Recently the media hype about the tiny living things known as microbes has blown up, including controversy over antibiotic-resistance, and new research on bacteria that live in the human gut. The main punchline from stories like these: not all microbes are bad. In fact, they do essential things for our bodies, like help us digest food. They also make some popular food items, like beer, wine, bread, and chocolate, just to name a few. Microbe is a general term that refers to any organism that can only be seen using a microscope. Teams of scientists have taken to studying the microbes on our foods in hopes of finding new techniques to discover bacterial and fungal diversity. One great candidate for this research happens to be cheese!
Fig. 1 A variety of cheeses displaying the diversity of microbial rinds. The bacteria and fungi that make up these rinds are responsible for the colors and textures on the surface of cheese. (Source: Jorge Royan on Flickr https://www.flickr.com/photos/90129630@N00/ )
Think about all the varieties of cheese – from Camembert to Grueyère– which are teeming with billions of bacteria and fungi that give each cheese its unique flavor, color, and smell. Artisan cheeses, like many of the foods we eat, are not produced in a sterile environment, providing opportunities for microbes to colonize the surface. The microbes that cover the surface of cheese produce the rind, which is a type of biofilm, a mixture of sugars, bacteria, and fungi in a gelatin-like substance that enables the microbes to attach to moist surfaces. Microbes form biofilms in nature in order to protect themselves from toxins and antibiotics, to have easy access to food, to prevent drying out, and to easily communicate and exchange DNA. Some of the most pathogenic microbes are capable of producing these sticky substances, including the bacteria responsible for staph infections and stomach ulcers . In the case of cheese, the bacteria and fungi in biofilms are intentionally introduced from starter cultures applied by the cheese maker or from the environment where the cheese is made. These starter cultures are mixtures of good bacteria and fungi that prevent the bad microbes that cause disease from living on the surface of cheese. Biofilms such as cheese rinds are of interest to scientists because they provide a unique opportunity to study the diversity of microbes and the relationships and interactions between them.
Fig. 2 A microscpic view of the combination of bacteria and fungi within a biofilm. (Source: AJC on Flickr https://www.flickr.com/photos/ajc1/)
There are many types of bacteria and fungi that comprise the diversity of microbes on Earth. One of the major ways that microbiologists study these microbes is by isolating one type of microbe and growing them in the laboratory. Unfortunately many of these microbes are not easy to grow because they might require the presence of other microbes or an unknown mixture of food and vitamins, which limits scientists’ ability to study them. In addition to studying microbes in the lab, scientists also use genetics in order to determine which microbial species are present. This is essential for discovering the microbes that cannot be grown in the lab because it gives scientists a window into the microbial world which are otherwise too small to be seen. These two approaches are used on samples from environments other than cheese surfaces, like soils and water. Samples taken directly from the environment have more species than cheese, making them incredibly difficult to study.
Fig. 3 A collection of diverse cultured fungi found on the rinds of cheeses. (Source: Dr. David Midgley on Wikipedia https://en.wikipedia.org/wiki/Penicillium#/media/File:Ascomycetes.jpg)
Cheese has been made the same way for centuries and the cheese makers (and the microbes!) have a recipe that is proven to work. That means that the same microbes are likely to be found on the same types of cheeses, making them a predictable study system for scientists. In fact, after scientists sampled cheeses worldwide to determine the types of bacteria on the rinds, they found that most of the same species kept reappearing. They discovered that no matter where cheeses were produced across the world, there was a main mixture of microbes that kept showing up again and again. Cheeses from opposite corners of the globe were similar in the bacteria and fungi that they contained, sometimes even more similar than cheeses that were produced nearby . Scientists believe that this is due more to the manufacturing environment where cheeses are made rather than the geographic location of the cheese factory. Many artisan cheese makers apply salt washes or other treatments which influence the pH and moisture of the cheese. These are known to be controlling factors in the types of bacteria and fungi that can live in a certain area .
Through growing many of the major players in the cheese rind community, scientists were able to determine which bacteria and fungi like to grow together, and which species might depend on others in order to grow. This means that finally scientists are able to reconstruct a microbial community similar to what would be found in nature! This opens up novel avenues for exploring new microbes and figuring out what their capabilities . Scientists can then use the knowledge from simplified systems, such as cheese, and apply it to more complex environments like soil or the human digestive system. Cheese has always been a delicious and complex food, and now it is a scientific model for future research on environmental and health impacts. So the next time you dig in to that melty baked brie, thank a microbe!
Fig. 4 A slice of brie cheese with a white, bloomy rind, which is composed mainly of a fungus. (Source: Jennifer on Flickr http://chezlouloufrance.blogspot.com/2008/08/la-fte-du-fromage-brie-de-melun.html)
 Button, Julie E., and Dutton, R.J. “Cheese Microbes,” Current Biology 22(2012):R587-R589. http://www.sciencedirect.com/science/article/pii/S0960982212006598.
 Donlan, Rodney M. “Biofilms: Microbial Life on Surfaces,” Emerging Infectious Diseases 8 (2002): 881-890. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2732559.
 Benjamin E. Wolfe, Button, J.E., Santarelli, M., and Dutton, R.J. “Cheese Rind Communities Provide Tractable Systems for In Situ and In Vitro Studies of Microbial Diversity,” Cell 158(2014):422-433. http://www.cell.com/cell/fulltext/S0092-8674(14)00745-4.
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