Between the discovery of listeria-laden Colorado cantaloupes and the release of Steven Soderbergh’s film “Contagion,” in which a virus kills millions of people, it’s been a rough season in PR for microbes. Faced with such reminders of their deadly potential, you may well have a natural urge to throw up some firewalls: No more handshakes, no sharing of the cellphone, and, God forbid, no sprouts.
But scrubbing your life of microbes is impossible. Microbes — bacteria, fungi, and other microscopic organisms — are the dominant form of life on earth. In fact, to a significant extent, you are microbes. About 90 percent of the cells, and 99 percent of the genes, in “your” body belong to bacteria, not you. Because bacterial cells are smaller than human cells, they make up only 10 percent of your body weight, but almost all the cells you’re carrying around have their own agenda.
The problem is, we have only the vaguest sense of that agenda. Despite their omnipresence, microbes are hard to study. They are inconveniently small. The traditional solution has been to isolate a single species and culture it in a lab. But microbes, just like other forms of life, live in communities. And just as a bored chimp in a zoo acts very differently from a wild chimp confronted with a fig tree, a leopard, or another chimp, a microbe monocultured in a petri dish won’t exhibit the wide range of behaviors it does in its natural environment. What’s really interesting about any organism is how it responds to other organisms — does it eat them, run away from them, or start a business with them?
Unfortunately, microbial communities are so complex — there may be a thousand different species in your gut or in any cubic inch of soil — that it’s virtually impossible to tell who’s doing what to whom. Which of the 99 different species in the vicinity caused that mold to start producing antibiotics? What made this dormant virus start reproducing like mad?
To start getting a grasp on microbial interactions, we need to study microbial communities that are simplified, but still real. That was the challenge facing Rachel Dutton, a Harvard microbiologist who was searching for a community to study that was complex, but not too complex, and that was naturally isolated. One day, she realized that she’d been eating her ideal subject all her life: cheese.
Artisanal cheese isn’t made of milk so much as it’s made of bacteria, fungi, and their byproducts — the milk is just the culture to grow the microorganisms. Each cheese is like a tiny, resource-rich island on which a collection of microbial species are thrown together, “Survivor” style. Along with postdoctoral fellow Benjamin Wolfe, Dutton is now in year one of a five-year project at Harvard University’s Center for Systems Biology to re-create those island communities in the lab and see who prospers, who gets double-crossed, and who gets voted off the island. To do that, they need to isolate all the organisms from a particular cheese, culture them in the lab, and then reintroduce them to each other in a number of different trials under slightly varied circumstances, and watch what happens.
“Eventually we’d like to understand the genes and pathways that are responsible for how these organisms live together,” Dutton says.
That could have important implications for our health, as well as our more general understanding of how microbes interact. Learning how microbial communities first form, for example, could help us to understand how infections take hold, why certain pathogens suddenly proliferate, and what we can do to stop them. It could also help us to cultivate our inner microfloral gardens in more precise ways than the yogurt carpetbombing currently in vogue.
Dutton and Wolfe began their project by visiting Jasper Hill Farm, a Vermont cheesemaker known for having the most diverse cheese cellar in America, and scraping samples from its cheese rinds. They’ve already found 15 different species of microbes on Winnimere, a washed-rind cheese known for its multifaceted flavor and cantankerous aroma. Some of their findings were unsurprising, such as a bacterium previously found on Europe’s most delicious washed-rind cheeses. Others were revelations, including several bacteria previously found only in extreme environments like the Arctic Ocean and Norwegian fjords. Some of those species persist, covering the rind in colorful blooms, while others give way to new species, the way a grassy pasture gives way to trees.
According to Dutton, that microbial community is the essence of the cheese. “It’s the microbes that smell, not the cheese. It’s the microbes we’re tasting.” (In fact, when we eat the blue veins in Gorgonzola, the downy fuzz on Brie, or the orange goop on Limburger, we’re wolfing down millions of living microbes on a cracker.) “When we isolate these organisms in the lab, they actually smell like cheese. A lot of times we’ll smell them and say, ‘OK, that’s Winnimere!’” In fact, their fridge has become a bit of a sore spot with their lab neighbors. “The cooler does not smell pleasant around here,” Wolfe admits.
