August 8th, 2016

By Emily Pierce, PhD Student

One of my favorite parts of working in Rachel Dutton’s lab (besides having my boss bring cheese into the office on a regular basis) is getting to see people react to the statement “I’m doing research with cheese.”

This reaction usually occurs in three phases. First is the initial surprise, followed by a momentary doubt that this is a legitimate scientific endeavor, and finally there is the exclamation of “That’s really cool!” I couldn’t agree more; it is cool, and when you think about it, cheese is a great system for studying microbiology. Cheese, like other fermented foods and like our gut, is home to a diverse community of bacteria and fungi. Using cheese as a model, we are able to study both the mechanisms that drive the formation of these communities and the interactions between community members. For me, this research is the perfect pairing of my love of food and my love of interesting biology, and although it may sound cheesy, I feel like it was fer-meant to be.

Microbial rinds form on the surface of cheese during the aging process. The microbes that make up these rinds can come from intentionally added starter cultures, the milk or containers used, or from the surrounding environment. By altering characteristics of the cheese such as salt, pH, and moisture, cheesemakers can shape the microbial communities that form. The amazing diversity that you see when drooling over the cheese case at your local grocery store is largely a result of the various microbes that give each cheese its unique character. These microbes influence not only the appearance of the rind, but also the flavor of the cheese. Enzymes produced by microbes help to digest components of the cheese curds into smaller compounds that have distinct sensory properties. For example, Penicillium roqueforti, a fungus added to blue cheeses, produces a molecule called 2-heptanone that gives these cheeses their recognizable “blue” aroma. These microbial rinds also help to maintain a protective barrier that prevents pathogens from colonizing the cheese.



Left: This is a cross-section of an aged cheese showing a microbial rind biofilm on the surface. Image from Wolfe, et al. Cell 158.2 (2014): 422-433. Right: Here you see some examples of microbes isolated from cheese that can be cultured in the lab.

Using some of the same tools that are used by the American Gut project to look at the human microbiome, our lab has been able to characterize the microbial diversity of cheese rinds from all over the world. Interestingly, these studies showed that worldwide there are 24 genera of bacteria and fungi that consistently dominate cheese. Luckily for us, we are able to grow representatives of these genera in the lab, which means that we can reconstruct their communities and study how these microbes interact in the context of their natural environments.



This figure shows the results of a study looking at microbial diversity present in 137 different cheeses based on sequencing of bacterial 16S rRNA and fungal ITS markers. Each column in this figure represents an individual cheese. The bacteria and fungi listed at the bottom are frequent cheese inhabitants. For more information, see Wolfe, et al. Cell 158.2 (2014): 422-433.

One of the other interesting findings of this study was that there is a reproducible pattern of microbial succession on the surface of the cheese. As the cheese ages, new microbes establish themselves and replace the original pioneers in a systematic way. This makes cheese a good system for investigating how microbial communities initially form.



Cheese is therefore not only rich in flavor, but also rich in opportunities for studying microbial life. Although I am a relative newcomer to the field, this is certainly an exciting time to be involved in researching microbial communities. Through our collaboration with the Knight lab and the American Gut project, we hope to gain a better understanding of the microbial diversity present in fermented foods and to start to make connections between these microbes and our health. This spring, I was able to join the American Gut project at the Santa Barbara Earth Day Festival and was inspired by the interest that fermentation enthusiasts showed in the science behind these foods. I’m looking forward to the Santa Barbara Fermentation Festival in September as another opportunity to learn from the fermentation community and to encourage their involvement in the American Gut project.

The Dutton lab. Blog author Emily Pierce is second from right.

Emily Pierce is a second-year PhD student in Rachel Dutton’s lab, in the Division of Biological Sciences at the University of California San Diego.