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Tag: JessicaHuang

Say Cheese! A Snapshot of Microbial Communities on Cheese

Author: Jessica Huang

Editors: Keith Fraga, Hongyan Hao, Sharon Lee


I love eating cheese. If you set a block of cheese in front of me, I will probably not stop eating. One of my favorite memories from taking French in high school, besides singing a bunch of Disney songs in French, was the time my teacher brought a few different cheeses for us to try out. I have briefly thought about getting a cheese wedding cake if I ever manage to get married.

But what makes cheese so cheesy? The answer is, surprisingly, microbes.


How is cheese made?

Before we delve into the contribution of the microbial community within cheese, it’s important to know a bit about how cheese is made. The key component in milk for making cheese is the protein casein. Normally, casein is found in a micelle form in milk, which means that several caseins aggregate together into a spherical form. Since casein is negatively charged, the spherical micelles repulse one another. However, if acid is added, the negative charge is neutralized, allowing for coagulation, which is the thickening of milk into solid curds that are used to make cheese. Using this method alone will produce softer cheeses.

Comic about caseins coming together.


Another way to promote coagulation is to use rennin, which contains a protease called chymosin that breaks down κ-casein, a soluble protein that forms a protective and stabilizing layer around casein micelles. This formation of the solid milk curds is the first step in making cheese. The curds are then separated from the whey, which is a liquid byproduct composed of proteins that remain soluble even after acidification and rennet treatment. Whey can be used for several things, such as protein shakes. Meanwhile, the curds are processed in various ways to make different types of cheeses. The last step is the maturation of cheese, which contributes most to the distinct flavor of cheese and can last anywhere from several months to several years.


So where do microbes come into the picture?

While vinegar or lemon juice can be used to acidify milk, another common method is to use microbial starter cultures instead. Some of the most commonly used strains in starter cultures include Lactococcus lactis (used for cheddar), Streptococcus thermophilus (used for mozzarella), and the Lactobacillus species (used for Swiss cheese). These bacteria help acidify milk by converting lactate into lactic acid.

Microbes also play a significant role during the aging process of the cheese. During this time, bacteria added from the starter cultures begin to die off, while other microbes that were either already in the milk from the beginning or joined in from the environment along the way begin to flourish.

Sometimes additional microbes known as adjunct cultures are added. Their main purpose is to enhance the flavor or texture of the cheese rather than to produce lactic acid. One example is the mold Penicillium roqueforti, which puts the blue in blue cheese through its formation of spores. The unique flavor of blue cheese comes from the conversion of fats into flavorful free fatty acids and methyl ketones by lipases produced by P. roqueforti. Another example is Penicillium camemberti, which gives cheeses like camembert and brie their soft, gooey texture. Its preference for the surface of the cheese allows for the development of a characteristic soft, white, bloomy rind. The holey appearance of Swiss chese is thanks to Propionibacterium freudenreichii. These bacteria convert lactic acid inside the cheese into carbon dioxide, which becomes trapped and forms bubbles. Acetate and propionic acid are also produced as byproducts and contribute to the flavor of the cheese. P. freudenreichii is often used together with Lactobacillus helveticus, a strain that can also be used when making cheeses like cheddar and that helps produce a nutty flavor.

A) Spores formed by  roqueforti throughout blue cheese. B) Bloomy rind of brie formed by P. camemberti.


Of course, there are many other microbes present in cheeses. In addition to those that are added, there are also microbes that were present from the very beginning in the milk, as well as ones that were acquired throughout the cheese-making process. Furthermore, many factors such as pH, temperature, and salt content affect which microbes are capable of forming colonies in the cheese. The presence of the microbial community, the metabolic byproducts they produce, and their interactions with one another in turn produce the distinctive flavor, aroma, and texture of many different cheeses.


A cheesy model system?