That scent, however, may be the sweet smell of success for American cheesemakers, who have long sought to duplicate the complex flavors of traditional European cheeses. Those traditional cheese varieties were established centuries before any understanding of microbiology; cheesemakers simply learned that certain practices would produce cheese with particular flavor. Parmesan makers, for instance, learned to inoculate the milk for each day’s cheese with the whey from the previous day. The greatest cheeses were happy accidents of geography. Leave a young sheep’s milk cheese in the caves near the French town of Roquefort-sur-Soulzon, for instance, and when you return in a few months you’ll have a blue-veined masterpiece on your hands, thanks, we now know, to the indigenous Penicillium mold that lives there. Later, cultures were made from the famous cheeses so that their flavors could be reproduced elsewhere.
Yet, even once the role of microbes was understood, cheesemakers were able to identify only the most obvious players in their cheese, which is why none of the lab-derived starter cultures can re-create the diverse flavors produced by the microbial community in a real, ancient European cheese cave. This is one reason why few American cheeses have achieved the intensity and complexity of the great European cheeses. Europeans chalk this up to “terroir,” the semi-mystical uniqueness of the land, but the local microbes are probably the real muses.
Dutton and Wolfe are now beginning a large survey of both American cheeses and classic European cheeses such as Valençay, St. Nectaire, and Stilton, with the goal of identifying all the microbes present in each. “We’re hoping to see distinct signatures of the microbial communities based on the different styles of cheese,” Wolfe says. If they can connect certain microbes with certain flavors and textures, Dutton and Wolfe may serve as a Prometheus to American cheesemaking, handing American cheesemakers powerful new knowledge that the European gods have kept all to themselves. “We’ll be able to tell cheesemakers that if you add this strain of Geotrichum, you get more of Species X,” Wolfe speculates, “and Species X is known to produce floral flavors. You can hopefully get to a point where you can make predictions. Nobody in the cheese world has this knowledge at the genomics level. They have their cultures that they use, but it’s been hit and miss, because they’re tossing them into an unknown community.”
Such knowledge could help American cheesemakers to emphasize their own unique terroir. Wolfe has already found a new strain of Geotrichum, the fungus responsible for the quilted texture of many goat cheese rinds, that appears to be native to Jasper Hill Farm. “The cheesemakers want a good product,” he says, “so it makes sense that they’ve been using what was used in France, but it’d be cool to break away from that. Maybe we’ll find really cool strains in our survey that could be useful to cheesemakers, and even make it more regional. Maybe there are West Coast strains and East Coast strains. Who knows?”
All this has made Dutton and Wolfe accidental cheese celebrities. When the two scientists attend American Cheese Society meetings, cheesemakers line up with their cheeses for analysis in a sort of microbial version of “Antiques Roadshow.” Their microscope images have been featured in Culture magazine, and Dutton has been sharing lecture stages with Sister Noella Marcellino, the much-celebrated “Cheese Nun” who received a Fulbright scholarship in microbiology while making cheese at a Benedictine abbey in Connecticut.
Now, their fame is spreading beyond the world of cheese, which is, of course, only one of microbes’ great culinary creations. Yeasts, which are single-celled fungi, give us bread, wine, and beer; mold produces soy sauce and miso; bacteria are responsible for the fine flavors of chocolate, kimchi, vinegar, and salami. The Manhattan chef David Chang, of Momofuku fame, recently enlisted Dutton and Wolfe to ensure that the pork loin he had fermented wasn’t going to kill anyone. That collaboration went so well that he now has them helping him to grow koji, the mold used to ferment soybeans, so he can make his own miso, among other things.
“It’s been a real blessing to have Rachel and Ben as a resource,” Chang said. “They’ve opened all kinds of doors for us. There’s no way we would have found out anything without their help. Outside of some basic knowledge about cheese and wine and brewing beer, there’s not much info [about microbes] out there for chefs.”
Chang believes that learning to work with microbes may be the next great culinary revolution. Being able to control fermentation gives chefs a new set of flavor and texture tools within a traditional framework. “Every chef I ever worked for told me ‘Here’s how you make sauerkraut,’ but he never said why. He never said it has to do with the bacteria already present in the cabbage. Everyone always says to hang the duck by the neck until the head falls off, but no one ever knew why. Now, understanding how bacteria work, what if we can make an aged Parmesan in six months instead of two years? What if I can age beef in six days instead of 60? Is that good? I don’t know, but it will make us ask many fundamental questions about how we make stuff. It’s going to force chefs to become more knowledgeable, and knowing is never a bad thing.”