Cheese provides unexpected vehicle for microbial research

While many science laboratories enforce a strict “no food in the lab” policy, Assistant Professor of Biology Benjamin Wolfe’s lab almost always contains at least one kind of food: cheese. Wolfe studies how microbial communities assemble, and he often uses food in his lab, especially cheese, which contains live microbial communities.

“We use cheese because it’s delicious and interesting, and there aren’t that many microbes in it, so it’s low in diversity and easy to take apart,” Wolfe said.

After “taking apart” the microbes in the cheese, Wolfe and others who work in his lab then reassemble them.

“During that process, you can understand what is the order that things go, where things go and how they fit together,” he said.

Wolfe compared the process to assembling a car: every part, he said, must be placed in a specific location and in the correct order.

“We’re trying to address that same question with microbial communities -- species of microbes, bacteria and fungi that live everywhere, such as in soil, in food and in the air,” he said. “We’ve become really good at describing that diversity, and we can measure it really easily, but the challenge is how to understand where the diversity comes from. Why do we see different diversity in different places -- in Medford, Cambridge and Lincoln, Mass., for example?”

Most microbial communities are highly complex, so this question is often difficult to answer, according to Wolfe. But microbial communities in cheese and other fermented foods tend to be relatively simple, and Wolfe is able to grow all the microbes that live on the cheeses in his lab.

Wolfe, who started working at Tufts in September 2014, currently has seven undergraduate students and one rotating graduate student working with him in the lab.

“They keep the lab going,” he said. “They’re always in and out doing various projects. I had a huge response for lab workers and had to turn some people away because we have limited space.”

Michael Zalesne, a junior majoring in biology, first got involved with Wolfe’s “cheese lab” through working in a synthetic biology lab at Tufts. After meeting Wolfe, he decided to get involved with his lab as well.

“I’ve always really liked food -- food and cheese are some of my favorite things in the world,” Zalesne said. “I wanted to learn some microbiological techniques in the lab, and get to eat some.”

Zalesne’s work focuses on discovering the cause of an unusual purple-colored culture in a raw goat milk cheese.

“Purple is a unique color in the microbial community, so it’s an interesting endeavor,” he said. “The cheese maker cannot get it to go away. We don’t know if it’s infectious, but it’s not sellable.”

He added that the shade of purple is similar to the color that emerges during purple urine bag syndrome, a rare syndrome that usually occurs in older women. The problem could be caused by similar bacteria, he said.

Zalesne is also working on a side project in the lab, in which he works to produce miso-flavored cheese.

“Experimental evolution was one of the big selling points of joining his lab,” he said.

Junior Ina Bodinaku, who majors in women’s studies and biology, joined Wolfe’s lab last October.

“I want to be a medical student, so I felt like learning about how microbes interact with each other in communities you don’t think of -- like cheese -- could be beneficial for seeing how they behave in the human body as well," she said. "I thought it was cool how [Wolfe] worked with cheese, that’s something people don’t really think of when they think of microbes.”

Bodinaku’s work focuses on one specific fungus: penicillium.

“It’s a problematic fungus that grows in cheese, and it’s becoming really invasive,” she said.

Normally, penicillium is not found in places where cheese is produced, Bodinaku said, and it likely comes from outside sources, like soil, that come into contact with cheese caves where the cheese ages. Bodinaku plans to continue working in the lab this summer, expanding on her current work with penincillium.

“I’m going to look to see if penicillium was grown with other microbes, how this would affect its invasive capabilities,” she said. “Maybe there is one type of bacteria that could prevent the species from ruining the cheese. I’ll also be looking at how this could be applied to microbe communities that grow in other environments, like the human body.”

Bodinaku currently spends about three hours a week in the lab, but this summer, she’ll be working full-time for 10 weeks. Zalesne estimates that he spends at least 15 hours a week working in the lab.

Wolfe said that he is very impressed by the work the undergraduate students have produced.

“They’ve had to trek all the way through the snow to get here,” he said, referring to the location of the lab at 200 Boston Ave., several blocks off campus.

Though the main research involves cheese production, Wolfe’s lab also deals with other fermented foods such as salami, fermented meats and kombucha.

Though Wolfe enjoys conducting research, he is also passionate about teaching. This semester, he teaches Biology 106: Microbiology with Lab, a required course for many students planning on attending medical or veterinary school that covers microbial genetics, diversity and functions, he said. Next fall, he’ll teach a course on the microbiology of food, which will be catered toward non-biology majors.

“It’s an exploration of the role that microbes play in the production, processing and consumption of food -- a farm-to-gut study of microbes,” he said. “We will use food as our lens into the microbial world. It’s a fun way to see how every day, throughout the entire day, as we eat yogurt or eat a sandwich, microbes play a role in our lives. Any undergraduate at Tufts could take this course if they’re interested in microbiology.”

Wolfe’s lab is also interacting with researchers at the Friedman School of Nutrition Science and Policy, examining the health impacts and digestive properties of foods like cheese.

Wolfe said that the Tufts Biology Department is an ideal place to conduct this type of research with the help of dedicated, enthusiastic undergraduate students. His only complaint is that he wishes he had more time and more people working with him in the lab.

In addition to conducting research and teaching courses, Wolfe also strives to educate the public about microbes.

"Talking to people about microbes can be challenging, because many people are only exposed to the topic through visits to the doctor and news about infectious diseases like Ebola," he said. "Cheese, on the other hand, is more accessible and less threatening ... These foods have interesting, calming, delicious stories to tell,” Wolfe continued. “So you can use them as a tool for teaching the world about how microbes work.”