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The Microbiologist Sniffing Out the World’s Perfect Cheese

Rachel Dutton’s studies of bacteria may have a huge impact on dairy as we know it.

Rachel Dutton, surrounded by oodles of cheese.
Rachel Dutton, surrounded by oodles of cheese. Erik Jepsen, UC San Diego Publications

Underneath a laboratory’s fluorescent lights, Rachel Dutton examines a cheese morsel. It’s not so much a treat as it is a mystery. That’s because Dutton is a scientist—a molecular biology detective of sorts—who has devoted her career to studying the tiny bacterial communities that live in and on cheese. Her tool of choice is a microscope, which she uses to pore over evidence hidden within microscopic crumbles. Ultimately, she hopes to uncover how these microbes create colonies within these creamy and waxen morsels.

From Camembert to cotija, making any type of cheese essentially starts in the same way. Cheesemakers take fresh milk, then curdle it. The mixture separates into solid clumps, known as curds, and a watery substance, whey. They then mold the curds into shape.* From there, all the cheese has to do is sit and age. Yet it’s the near-invisible community of bacteria that not only gives cheese its funk, but is also capable of transforming a few simple ingredients into an addictive kitchen staple. Many mass-produced cheesemakers use packets of bacteria to form these cultures. But change the bacteria within cheese, and it becomes an entirely different beast.

Along with her lab crew at UC San Diego, Dutton has made immense progress in identifying the myriad bacteria, yeast, molds, and viruses that live on wheels and in wedges of cheese. Some bacteria and fungi stick together, forming the rind that lines a wheel of cheese’s exterior. Others devour the inside of the cheese, and create the kinds of lapis-hued blooms within blue cheese. And some burp carbon dioxide when they consume lactic acid inside the cheese, which is what gives Swiss cheese its distinctive interior.

Dutton believes that studying the minutiae of bacteria can teach us about the microbial communities—also known as microbiomes—found on virtually every conceivable surface, in the human body, and in the ocean. “We’re kind of using cheese like our lab rat,” explains Dutton. “The goal of using a simple microbiome, like cheese, is to understand how these communities are built and how to manipulate them if we want to.” It’s no wonder that her intriguing approach to food science has caught the attention of kitchen innovators, such as Momofuku’s David Chang, who Dutton collaborated with several years ago.

Rachel Dutton at work.
Rachel Dutton at work. Erik Jepsen, UC San Diego Publications

Dutton originally studied molecular biology at Harvard University’s medical school. After earning her PhD, she worked in the cellars of Vermont cheesemaker Jasper Hill Farm for several months; there, she marveled at how each morsel of cheese contained a tiny world within it. That fall, she went back to Harvard, this time starting her own lab focused on teasing out how these worlds form.

In 2014, Dutton’s lab studied some 150 types of cheese from 10 different countries to determine similarities and variances. Similar work had been done in France, but nothing on the same scale as Dutton. “A lot of what she’s doing is groundbreaking … it was a big project, big thinking,” says Mateo Kehler, co-owner of Jasper Hill Farm where Dutton began her research and a celebrated cheesemaker in the U.S.

During her tenure at Jasper Hill, Dutton found ample variances between microbes and types of cheese. For example, hard cheeses, such as cheddar, have a common bacterial makeup regardless of where they were produced. Cheeses with a washed rind—or those that have a sticky, fleshy exterior—can have colonies with 20 types of microbes living together, maybe more. The same goes for soft cheeses, including brie.

“How the cheese is made sets a very specific environment,” says Dutton. “These microbes are eating the protein and fat in the milk and breaking those down into flavor molecules, using the cheese as food for themselves. In the process of doing that, they spit out all these byproducts which we perceive as interesting smells and flavors.”

The resulting gases, enzymes, and molecules are what create pungent, cauliflower-like smells or the veins within blue cheese. “Each microbe is different, so it’ll do slightly different things depending on the microbes you have,” Dutton explains. Cheese isn’t unique in hosting microscopic living organisms, though. These ecosystems also exist in other fermented foods. “The production of fermented foods relies on highly reproducible communities on a fast timetable,” Dutton says.

Dutton’s stint at Jasper Hill Farm proved formative, not only for her research but for the creamery, too. While Dutton was the first microbiologist to work there, Jasper Hill has hired a full-time microbiologist since her departure. Through this, the creamery has learned, for instance, that 80 percent of the microbes in raw milk come from the outside of their cows. Incremental changes that happen while feeding livestock, and even in the cows’ bedding, can dramatically change milk’s microbial composition.

Wheels of Harbison cheese age at Jasper Hill Creamery.
Wheels of Harbison cheese age at Jasper Hill Creamery. U.S. Department of Agriculture / CC BY 2.0

“It was all chance,” Kehler says. “We stumbled into this relationship with her and it’s really changed our business. She called us up and we didn’t really have any intention of building a microbiology lab or doing any of the work.” He adds: “I credit her to a large degree with setting us up to do really interesting things.” These days, the creamery is especially interested in exploring the flavor profiles associated with brachybacterium, one particular strain of bacteria that can impart a strong broccoli or clam-like flavor profile. Through this newfound focus, the creamery was also able to entirely eliminate listeria, a potentially deadly contaminant, from their farm.

Panos Lekkas currently works as Jasper Hill Farm’s staff microbiologist. Lekkas, who has a background in agriculture and in researching human pathogens, now hunts for bacteria hidden in the creamery’s barn and among its hay. To do so, he swabs surfaces and exposes petri dishes to the elements to catch any bacteria cruising through the air.

Sometimes, this testing results in happy accidents. “There’s one bacteria that I grew a lot of people smell it and they say it smells like Ovaltine. I don’t try to understand it,” Lekkas says. “I just say ‘Oh, great.’” Eventually, Jasper Hill hopes to create a cheese using only native cultures from the farm. To get there, Lekkas is experimenting with the different strains of bacteria in the cheesemaking process. “There are so many strains where we don’t even know what they do, but they’re there. And they give us a great taste and aroma and appearance and texture,” Lekkas says.

Over thousands of years, humans have learned how to harness microbes to create a varied—and delicious—product. For contemporary food scientists like Lekkas, examining cheese at the microbial level reinforces a return to early cheesemaking techniques when bacteria came from local environments rather than mass-produced packets. “Nature knows its balance, and we’re trying to imitate that,” says Lekkas.

The implications of understanding microbes goes far beyond making the perfect cheese. But it’s through cheese that Dutton hopes to learn about the formation of bacterial colonies, and ultimately how they can be manipulated. That could translate to improving human health, and the health of the world around us, too. “I have a different perspective on cheese,” Dutton says. “As a microbiologist, you learn to appreciate that microbes are wonderful and everywhere and they’re just a part of our world.”

Updated 4/18: The article has been updated to reflect the fact that cheese results in both curds and whey, but that cheese is most often made from the curds.

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