Cheese is home to many different microbes, and the rind is especially rich in microbial diversity. This makes cheese a potential model system for studying microbial communities. One of the labs that uses cheese for research is headed by Rachel Dutton at UC San Diego. Back in 2014, her lab successfully sequenced 136 different rind communities and found that they are highly reproducible. They discovered that the composition of the microbial community on cheese rinds and the relative abundance of individual microbes is correlated with the type of rind. For example, the bloomy rinds of camembert have a denser population of fungi, as would be expected of rinds produced due to the mold P. camemberti. The environment that the cheese is exposed to as it ripens is important too, but surprisingly, where the cheese was made does not correlate with the composition of the microbial community.

The Dutton group also found that many of the dominant species can be isolated and cultured, allowing them to easily recreate the communities in vitro. Thus, they were able to study interactions between different species, and observe how they affect one another in pairs. One of their findings is that the presence of fungi may promote an increase in pH, creating an environment that is beneficial to some bacteria. Overall, it looks like they’ve succeeded in creating quite the tasteful system.


Cheese is grate

Cheesy pun aside, cheese really is quite wonderful. It’s the basis of many delicious dishes and makes for a great snack by itself. On top of all that, it’s also making cool contributions to science. You gouda love it.

(P.S. Cheese can still go bad. If you see mold that isn’t supposed to be on the cheese, throw it out if it’s a soft cheese. For hard cheeses, which have lower moisture content, you should be able to cut off the moldy part and keep the rest. Bon appetit!)



  • Button JE, Dutton RJ. Cheese microbes, Current Biology 22 (2012) R587-R589.
  • Wolfe BE et al. Cheese Rind Communities Provide Tractable Systems for In Situ and In Vitro Studies of Microbial Diversity. 158 (2014) 422-433.


Finding Your Way: Choosing a Thesis Lab

Contributing authors (alphabetical order): Emily Cartwright, Anna Feitzinger, Keith Fraga, Hongyan Hao, Jessica Huang, Sharon Lee, Linda Ma


Congratulations, you’ve made it past the harrowing applications, nerve-wracking interviews, and awesome recruitment food! The first year in graduate school can be difficult, as you juggle coursework with organizing rotations and looking for the lab you’ll be dedicating the next 4-6 years of your life to. The question of which lab you will join is the question that you think about all the time, and rightfully so. The experience and relationships you make during your PhD are transformative. But there are many variables to consider and reaching a final decision on which lab to join can be a challenge!

All of us here at BioScope have gone through the same process, and we have some ideas that just might give first-year graduate students another perspective on deciding on a lab. In some ways, this is an advice column, but definitely not a “How to” article. We don’t know of a magic bullet that makes this decision easy. Part of the process is actually experiencing the process itself: all of the highs and lows, all of the epiphanies and backtracking, and the feeling of finally deciding. So let’s get started!

Getting through rotations!

Perhaps the first step in deciding on a lab is doing rotations. Granted, some disciplines and graduate programs do not operate on a formal rotation schedule. However, in general, there is a period of time during the first year where you will have the chance to rotate with a lab that you are interested in. The “Car Dealership Test Drive” analogy works perfectly here. What better way to experience a lab environment, the research they do, and how you work with the PI more than doing a rotation with them?

Specifically, here at UC Davis, many graduate programs provide great resources for finding faculty to rotate with. Don’t forget that you can look in other departments as well! UC Davis has diverse faculty, covering a range of fields that you will definitely find something that you’re interested in pursuing.

While shopping for a car, you can test drive as many cars as you want, which is not the case in graduate school. You can only participate in a limited number of rotations. Therefore, there can be a lot of planning and reflection that goes into who you should rotate with. There are two things we want to stress about managing rotations:

(1) Know what you want to study – or what you DON’T want to study – to a point where you can narrow down the labs you are interested in. Having the self-discipline to focus your interests is critical for decisive rotation decisions.

(2) Rotations are less about the progress you make in the short amount of time in the lab, and more about getting a feel for the lab. In the rotation, you receive a small project, and in the hopes of impressing the PI, the lab, and your peers, you devote a lot of energy to generating results. Striking gold during a rotation (such as getting results that will contribute to a manuscript) is rare, and not something to bet on. Instead, it is much more efficient to devote your attention to being in lab, experiencing the group, learning how you work with the PI, and gaining a solid grasp of the research program.

