Cheese cultures are living bacteria, originally wild microorganisms that were naturally present in raw milk, on the skin of animals, in the air of dairy environments, and on the surfaces of traditional cheesemaking equipment. Over centuries of repeated use, these bacteria were unknowingly selected and domesticated by cheesemakers long before anyone understood microbiology. Today, most commercial cheese cultures are produced by specialized laboratories that have isolated, purified, and freeze-dried specific bacterial strains, but their ancestry traces back to those same wild populations.
The Wild Bacteria in Raw Milk
Before refrigeration and pasteurization, milk arrived in the cheese vat teeming with bacteria from multiple sources: the cow’s udder and skin, the grass she ate, the hands of the person milking her, and the wooden buckets used to collect the milk. Among these microbes were lactic acid bacteria from genera like Lactobacillus, Lactococcus, Leuconostoc, Pediococcus, and Streptococcus. These bacteria naturally ferment lactose (milk sugar) into lactic acid, which drops the milk’s pH toward 4.6. At that acidity, the milk’s protein structure changes: casein molecules lose their ability to stay dissolved in water and begin clumping together, forming the solid curds that become cheese.
This process happened spontaneously in warm raw milk. Early cheesemakers didn’t add cultures. They simply created the right conditions (warmth, time) and let the indigenous bacteria do the work. The specific mix of microbes varied by region, season, and animal species, which is one reason traditional cheeses from different places taste so different from one another.
How Backslopping Domesticated Wild Bacteria
At some point, cheesemakers noticed that saving a small amount of whey or curd from a successful batch and adding it to the next day’s milk produced more consistent results. This technique, called backslopping, is one of the oldest forms of culture propagation. It’s the same principle behind sourdough starters and sauerkraut fermentation.
Each time a cheesemaker backslopped, they were applying selection pressure. Bacteria that thrived in milk, tolerated salt, and produced good acid and flavor were carried forward. Bacteria that couldn’t compete died off. Over hundreds or thousands of generations, this created increasingly specialized populations of bacteria, essentially domesticated strains that were optimized for cheesemaking without anyone consciously engineering them. Many of the starter cultures used in industrial cheesemaking today descend from these traditional backslopped populations, isolated and purified in the 20th century.
Geography, Tools, and “Terroir”
The concept of terroir, usually associated with wine, applies to cheese as well. Large-scale research comparing cheeses across regions has shown that bacterial and fungal communities in both milk and cheese differ significantly depending on geographic area, animal species, and local cheesemaking practices. A high proportion of the microbes found in finished cheese can be traced directly back to the milk, but the cheesemaker’s environment adds its own signature.
Wooden vats, aging caves, and even the air inside a dairy harbor resident microbial communities that colonize each new batch. This is why many protected-designation cheeses (like Comté, Parmigiano-Reggiano, or Roquefort) insist on traditional tools and facilities. The regional know-how and physical environment actively shape the cheese microbiota in ways that can’t be replicated by simply shipping the same starter culture to a different location.
The Five Primary Starter Species
Despite the enormous diversity of cheese varieties worldwide, only five bacterial species do most of the heavy lifting as primary acid producers. These are the organisms responsible for the critical first-day fermentation that transforms liquid milk into solid curd.
They fall into two temperature groups. Mesophilic cultures prefer moderate warmth (around 20 to 32°C, or roughly 68 to 90°F) and are used in cheeses like cheddar, Gouda, and Colby. The two key mesophilic species are both strains of Lactococcus lactis. Thermophilic cultures work at higher temperatures and are essential for cheeses like mozzarella, Parmesan, and Swiss. The primary thermophilic species include Streptococcus thermophilus, Lactobacillus delbrueckii, and Lactobacillus helveticus.
Secondary and “Wild” Cultures
Beyond the primary starters, a second wave of microorganisms shapes a cheese’s final character during aging. Some of these are intentionally added. The bacterium responsible for the eyes (holes) in Swiss cheese, for instance, is Propionibacterium freudenreichii, which ferments compounds in the curd and produces carbon dioxide gas bubbles. Blue cheeses rely on molds like Penicillium roqueforti, while the sticky orange rinds on washed-rind cheeses come from surface bacteria deliberately encouraged during aging.
Other secondary organisms arrive uninvited. Non-starter lactic acid bacteria (NSLAB) are naturally present in most cheese varieties and dominate the microbial population during ripening. Species like Lactobacillus casei, Lactobacillus plantarum, and Lactobacillus curvatus aren’t added as starters, but they tolerate the harsh, low-moisture, salty, acidic environment of aging cheese remarkably well. They break down proteins and fats in the curd, generating the complex flavor compounds that distinguish a sharp aged cheddar from a mild young one. Some cheesemakers now add selected NSLAB strains as adjunct cultures to steer ripening in a desired direction or to add probiotic benefits.
How Modern Culture Companies Produce Them
Today, most cheesemakers purchase freeze-dried or frozen cultures from a handful of specialized companies. These firms maintain libraries of bacterial strains, many originally isolated from traditional European dairy environments decades ago. The production process involves growing a pure strain in large fermentation tanks under controlled conditions, then concentrating and preserving the bacteria through freeze-drying or deep freezing.
The result is a packet or canister of dormant bacteria that a cheesemaker can add directly to pasteurized milk, replacing the wild populations that pasteurization killed. This gives industrial producers consistency and predictability, since the exact same strain blend can be used batch after batch. In the United States, starter culture organisms carry “generally recognized as safe” (GRAS) status from the FDA, a classification based either on a long history of safe use in food prior to 1958 or on formal scientific safety evaluation. The regulations require that only nonpathogenic, nontoxic strains are used.
Artisanal vs. Industrial Sourcing
The distinction between artisanal and industrial cheese often comes down to where the cultures originate. A farmstead cheesemaker working with raw milk may rely heavily on the indigenous bacteria already in that milk, supplemented by the microbial community living on their equipment and in their aging room. Some still practice backslopping, maintaining a living culture that evolves slowly over time. These cheeses tend to have more complex, variable flavor profiles because the microbial community is more diverse and less controlled.
Industrial operations, by contrast, pasteurize the milk (killing native bacteria), then add a defined starter culture with a known composition. This produces a more uniform product but sacrifices some of the microbial complexity that gives traditional cheeses their depth. Many mid-scale and craft cheesemakers split the difference: they use a commercial starter for reliable acidification but work with raw or lightly pasteurized milk, wooden tools, or natural rind techniques to invite environmental microbes into the process.