Integrating shotgun metagenomics and wine metabolomics links terroir-driven microbiome functions to nucleotide, amino acid, fatty acid, and carbohydrate pathways

Abstract

Microbial terroir is increasingly linked to wine typicity, yet the chemical mechanisms connecting regional microbiomes to the wine phenotype remain incompletely defined. This stud focused on untargeted metabolomics to track terroir expression during alcoholic fermentation, supported by shotgun mycobiome profiling. Muscat (Vitis vinifera L.) grapes from two terroirs (Piedmont, Italy and Limnos Island, Greece) were vinified under comparable white-winemaking conditions and inoculated with the same Saccharomyces cerevisiaestarter. Samples were collected before inoculation, after 72 h, and at end of fermentation, having three biological replicates per each time point/region. The samples were analysed by shotgun metagenomics and LC-MS based metabolomics. Shotgun metagenomics showed clear terroir separation of fungal communities in musts, followed by a marked reduction in diversity during fermentation consistent with starter dominance. Differential abundance analyses highlighted Torulaspora delbrueckii enrichment in Greek samples and Kluyveromyces spp. enrichment in Italian samples. Functional profiling revealed terroir- and time-dependent shifts across core metabolic categories, including significant variation in amino acid, carbohydrate and energy metabolism. In parallel, UHPLC–QTOF-MS untargeted metabolomics generated broad chemical fingerprints, with unsupervised models separating samples primarily by terroir and secondarily by fermentation stage and showing larger divergence between terroirs in wines than in musts. Discriminant metabolite classes included oligosaccharides, glycosylated phenolics that decreased during fermentation but remained overall higher in Greek samples, and nitrogen-containing metabolites reflecting amino acid/peptide turnover and redox-related trajectories1. Overall, the multi-omics integration links terroir-driven microbiome functions to coherent pathway-level shifts in the wine metabolome, providing new tools that could be used to ensure wine authenticity and quality control.

References

Di Gianvitoa, P.; Saez, V.; Dimopoulou, M.; Papandreou, C.; Francesca, N.; Vrhovsek, U.; Rantsiou, K.; Cocolin, L.; Arapitsas, P.; Englezos, V. (2026). The role of mycobiome in terroir and during Muscat grapes fermentation unveiled by multi-omic analysis. Food Res. Int., in press.