Microbes 101

Microorganisms found in cheese are responsible for much of the uniqueness and character that we all know and love

What are Microbes?

“Microbe” is short for microorganism -- any microscopic living organism*. There are many things found in this branch of the evolutionary tree. In cheese we usually find bacteria, yeasts, and molds. Even looking at just these categories leaves thousands upon thousands of microbes that could potentially be found cheese. For brevity's sake, we're going to cover just the basics (thus the “101”). There is a lot we won't cover here. If you're looking for a more in-depth review of microbes and cheese, check our MicrobialFoods.org.

*To avoid excessive repetition we'll be using “microbe”, “organism”, and “bug” interchangeably. I'll try my best to get the spelling right and not say how important orgasms are to cheese making.


Microbes in Cheese

The bacteria, molds, yeasts, etc. that find their way into cheese can be added intentionally by the cheesemaker or affineur. And by intentionally, I mean a person made a judgement call and chose which organism to add to the cheese. Of more interest and import are the multitude of microbes that are introduced into the cheese without any direct decision making from the cheesemaker/affineur. This is where a cheese takes on its so-called “terroir”. Microbes native to the milk will be carried over to the cheese and as cheese is being made and as it is being aged there are many ambient organisms that weasel themselves in.

Where microbes come from

Microbes are introduced into cheese at every step in the cheese making process


Lactic Acid Bacteria

These are the microbes (bacteria) that are added to the milk very early in the cheese making process that induce the fermentation process. The main reaction taking place here is the conversion of lactose to lactic acid, acidifying the milk, which explains how they get their name. You may have also heard of these guys referred to as “starter cultures”. Examples from this category include:

  • Lactococci - Lactococcus lactis ssp. lactis and Lactococcus lactis ssp. cremoris are common lactic acid bacteria that are used to make cheeses like cheddar
  • Streptococci - Streptococcus salivarius ssp. thermophilus is an example of a culture used in cheese like mozzarella
  • Lactobacilli - Lactobacillus helveticus is an example of a culture commonly used in Swiss and alpine cheeses. L. helveticus is also commonly used as an adjunct. (below)


Lactic acid bacteria are a ubiquitous starter culture

Adjunct Cultures

Adjuncts are microbes that are added for reasons other than just producing lactic acid. In many cases, adjuncts are added to encourage flavor development in the cheese. Lactobacillus helveticus (see above) is a common example, often giving cheeses a pleasant sweet flavor and promoting the growth of tyrosine crystals.


Lactobacillus helveticus often gives a sweet flavor to cheeses like aged Gouda


Related to adjuncts, Non-Starter Lactic Acid Bacteria are lactic acid bacteria that grow as cheese is ripened that weren’t added for the express purpose of acidifying the milk. Usually these microbes are present naturally in the milk or get picked up along the way during cheesemaking. As cheese ages, the numbers of NSLAB increase while starter cultures die off. Each of their exact roles in cheese flavor development is still trying to be understood completely. Examples include:

  • Lactobacillus casei ssp. casei
  • Lactobacillus plantarum

Eye Formers

Swiss cheese (and Gouda to a lesser degree) have pronounced eye (hole) formation due to the action of certain bacteria. Propionibacterium freudenreichii ssp. shermanii is a specific bacterium that converts lactic acid into carbon dioxide, propionic acid, and acetic acid. The carbon dioxide seeps into the cheese body and produces the eyes we all know and love. The other products of Propionibacterium metabolism also give the characteristic flavors commonly associated with Swiss cheeses.


Propionibacterium produce CO2 and form the eyes in Swiss

Gouda cheese often have eyes as well, although usually to a smaller degree than Swiss. In this case, it’s not propionibacteria that is responsible, but usually bacteria such as Leuconostoc mesenteroides and Lactococcus lactis ssp lactis biovar. diacetylactis. In this case it is citric acid that is converted to carbon dioxide and diacetyl (buttery flavor).



The two main molds that are found in/on cheese are blue and white, respectively. While there are specific molds cheesemakers add to get the cheese they want, there are many molds that grow naturally on the surfaces of cheese during affinage. We’ll be covering the former.

White Mold

Penicillium camemberti (fka Penicillium candidum) is the most popular mold species that is responsible for the nice white lawn on the surfaces of cheeses like camembert and brie. The metabolism of this mold is responsible for some of the characteristic aromas associated with white mold cheeses (mushroom, ammonia, etc.) as well as the texture (soupy goodness). You can often see this by looking at a cross section of a piece of young brie. You’ll observe a translucent soupy boarder surrounding a chalky center.

penicillium camemberti

Penicillium camemberti covers Brie and Camembert

Blue Mold

Penicillium roqueforti and Penicillium glaucum are the big players in the blue mold worlds. These are what give bleus the blues. The pigments are created by the molds as well as the unique flavor and distinctive texture. As mentioned in the opening paragraph of the post, these molds are living breathing organisms. Starving them of oxygen will change their metabolism and they will change color as well as produce off-flavors. For this reason it’s best to never vacuum package blue cheeses (or any mold-contain cheese for that matter). A common misconception is that when blue cheeses are pierced during the aging process that mold is being injected. Actually, those needles are there to create air channels. The mold is usually added to the milk during the preliminary cheese making steps or to the curds before they're hooped. The piercing only serves to encourage mold growth by introducing oxygen.

penicillium roqueforti

Penicillium roqueforti is a common blue mold added to cheese
Bayley Hazen Blue - Jasper Hill

Mold-like Yeast

I’d also like to mention Geotrichum candidum which is a yeast that exhibits mold-like tendencies. This microbes is responsible for the “brainy” appearance some cheeses have.

geotrichum candidum

Geotrichum candidum is responsible for the brainy appearance of some cheeses


Surface Ripened Bacteria

Brevibacterium linens is one of the most common bacteria that make up “smear” bacteria. It is also responsible for foot odor, which explains the smell of many surface ripened cheeses. This bacterium produces a multitude of compounds including ones that give rise to the distinctive aroma. Corynebacteria are another class of bacteria commonly found on these cheeses. It's important to remember that the combination of microorganisms is what makes the magic happen for many cheeses.

Brevibacterium linens

Brevibacterium linens and yeast often produces orange colored pigments



Often forgotten, but yeast are commonly used in the molded and surface ripened cheeses. They are also naturally present in many natural rind cheeses. These are important parts of the aging process of many cheeses. In many cases, there is a careful balance of yeast, mold, and bacteria that give rise to natural rinds. This will have its own post one day.



Here we talked about microbes seperately for the most part. It's important to remember cheese is often teaming with a whole slew of microbes interacting with each other and the environment. It's the combination of bacteria, yeast, molds, etc. that make the magic happen.

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Infographic summary of the information contained in this post.