness of this multi-omics approach in identifying product-specific fungal communities and wine metabolite signatures, providing new tools that could be used to ensure wine authenticity and quality control.