Illustration by Justin Renteria

The Bugs that Give Wine Its Flavor

Can sequencing a vineyard’s microbiome make it possible to reverse engineer a fine wine?

Marcus Woo
Apr 19, 2018 · 5 min read

For the uninitiated, wine talk can be puzzling. Oenophiles gush over hints of tobacco, pencil shavings, charred herbs, and loamy soil. It’s brawny, chewy, cedary, or raw. Whether these descriptions are perceptive or pretentious, they all get at something subtle and complex about wine, notably terroir: the idea that a wine’s characteristics are an expression of the place where the grapes grow.

Soil, climate, geology, topography, elevation, and local winemaking traditions and techniques all make a particular wine different from others made with the same grapes. But now scientists are finding another factor contributes to terroir: microbes.

Every winemaker already knows that microorganisms drive the fermentation process that turns grape juice into a potent potable. But they’ve had little insight into the thousand species of fungi, bacteria, and archaea that teem in the soil, on the vine and the fruit, and even in the cellar, forming communities known as microbiomes. In the soil, these microbes can alter how roots grow and absorb nutrients, which affects the quality of the grape. Although microbes are filtered out of the finished product you drink, they persist through the fermentation process, producing chemicals that taste of, say, vanilla or butter.

What most of these microbes do, exactly, is still a bit of a black box. But a San Francisco-based startup called Biome Makers wants to help growers and winemakers better understand how these critters affect their product. For $199 a pop, vintners can submit a sample of their soil, vine, grape, unfermented grape juice, or any other part of the fermentation process. By sequencing the microbial DNA, Biome Makers provides an analysis of the sample’s microbiome, giving growers a potentially powerful new way to manage their grapes and winemaking process.

“Now we have the possibility to understand the microbiome and the microbes of wine,” says Francisco De Frutos, the U.S. business development manager for Biome Makers. Researchers are still teasing out the details for how specific microbes affect wine, and even De Frutos admits that precise prediction and control is not yet possible. But someday, scientists’ understanding of the wine microbiome could allow for fine-grained manipulations of terroir.

Biome Makers can sequence the soil, vines, grapes, or fermented liquids from a vineyard to identify its microbiome. It plans to expand to other crops such as sugar cane, apples, and pecans. (Photo courtesy of Biome Makers)

The startup, founded in 2015, is part of a wave of companies trying to make better use of the microbiome for agriculture. Startups and big corporations such as Bayer think that manipulating microbes will boost crop yield and quality and help manage diseases. In one ambitious partnership, Bayer and a synthetic biology company, Ginkgo Bioworks, that will enable a wide variety of plants to get nitrogen from the air rather than requiring fertilizer. In March, Bayer established a new lab space for biotech startups, with Biome Makers as its first tenant. Startups such as Trace Genomics also sequence soil microbiomes to help growers ensure healthy soil. A company called MicroTrek samples microbes to monitor fermentation and spoilage during food and beverage production.

As part of its service, called WineSeq, Biome Makers provides a website that vintners can use to understand their wine microbes. The site identifies microbes that may muck up fermentation — an abundance of a bacterium that produces acetic acid, for example, leading to an overpowering taste of vinegar. The company also flags pathogenic microbes that could cause diseases on the vines.

Then there’s terroir. Researchers that grape microbiomes in California’s Napa and Sonoma counties depend on the type of grape, where it’s grown, and the climate. They have also variations in grape microbiomes and the chemical composition of wine to specific vineyards in Napa. Scientists have also that certain strains of S. cerevisiae, the primary yeast that ferments wine, vary from region to region in New Zealand. Biome Makers can identify a few specific yeasts that it says have been linked to certain flavors, such as a zinfandel’s body and its spicy, floral, or earthy qualities.

Left: The front end of Biome Makers’ vineyard sequencing app, which can include sample results, diseases, treatments, and microbiome diversity. Right: The raw data. (Photo courtesy of Biome Makers)

Still, these types of studies only highlight correlations between microbiomes and particular locales and soils. Microbes produce lots of chemicals, and they likely interact with one another in myriad ways. Identifying cause-and-effect connections between specific microbes and the aromas of a riesling is not yet something scientists can do, let alone predicting or even manipulating a microbe’s influence on wine.

“Microbial terroir is a measurable thing; it’s just that understanding the implications of that are challenging at this point,” says Reid Griggs, a graduate student in enology at the University of California, Davis.

Griggs says he doesn’t know Biome Makers’ exact methods, but he’s skeptical that identifying a few bugs can really predict flavor. So much of fermentation, for instance, depends on environment. “The same yeast in two different juices is going to produce two different wines,” he says. Standard sequencing techniques also don’t provide a complete picture of all the compounds a microbe can produce. For a winemaker, he says, applications of sequencing technology at this point might not go much beyond identifying pathogens that could cause disease in grapevines.

But despite the uncertainty so far, some winemakers are already recognizing the potential of the wine microbiome, says Jean Michel Valette, the CEO of Vinfolio, and the former CEO of Franciscan Estate Winery and managing director of Robert Mondavi Winery. “We don’t always know what to look for, or what to look at,” he says. “But we know we need to be looking.”

Identifying microbes may be especially useful for people like David Olson, owner of Sustainable Growing Solutions in California and one of Biome Makers’ clients. Olson’s company, founded in 2013, sells diverse microbial communities — nurtured in rich compost, for example — that go into irrigation systems to help crops grow better. A third of his customers are wine-grape growers. But no one really knows how Olson’s products work. Enter Biome Makers: it was able to identify the microbes that produce certain compounds that help the vine grow.

Olson says the data he gets from Biome Makers helps him choose the best mix of bugs for a particular crop. “It gives us a quantitative tool we just didn’t have before,” Olson says.

For wine tasters, microbiome analyses might someday provide yet more complexity — and verbiage. If those notes of blueberry and black pepper weren’t subtle enough, you might bring up the full body and spicy, vegetal undertones of M. pulcherrima and H. uvarum.

NEO.LIFE

Making sense of the Neobiological Revolution.

Marcus Woo

Written by

Science journalist

NEO.LIFE

NEO.LIFE

Making sense of the Neobiological Revolution.

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