Gene-Swapping Cheese Molds are Ripe for Investigation

For Tatiana Giraud, cheese isn’t just an emblem of French cuisine—it’s a complex and evolving world of microorganisms.

So when Giraud, a microbiologist at the French National Center for Scientific Research, stocked her lab’s fridge with wheels, wedges, and rounds of cheese ordered online, it wasn’t just to spread globs of the dairy product on crackers. (But rest assured: “We took all the samples we needed,” Giraud says, “and then we ate the remaining.”).

Instead, Giraud and her colleagues were looking for traces of evolution in the molds that make up Camembert’s rind, and that marble Roquefort with blue streaks. And they found something surprising: These distantly-related species of fungi have somehow recently swapped chunks of their DNA. Giraud and her co-authors published their findings earlier this month in the journal Current Biology.

For such a simple dietary staple, cheese turns out to be a miniature barnyard, teeming with microorganisms. These cheese microbes have been domesticated by centuries of cheesemakers, tweaking recipes and conditions to nurture the little bugs that create perfect levels of creaminess or hardness, sharpness, or smoothness.

So cheese is ripe for investigations into how an environment created by humans can shape microbial genes. Giraud and her colleagues rounded up ten species of Penicillium fungus—six of which like living in cheese—and took a look at their genomes.

They discovered that Penicillium roqueforti—blue cheese’s blue streak—share almost identical swathes of genes with Camembert’s crust of Penicillium camemberti. These genes help the fungi thrive in the cheesy environment: One encodes an antifungal protein to ward off other species that might want to use the cheese’s resources, and others help the fungi feed on lactose, a sugar in milk.

This isn’t the first time organisms have shared genes with each other some way besides procreating. Bacteria, for example, can scoop up DNA from their environments and pass traits like antibiotic resistance from one species to another. But Wolfe says this isn’t something you usually see in fungi.

Stranger still, it looks like this gene swap happened recently, and almost exclusively in fungi that live in cheese. The shared regions are too similar to have evolved independently or been transferred long ago—the code is still too shiny and new. But exactly how new is still up for debate, partly because the researchers still need to catch the fungi in the act of passing chunks of DNA from one to another.   

“They’ve shown that in a really short period of time, in a human made environment, that you can have genes moving across species boundaries,” says Benjamin Wolfe, a microbiology professor at Tufts University. But here are still a few open questions. “Where did these horizontally transferred genes come from originally? Are they actually part of these fungi and relatives of Penicillium in nature? Are they coming from other organisms?” Wolfe says. “That’s another future study.”

These findings are a mixed bag for cheesemakers. On one hand, they may give cheesemakers greater control in a process that has been based on intuition, trial, and error for centuries.

“I used to describe being a cheese maker as like being God, except blind and dumb,” jokes Mateo Kehler, a cheesemaker at Jasper Hill Farm in Vermont. “The technology that exists now is making it possible to really see for the first time exactly how these [microbial] communities are put together, who’s there, who survives and who doesn’t,” he says.

Mother Noella Marcellino, a cheese-making scientist and a Benedictine nun at the Abbey of Regina Laudis in Bethlehem, Connecticut who prefers to go by Sister Noella, says that identifying these survival genes might help cheesemakers cultivate hearty fungi that are more competitive, breeding ones that also have desirable flavors or colors.

But it’s not without caveats.

“Are we also going to allow a specific species that could have […] metabolites that could be toxic or dangerous?” Sister Noella says. “I’m sure that they will continue testing the microbes to make sure they’re safe. But it shows you how complex it is.”

Rachel Becker is the daily news intern for National Geographic and a science writer based in Sacramento, California. Follow her on Twitter.