Many of our favorite foods, from beer and chocolate to cheese and coffee, are actually made by microbes. This microbial help in our kitchens has historically been rather slapdash and imprecise. People simply used the microbes that were available, often not even realizing that tiny bacteria and fungi were actually helping. Even now, some of the best cheesemakers and brewers still don’t know exactly how the microbial magic happens.

A new startup called Afineur wants to change all that. By using specific bacterial strains in its coffee fermentation process, they hope to create precise flavor profiles in batch after batch.

“We ferment the beans just before roasting, selecting specific strains of microbes to produce specific flavors,” said Camille Delebecque, co-founder of Afineur.

The popularity of such an endeavor is obvious: Within just a few hours, Afineur had funded the entirety of its $15,000 goal on Kickstarter. Within a week, they had raised nearly $40,000.

Cheesemakers are beginning to experiment with similar types of targeted fermentation, and so are beermakers, as microbiologists dig deep into the diversity of tiny critters that provide some of our favorite flavors and foods. By understanding the chemicals they make and the flavors these microbes produce, researchers and foodmakers like Delebecque and his partner Sophie Deterre, a flavor chemist, hope to completely transform our palates.

Every morning, my routine is the same. After smacking the snooze button an interminable number of times, I shuffle downstairs, feed the cat, and make a cup of coffee. Getting anything else done for the rest of the day depends on that first cup. Unlike some, I am not a coffee snob. I used to guzzle the swill at a previous office because it was hot, caffeinated, and free. Although I have my preferences, mostly I stick to the comfort and convenience of my home brewer.

Still, I’ve consumed enough of the stuff over my lifetime to understand the differences between dark roasts and light roasts, Starbucks and Dunkin’. I might not be able to pick out the floral and fruity notes of the organic, shade-grown Guatemalan coffee I tried on vacation, but others can and do. One of them is Delebecque, who began his road to fermented bliss by roasting his own beans in his tiny apartment kitchen.

“It started off as a hobby, a side project after I learned about the wonderful world of specialty coffee. And then I learned that some types of coffee are actually fermented,” Delebecque said.

His experience working with microbial fermentation in the production of biofuels sparked his interest in the fermentation process that happens in some types of coffee. Coffee beans grow inside a fruit called a cherry, and the coffee is harvested, cherry and all. Growers and roasters have developed a variety of techniques to remove the cherry and surrounding slime from the coffee bean, explains Tufts University microbiologist Benjamin Wolfe, one of Afineur’s scientific advisers. One of those ways is to ferment the cherry until it essentially dissolves away.

Initially, fermentation was used as a practical measure, whether to dissolve unwanted fruit or, more commonly, to preserve easily spoiled foods like milk and produce. “Historically, fermentation was a necessity. Now, it’s a luxury that we can use to generate novel foods and novel flavors,” Wolfe says.

But what began as purely a practical measure has coffee aficionados like Delebecque excited for its potential impacts on a coffee’s flavor. When microbes break down the cherry, they aren’t just treated to an all-you-can-eat buffet. The chemicals they produce as a byproduct of their feasting can create a huge variety of flavors. But instead of relying on “whatever microbes happen to be in the forests of Guinea that day,” as Wolfe puts it, he wants to be a lot more strategic. He sprays solutions of non-disease-causing strains of bacteria directly onto green, unroasted coffee beans, which then work their microbial magic. The idea is that as long as Delebecque sprays the same microbes on his coffee in the same conditions, he will be able to produce the same flavors in the final product.

Wolfe calls Afineur’s science “cutting edge.” He would know. Wolfe has spent the last several years studying how the microbial zoo that helps create various types of cheeses from cheddar to camembert, and he says that scientists are moving ever closer to understanding which sets of microbes produce which types of flavors from which starting ingredients.

“Imagine if you went out to garden blindfolded. You’d probably do a pretty bad job of managing your roses and hydrangeas and daffodils because you might be putting the wrong treatments on the wrong plants or using the wrong type of fertilizer. But if you take the blindfold off, you can do a much better job. Our lab is trying to do the same thing with cheese microbes,” Wolfe says.

Afineur isn’t just hoping to be a novelty item. It is posing itself to be a cheaper, better-tasting, and more humane alternative to gourmet coffees like kopi luwak. In the world of exotic coffee, it’s hard to beat kopi luwak, an Indonesian coffee whose beans are fed to civet cats, partially digested, and extracted from their poo before roasting.

I have gone to many extremes for my morning cuppa, but I have not picked beans out of cat poo.

No one really knows what gives kopi luwak its signature taste, but researchers believe that it’s a combination of stomach acids etching the beans and the microbes in the civet cats’ guts fermenting them that provides the basis for the flavor profile. Besides being almost prohibitively expensive (at a London coffeehouse, coffee enthusiasts can expect to fork over as much as $100 per cup of kopi luwak crap-occino) and rife with imposters and fraud, according to a study in the Journal of Agricultural and Food Chemistry, it’s also inhumane, as civets are kept in unsanitary conditions where they are force-fed beans.

“Most people have no idea what is going on. They think the picture of the civet on the package is just a logo. If they knew, they would probably stop using it,” said Chris Shepherd, regional director of Southeast Asia for Traffic, a conservation group that monitors trade in plants and animals.

Afineur doesn’t intend to directly replicate the flavors of kopi luwak, but instead create a better option that’s easier on the pocketbook and the conscience.

“This is a lot more intelligent than civet coffee, and I really hope it replaces current methods,” Shepherd says. “I just can’t imagine plucking something out of a small carnivore’s feces and putting it in my mouth.”

Whether Afineur ultimately succeeds or not remains to be seen. But their ideology is at the leading edge of food science with a very simple goal.

“We’re creating better conditions to make better food,” Delebecque says. And who can argue with that?