Who Put the Holes in Swiss and the Blue in Blue? The Named Microbes Behind Your Favorite Cheese

Specific microorganisms are directly responsible for the iconic characteristics of popular cheeses, from the holes in Swiss to the blue veins in Roquefort and the rinds of washed-rind varieties. Understanding the roles of starter and secondary cultures, like Propionibacterium freudenreichii, Penicillium roqueforti, and Brevibacterium linens, transforms cheese tasting into an appreciation of microbial craft.

Shira Golan

October 28, 2026 · 5 min read

The holes in Swiss cheese, the blue-green marbling of a Roquefort, and the rust-orange rind and penetrating smell of a washed-rind wheel are not accidents of terroir or mystique. Each is the visible signature of a specific, named microorganism at work. A scientific review of the cheese ecosystem published in the journal Microorganisms traces these characteristics directly to individual species: Propionibacterium freudenreichii for the eyes and flavor of Swiss-type cheeses, Penicillium roqueforti for the veins and pungency of blue cheeses, and Brevibacterium linens for the color and aroma of smear-ripened varieties. Understanding those names, and what each one actually does, turns tasting from passive enjoyment into recognition.

Starter vs. Secondary Cultures: Different Roles, Distinct Outcomes

Cheesemaking is a relay race between two very different microbial teams, and confusing them is the most common misunderstanding in cheese appreciation. The first leg belongs to the primary, or starter, cultures: lactic acid bacteria such as Lactococcus lactis subspecies lactis and cremoris, used in most cheeses, and the pairing of Streptococcus thermophilus with Lactobacillus delbrueckii subspecies lactis in Italian and Swiss types. Their job is fundamentally structural: they convert milk sugar into lactic acid, acidifying the milk, firming the curd, and setting the stage for everything that follows. Flavor development begins here too, but acidification is their defining contribution.

The second leg belongs to secondary, adjunct, or ripening cultures, and this is where a cheese's identity is written. These microbes arrive on the scene after acidification has done its work, often on the surface or deep within the paste during the ripening months. Propionibacterium freudenreichii in Swiss-type cheeses, Brevibacterium linens and Corynebacterium casei in smear-ripened wheels, Penicillium camemberti on white moldy cheeses, and Penicillium roqueforti in blue-veined varieties all play this role, according to the microbial survey compiled from research by Fox and colleagues and by Parente and Cogan.

The distinction matters because the two teams respond to different conditions and produce different results. Acidification is fast and largely a matter of days; ripening is slow, unfolding over weeks or months at low temperatures and high humidity. The review emphasizes that the environment, from whether starters were used at all to ambient conditions in the aging room, modulates which microbes implant and how active they become. Those variables, not just the ingredient list, determine the "unique appearance, texture, aroma and taste properties of each cheese variety."

How Specific Microbes Shape Cheese Identity

What elevates cheese appreciation from trivia to understanding is the causal chain: a named species performs a specific biochemical action, and that action produces a characteristic you can see, smell, and taste. Consider blue cheese first. The mold Penicillium roqueforti is added to the milk or curd, but the famous veining depends on a deliberately physical intervention: piercing the wheel to create air tunnels. Only when oxygen enters does the mold grow along the curd-air interface and develop the blue veins. Wisconsin Cheese's cheese-science guide credits P. roqueforti with creating blue cheese's "distinctive smell, flavor, and blue veins," noting that other species such as Penicillium glaucum, most associated with Gorgonzola, appear in some blues with a greener cast.

The mold's flavor work is biochemical. During ripening, P. roqueforti breaks down fat, increasing the free fatty acids that contribute the characteristic sharp flavor of blue cheeses. The veins themselves are also responsible for much of the aroma. In blue cheese production, ripening then proceeds at around 10°C and 85–95% humidity for at least one to two months, conditions that let the mold do its work slowly.

Swiss-type cheese offers an equally legible chain. Propionibacterium freudenreichii is a secondary ripening culture whose documented roles are hole formation and flavor development. The eyes that make a wheel of Emmental recognizable and the nutty note that accompanies them trace back to this single species acting during the warm ripening phase. Smear-ripened cheeses complete the picture: Brevibacterium linens, a ripening bacterium, contributes color and flavor development on the washed rind. Smithsonain Magazine's reporting on the science behind cheese describes how yeasts first neutralize the acidity created by lactic acid bacteria, which is what allows B. linens to join the community at all, a vivid illustration of how ripening cultures depend on the starter cultures that preceded them.

From named microbe to the characteristics in your slice
Microbe	Cheese example	Key action (biochemical process)	Resulting flavor/aroma	Resulting texture/appearance
Propionibacterium freudenreichii (secondary ripening bacterium)	Swiss-type cheeses	Ripening activity during the warm phase of aging	Characteristic Swiss-type flavor development	The holes ("eyes") that define the style
Penicillium roqueforti (ripening mold)	Blue-veined cheeses	Breaks down fat, increasing free fatty acids; grows only where oxygen reaches it via pierced air tunnels	The distinctive pungent smell and sharp flavor of blue cheese	The blue veins growing along the curd-air interface
Brevibacterium linens (secondary ripening bacterium)	Smear-ripened (washed-rind) cheeses	Colonizes the rind after yeasts neutralize acidity; flavor and color development on the surface	Flavor development characteristic of the style	Surface color of the smear-ripened rind

Beyond Fermentation: The Science of Cheese Flavor

It is worth pausing on what "flavor development" actually means chemically, because the phrase hides the real machinery. A cheese's sensory profile is not one compound but a portfolio of biochemical changes, driven during ripening by whatever microbes are present and active. Fat breakdown liberating free fatty acids is one documented route, as in blue cheese. Proteins are another frontier: enzymatic action on proteins produces the volatile compounds behind many aromas, which is how surface bacteria such as B. linens shape the smell of a washed rind.

Microbes also compete. A 2020 study of 55 artisanal Irish cheeses, cited in Smithsonian Magazine's coverage, found that almost one in three cheese microbes carried genes for producing chemical compounds that kill off microbial rivals. The final community in a wheel, and therefore the final flavor, reflects both cooperation and conflict, shaped further by technological choices and environmental conditions during ripening.

There are honest limits to how far this story goes. Cheese character also depends on milk, rennet, salt, and the affineur's technique, and this account focuses on the microbial contribution. Nor is every microbe in a wheel welcome; the same open surfaces that invite B. linens can admit contaminants. But for the enthusiast, the microbial lens is the most direct one available: these three species alone explain three of the most recognizable cheese families in the shop.