Grape Microbiomes Shape Wine Characteristics

The complexity of wine—from its aroma to its acidity to its flavor profile—is influenced by microbial metabolisms during the fermentation process. While the alcohol-producing Saccharomyces cerevisiae has a dominant role in this profile, increasingly, the role of fungi and yeast introduced from the original grapes, called microbial terroir, has been appreciated.¹

As geographical conditions, like temperature and climate, influence which microbes are present on the fruit, it’s possible that geography could represent another contributing factor to a wine’s final aroma, taste, and appearance. However, whether these native microbes survived through commercial fermentation processes, during which producers introduced S. cerevisiae into crushed grapes, to give rise to regional variations remained unknown.

Kalliopi Rantsiou, a microbial ecologist at the University of Turin, and her team put this question to the test. After collecting red grapes from three distinct regions in Italy and fermenting them into wine using the same process, the researchers showed that parts of the fruit’s original microbiome remained intact throughout fermentation.² Although the same kind of grape was collected from all of the vineyards in the same time period, Rantsiou and her team also observed differences in the aroma and metabolite composition of the final wine.

The findings, published in Applied Environmental Microbiology, suggest that geographic conditions that shape fruit microbiomes can influence wine’s profile.

The team collected the same variety of grapes from several vineyards across three distinct geographical regions in northern Italy: North Piedmont, South Piedmont, and Valtellina. The red grape variety, Nebbiolo, is well-defined and has its own unique features, which made it a good candidate to explore possible differences in wine profiles from microbes.

Using ribosomal RNA sequencing, the researchers found 451 bacterial sequence variants and 290 fungal sequence variants. After matching these to reference databases, the team identified eight fungi species and bacterial genera that were present in 50 percent or more samples. They used a principal component analysis to study the shifts in the fungal and bacterial communities from each vineyard through fermentation. While the communities shifted over this time course, these eight core fungi and bacteria taxa remained detectable.

Studying the vineyards’ microbiome diversity prior to fermentation, the researchers saw that while the fungal and bacterial community compositions were similar between Valtellina and North Piedmont samples, these microbial distributions were distinct from those of South Piedmont samples. Over the course of fermentation, though, the team observed distinct changes in the variation of microbial taxa in samples from the different regions. The researchers concluded that both geographic origin and fermentation influenced the overall microbiome of the samples.

To explore how these differences may have influenced the chemical properties of the final product, the researchers assessed the acid and sugar content at the end of fermentation and then used gas chromatography mass spectrometry six months after bottling the wine to study the metabolites present.

After fermentation, samples from the Valtellina region had a higher total acidity content, while South Piedmont samples had higher sugar contents. The type of predominant acids in the wines from the different regions also varied. Those made from grapes from South Piedmont vineyards had a higher content of acetic acid, which correlated with a higher abundance of acetic acid-producing bacteria. Meanwhile, North Piedmont and Valtellina wines had more malic acid that correlated with a lower abundance of bacteria that produced the enzyme needed to convert this acid into lactic acid.

The researchers also identified 39 volatile compounds, which influence a wine’s profile, in the bottled wines from all of the samples. Using a principal component analysis, the team found that wines produced with grapes from the North Piedmont and South Piedmont regions had distinct profiles based on their metabolite profiles, with high variation in these samples. Meanwhile, samples from the Valtellina region showed more homogeneity in their compounds.

Using another association analysis, the researchers showed that certain fungal species and bacterial genera correlated with compounds like alcohols, fatty acids, and terpenes that influence wine’s overall characteristics.

“The outcomes support the concept that microbial terroir is robust. Even when winemakers use commercial yeast inoculation—a widespread practice—the vineyard’s native microbial community still shapes fermentation trajectories and contributes to wine identity,” Rantsiou said in a press release.