Blessed are the (tiny) cheesemakers

Blessed are the (tiny) cheesemakers

By Ute Eberle

Some cheeses are mild and soft like mozzarella, others are salty-hard like Parmesan. And some smell pungent like Époisses, a funky orange cheese from the Burgundy region in France.

There are cheeses with fuzzy rinds such as Camembert, and ones marbled with blue veins such as Cabrales, which ripens for months in mountain caves in northern Spain.

Yet almost all of the world’s thousand-odd kinds of cheese start the same, as a white, rubbery lump of curd.

How do we get from that uniform blandness to this cornucopia? The answer revolves around microbes. Cheese teems with bacteria, yeasts and molds. “More than 100 different microbial species can easily be found in a single cheese type,” says Baltasar Mayo, a senior researcher at the Dairy Research Institute of Asturias in Spain. In other words: Cheese isn’t just a snack, it’s an ecosystem. Every slice contains billions of microbes — and they are what makes cheeses distinctive and delicious.

People have made cheese since the late Stone Age, but only recently have scientists begun to study its microbial nature and learn about the deadly skirmishes, peaceful alliances and beneficial collaborations that happen between the organisms that call cheese home.

To find out what bacteria and fungi are present in cheese and where they come from, scientists sample cheeses from all over the world and extract the DNA they contain. By matching the DNA to genes in existing databases, they can identify which organisms are present in the cheese. “The way we do that is sort of like microbial CSI, you know, when they go out to a crime scene investigation, but in this case we are looking at what microbes are there,” Ben Wolfe, a microbial ecologist at Tufts University, likes to say.

Early on, that search yielded surprises. For example, cheesemakers often add starter cultures of beneficial bacteria to freshly formed curds to help a cheese on its way. Yet when Wolfe’s group and others examined ripened cheeses, they found that the microbial mixes — microbiomes — of the cheeses showed only a passing resemblance to those cultures. Often, more than half of the bacteria present were microbial “strangers” that had not been in the starter culture. Where did they come from?

People have been making cheese for thousands of years. This illustration from a 14th century manuscript shows medieval Europeans making cheese — and eating it.

Many of these microbes turned out to be old acquaintances, but ones we usually know from places other than cheese. Take Brachybacterium, a microbe present in Gruyère, which is more commonly found in soil, seawater and chicken litter (and perhaps even an Etruscan tomb). Or bacteria of the genus Halomonas, which are usually associated with salt ponds and marine environments.

Initially, researchers were dumbfounded by how some of these microbes ended up on and in cheese. Yet, as they sampled the environment of cheesemaking facilities, a picture began to emerge. The milk of cows (or goats or sheep) contains some microbes from the get-go. But many more are picked up during the milking and cheesemaking process. Soil bacteria lurking in a stable’s straw bedding might attach themselves to the teats of a cow and end up in the milking pail, for example. Skin bacteria fall into the milk from the hand of the milker or get transferred by the knife that cuts the curd. Other microbes enter the milk from the storage tank or simply drift down off the walls of the dairy facility.

Every cheese is an ecosystem of bacteria and fungi. These microbes were isolated from the rind of a Vermont blue cheese. The orange colonies with ruffled edges are the bacterium Staphylococcus xylosus and the white ones are S. succinus. The small round colonies are several species of Brevibacterium, and the fuzzy white colony is a Penicillium mold.

As the various species settle in, territorial struggles can ensue. A study in 2020 that looked at 55 artisanal Irish cheeses found that almost one in three cheese microbes possessed genes needed to produce “weapons” — chemical compounds that kill off rivals. At this point it isn’t clear if and how many of these genes are switched on, says Cotter, who was involved in the project. (Should these compounds be potent enough, he hopes they might one day become sources for new antibiotics.)

But cheese microbes also cooperate. For example, the Saccharomyces cerevisiae yeasts that eat the lactic acid produced by the LABs return the favor by manufacturing vitamins and other compounds that the LABs need. In a different sort of cooperation, threadlike fungal filaments can act as “roads” for surface bacteria to travel deep into the interior of a cheese, Wolfe’s team has found.

By now you might have started to suspect: Cheese is fundamentally about decomposition. Like microbes on a rotten log in the woods, the bacteria and fungi in cheese break down their environment — in this case, the milk fats and proteins. This makes cheeses creamy and gives them flavor.


The microbes that colonize cheese come from many places. Some are intentionally added to the milk, while others drift there from the environment and from the cheesemakers themselves. Details of temperature, salt, acidity and other variables determine which of the colonists survive and dominate as the cheese matures.

Even the tiniest changes in how a cheese is handled can alter its microbiome, and thus the cheese itself, cheesemakers say. Switch on the air exchanger in the ripening room by mistake so that more oxygen flows around the cheese and suddenly molds will sprout that haven’t been there before.

But surprisingly, as long as the conditions remain the same, the same communities of microbes will show up again and again, researchers have found. Put differently: The same microbes can be found almost everywhere. If a cheesemaker sticks to the recipe for a Camembert — always heats the milk to the relevant temperature, cuts the curd to the right size, ripens the cheese at the appropriate temperature and moisture level — the same species will flourish and an almost identical kind of Camembert will develop, whether it’s on a farm in Normandy, in a cheesemaker’s cave in Vermont or in a steel-clad dairy factory in Wisconsin.

Some cheesemakers had speculated that cheese was like wine, which famously has a terroir — that is, a specific taste that is tied to its geography and is rooted in the vineyard’s microclimate and soil. But apart from subtle nuances, if everything goes well in production, the same cheese type always tastes the same no matter where or when it’s made, says Mayo.

By now, some microbes have been making cheese for people for so long that they have become — in the words of microbiologist Vincent Somerville at the University of Lausanne in Switzerland — “domesticated.” Somerville studies genomic changes in cheese starter cultures used in his country. In Switzerland, cheesemakers traditionally hold back part of the whey from a batch of cheese to use again when making the next one. It’s called backslopping, “and some starter cultures have been continuously backslopped for months, years, and even centuries,” says Somerville. During that time, the backslopped microbes have lost genes that are no longer useful for them in their specialized dairy environment, such as some genes needed to metabolize carbohydrates other than lactose, the only sugar found in milk.

But not only has cheesemaking become tamer over time, it is also cleaner than it used to be — and this has had consequences for its ecosystem. These days, many cows are milked by machines and the milk is siphoned directly into the closed systems of hermetically sealed, ultra-filtered storage tanks, protected from the steady rain of microbes from hay, humans and walls that settled on the milk in more traditional times.

Often the milk is pasteurized, too — that is, briefly heated to high temperatures to kill the bacteria that come naturally with it. Then, they’re replaced with standardized starter cultures.

All of this has made cheesemaking more controlled. But alas, it also means that there’s less diversity of microbes in our cheeses. Many of our cheddars, provolones and Camemberts, once wildly proliferating microbial meadows, have become more like manicured lawns. And because every microbe contributes its own signature mix of chemical compounds to a cheese, less diversity also means less flavor — a big loss.


Originally posted in full in Knowable Magazine

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