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    • May 10, 2021
    • 4 min read

MicroEducation - Cheese Microbiome

Recently in the MicroEducation series we’ve written a lot about food - coffee, sourdough bread, and even food composting. That’s because we rely on microbial fermentation to make a LOT of our food products. Sticking with the theme of microbes making delicious dishes for us, this week we are going to discuss the cheese microbiome (a community of different microbes that live inside/on cheese).


What exactly do microbes do for cheese?


It’s generally accepted that cheese was initially invented as a way to keep milk from spoiling. There are three major steps that occur in cheese production: 1) milk coagulates - resulting in two phases, solid curds and liquid whey; 2) curds are separated and processed; 3) processed curds (now what we’d call cheese) are aged (Button & Dutton, 2012).

The first and the third steps are where cheesemakers heavily rely on microbes. For milk to coagulate - form chunks of curds - our old friends, lactic acid bacteria (whom you may remember from our sourdough post) have to ferment the lactose in milk and produce lactic acid. Cheesemakers have special ‘starter cultures’ of lactic acid bacteria that they can add to the milk to aid this process (Button & Dutton, 2012; Wolf 2019). Now, the third step is where things get interesting, because it’s during the aging process where “cheese is truly transformed — from fresh cheese into the myriad flavors, aromas, and textures of mature cheese.” (Button & Dutton 2012). All of the microbes present in the cheese at this stage have time to grow both inside and on the surface - resulting in the funky, sometimes creamy, sometimes crispy/dry cheesy goodness we all enjoy.


Why do different cheeses have different tastes/textures/smells?


So we now know that cheese making involves three steps - two of which heavily depend on microbes. Which makes the answer to the question above quite obvious - because there are different microbes in different cheeses...duh! Actually, that’s only half right. Unlike other commonly studied microbiomes -e.g. the human intestinal/skin/oral microbiome - the cheese microbiome represents an almost perfect model system to study in the lab. This is because a large number of the microbes that colonize cheese during fermentation are culturable, they are dependable (they are pretty much always there - we call this “reproducible” in the lab), and cheese itself is a pretty easily manipulated ‘food’ source to grow these microbes on.

Most of the differences in cheese come from HOW they are handled during the first and third stages of production. Factors like pH, salt content, raw/pasteurized milk, etc all can naturally select for certain microbes. However, sometimes cheesemakers add specific microbes to their fresh cheeses to produce a particular type of cheese, for example, they use Penicillium roqueforti to produce the famous blue cheese, roquefort. A review from established cheese microbiome researchers - Button & Dutton, nicely outlined how some of the most famous/special cheeses are made, and we’ve condensed those findings in the image below.

If we know so much about cheese microbes, why are researchers studying them?


The cheese microbiome is unique because unlike most other microbial ecosystems, a large majority of the microbes in it can be grown in a lab and studied. This means that researchers can gain unique insights into how microbes interact with each other or just how they generally function. Furthermore, cheesemakers can make better tasting and more consistent cheese if they have a better understanding of which microbes are present and what exactly they are doing. Recently, a group of researchers looked at the genetic material of the microbiome of more than 200 cheese samples - these types of studies are called metagenomic studies - and found 47 potentially new species of microbes that may play major roles in a cheese’s taste and color! They also found evidence of microbes within the cheese microbiome competing with each other - for example they showed that bacteria were producing compounds that kill other bacteria as well as using special genetic modifications that could protect against viruses (Walsh, et al., 2020). Basically, these cheese bacteria are doing everything they can to ensure they are ‘the big cheese’ of the cheese microbiome.


The findings from studies like these can also help cheese producers alter how they make cheese to prevent something called ‘fermentation failures’ - basically when the cheese production goes awry. This can happen for a number of reasons, one which is the presence of undesirable bacteria. Previously, researchers identified a handful of spurious species of bacteria that could cause different problems. For example, bacteria from the genus Enterococcus which are sometimesdetected in reblochon, pecorino, or moriber cheeses may cause food poisoning by producing biogenic amines such as histamine and tyramine. Spoilage bacteria Thermus thermophilus are known for the production of carotenoids which may cause pink discoloration in the ripened cheese. Red-brown defects in italian fontina are linked with the presence of the genera Brevibacterium, Corynebacterium, and Microbacterium.


Take home message


Bacteria and fungi have long been known to confer unique flavors/colors/smells/textures to many tasty cheeses that are enjoyed world wide. While the cheese microbiome is often used as a model ecosystem in labs, because most of the microbes found there can easily be cultivated in a laboratory, recent studies have shown that there is still a lot that we can learn from these delicious ecosystems.


This article was written by Courtney Thomas and edited by Alex Vorobev.

 

Glossary:

  • A starter culture - a group of specific bacterial strains put together to initiate the transformation of milk into cheese.

  • Metagenomics - the study of the genomes of whole biological communities recovered directly from environmental samples.

 

References:

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