Honesty and Realism goes a long way

An important thing to remember when looking for rotation labs is to be realistic. You can’t be searching for a lab that studies microRNAs in brain development by day and cures Down syndrome by night. Even a lab with diverse projects maintains very specific and well-defined areas of interest. Having ambitious goals and ideas are great, but the key is to not pigeon-hole yourself to a point where every lab you come across doesn’t quite do everything you are excited about. Your perfect lab does not exist. You have to let your scientific interests grow and develop, and allow yourself to be mentored.

This goes to a deeper point about graduate school. It is not so much what you do, but how you do it and learning the skills to be a scientist. It is very common for individuals to work on something totally different from their thesis research after graduating. Doing a PhD helps you sharpen the tools to study a variety of problems. Getting a PhD is more about the training, and finding a lab is more about fit than it is about field.

Handling uncertainty is key

As mentioned above about rotations, knowing your interests is key to to deciding which lab to join. This is part of “Knowing yourself,” which consists of answers to questions like, “What am I interested in?”, “What type of research environment do I work best in?”, “Do I want a PI that is hands-on or hands-off?”, “What do I want to do after my PhD? And how can my thesis lab facilitate that?”, and many more. You can answer these questions by thinking back to labs you’ve worked in before and what you liked and didn’t like about them. With each rotation, you’ll be able to get a clearer idea of what your answers to these questions are.

Deciding on a thesis lab can be roughly split into concerns of two types: concerns that you can control, and concerns that are beyond your control. What we want to highlight is an appreciation of the difference between what you have control over (your attitudes, your interests, your effort) and things you cannot control or predict (how your relationship with your PI will develop, how funding will change, how experiments will go).

The major pitfall in deciding a thesis lab is being too worried about things that you cannot control. We are all concerned about choosing the “wrong” lab, becoming stuck in a situation where we need to switch advisors. In those cases, the relationship with the PI deteriorates due to a host of reasons. You cannot forecast these changes to your relationships. You do your best to address problems early on and find solutions. Appreciating the things that you can control gives you a tool in making your decision.

Things you should ask yourself

Choosing a thesis lab is a very personal process. It is about you, and you finding your way through graduate school. All of us here at BioScope arrived at our respective labs in different ways, and we pondered different concerns. However, we have recognized a few questions you should ask yourself. These are questions that you do not need the answer to right now. These are questions where your answer will change over time, maybe every 5 minutes! Nevertheless, these are some questions that are meant to get you thinking.

The Research

  • Do I love the science, and am I excited about the unanswered questions in the field?
  • Can I see myself truly enjoying reading papers in this field?
  • Am I willing to perform the literature searches necessary to fill in my gaps of knowledge?
  • Can I imagine performing the essential lab techniques on a daily basis, becoming an expert in the lab’s tools?

The Thesis Advisor

  • Can I see myself working with this PI for the next several years?
  • How comfortable do I feel communicating with the P.I.? Is it easy to have a conversation and brainstorm ideas?
  • Do I do better when the P.I. has an open door policy (questions always welcome), or can I be productive without meeting with my P.I. once a week?
  • What is the PI’s track record with other PhD students? What do other people say about the lab?
  • Is my PI supportive of my future goals?

The Environment

  • Can I have enjoyable and intellectual communications with the other students/post-docs, or do I feel like there are unpleasant interactions?
  • Do I prefer a lab that’s more social, or one where everyone goes into lab just to get the work done?

The grass on the other side is still just grass

Finally settling into a lab is a wonderful feeling; It’s like finally finding a home. And yet, we still have our difficulties. We still have our miscommunication. We still sometimes ponder if we made the right decision. It is very natural to have these questions because, like we said, there is no magic bullet, no recipe for doing this. And as scientists that strive for some degree of precision and exactness in our lives, this is hard to wrestle with. A lab is not perfect when you join. It takes dedication, patience, and communication to create a PhD training perfect for you. So keep calm, and carry on.



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