The rind of good cheese is a thriving microbial community. A single gram—a tiny crumb—contains 10 billion microbial cells, a mix of bacteria and fungi that contribute delicious and sometimes funky flavors. But even though humans have been making cheese for thousands of years, we know very little about what all those bugs are and how they interact.

Benjamin Wolfe and Rachel Dutton want to change that. The two scientists recently brought 137 cheeses from 10 countries into Dutton’s lab at Harvard University for genetic analysis. In a paper published July 17 in Cell, they and colleagues describe their findings, which include a few surprises—like the presence of bacteria commonly found in marine environments on cheeses made nowhere near an ocean.

"People have figured out how to do all these cool things to make different kinds of cheeses, but we don’t really understand what’s going on in terms of the microbes," said Jonathan Eisen, a microbial diversity researcher at the University of California, Davis. Eisen, who wasn't involved with the work, says to his knowledge it's the most comprehensive effort yet to characterize the microbial communities in cheese and the first to recreate those communities in the lab for further study.

The microbes that live on cheese turn out to be diverse, but not that diverse, Wolfe says. The researchers identified 10 types of fungi and 14 types of bacteria that tend to dominate (see the diagram below). Some of these were well known, like Penicillium fungus, a genus that includes the P. roqueforti that puts the blue in blue cheese and P. camemberti, which puts the white mold on the rind of camembert. Others, like the ocean-dwelling bacteria Pseudoalteromonas and Vibrio, were unexpected.

Each tiny column here represents an individual cheese. The colors correspond to different types of bacteria (top half) and fungi (bottom half) present in the rind. Wolfe et. al, Cell

Wolfe speculates that these bacteria were transferred to cheeses by sea salt used during the cheese making process. "All cheeses are salted in various ways," he said. In the ocean, these bacteria live on the chitin-rich shells of crabs and other marine invertebrates, he says. In cheese, fungi provide an alternative source of chitin: It's in walls of their cells. "We think cheese makers might be creating the same kind of environment that these bacteria love in the cold damp ocean."

Different types of cheeses, broadly speaking, had microbial communities dominated by different types of microbes. For example, bloomy rind cheeses, which are inoculated with mold to produce soft creamy cheeses with a fuzzy white rind (like brie), tended to have a different microbial makeup than natural rind cheeses, which are basically left alone and allowed to age (like traditional cheddars). The microbial mix on washed rind cheeses, super stinky orange and pink cheeses whose rinds are washed with brine during aging, appeared to be somewhere in between the other two.

Geography, however, didn't seem to matter. Wolfe and Dutton found no support for microbial terroir, the notion that different places have unique microbial populations that imbue a cheese with specific characteristics. What mattered far more than place was the microbial environment, especially the amount of moisture present.

Tiny wells of in vitro cheese with different combinations of microbes. Wolfe et al., Cell

Now Wolfe and Dutton want to study these communities in the lab. "In vitro cheese is the next step," said Wolfe, who'll be starting up his own lab at Tufts University in September. Petri-dish cheese may sound off-putting, but he says it smells amazing. It starts with freeze-dried cheese curd from a cheese maker in Vermont, which the researchers mix with water in a blender and pour into tiny wells in a rectangular plate like the one above. "It smells like a really fresh, buttery milkshake," Wolfe said. "Then we add the microbes and it starts to get funky. You get barnyard-y, mushroom-y aromas because we're adding all the microbes that make those aromas in cheese."

They've already used their lab cheese to re-create some of the microbial communities they found on cheese rinds and to study how those communities change as a cheese ages.

For Eisen, that's the most exciting part of the work. In the past 10 years, he says, there's been a growing realization that microbial communities have profound impacts on everything from human health to agricultural yields to ocean food chains. But while advances in gene sequencing have made it possible to identify and study many of the individual microbes involved, Eisen says, it's been much harder to study how they interact with each other and their environment.

For the kinds of carefully controlled experiments needed to demystify the microbial world around us, in vitro cheese may be a whiff of what's to come.