Operators at Ginkgo shuttle samples between workstations on the foundry floor. (Ginkgo Bioworks)

Thanks to recent advances in synthetic biology — a hybrid discipline of engineering and biology that makes possible the manipulation of DNA of microorganisms such as yeast, bacteria, fungi and algae — a new generation of “organism engineers” has already started experimenting with the creation of new flavors and ingredients. In doing so, they have the potential to transform synthetic biology into a new creative platform to enable chefs, bakers or brewers to create new flavor profiles for food and drink.

Imagine being able to create the next acclaimed ingredient that makes foods more savory, harnessing the power of the “noble rot” to make a wine the equal of a bottle of Château d’Yquem, or fermenting a new cheese that has more flavor complexity than Roquefort. Creative types in foodie capitals around the nation would no doubt be interested in experimenting with these new products and tastes, just as visionary chefs Ferran Adrià, Wylie Dufresne and Grant Achatz experimented with the molecular gastronomy trend when it first started to go mainstream.

One company at the forefront of using synthetic biology to create new types of “cultured ingredients” is Ginkgo Bioworks, a Boston-based start-up that emerged from Silicon Valley’s Y Combinator (the same incubator that gave us Airbnb and Dropbox). The company comes with a pretty impressive innovation pedigree — the company’s co-founder is Tom Knight, the MIT legend who played an important role during the 1960s and 1970s in the development of ARPANET, a precursor to the modern Internet. Knight then reinvented his career trajectory using biology, and by 2012, Fast Company was calling him the “godfather of synthetic biology.”

Backed by $9 million in new venture capital financing, Ginkgo has opened up a new 18,000-square foot facility in Boston — a facility that the company refers to as the “first organism engineering foundry” in the world. By taking advantage of software-directed robots, the plan is to scale up the production of engineered organisms that could eventually be used to make anything from designer fragrances to cheap biofuels. Unlike traditional factories, which one could imagine churning out huge vats of yeast, Ginkgo’s foundry has a wide range of test samples being refined at any time, none of them larger than a bottle of water.

Ginkgo Bioworks was founded by world-renowned computer scientist Tom Knight, center, along with MIT biological engineering PhDs Austin Che, Reshma Shetty, Jason Kelly, and Barry Canton (left to right). (Ginkgo Bioworks)

As Patrick Boyle, an organism designer at Ginkgo, told me, the company’s current showcase product is a “cultured rose product” that can be used to make new designer perfumes. Rather than relying on chemistry to create “rose mimics” artificially from a handful of chemicals or crushing 1,000 or more rose petals to make a single vial of rose oil naturally, Ginkgo is choosing a third way: using yeast to ferment these rose oils, which can then be used to create unique new perfume fragrances. The start-up says its method is more cost-effective, and provides a distinct scent.

And the same technology used to create new fragrances could also be used to create new food flavors by genetically modifying microbes. The most likely suspects, of course, are those food products that heavily rely on fermentation for their distinctive taste – think cheese, pickles, bread, beer, wine and yogurt. But that’s not all – there are at least 24 different types of food that result from fermentation – including some that have become favorites with the foodie set: kombucha, charcuterie and miso. Even coffee and chocolate can be considered “fermented food.”

Certain plant-based products, too, could be produced via the use of fermentation. For example, using synthetic biology, Swiss-based Evolva has created an alternative to artificial vanilla flavor (“vanillin”) that has already made its way into food products available to consumers. Boyle suggests that new “plant-based sweeteners” could become big. And a recent article in Perfumer & Flavorist by Reshma Shetty of Ginkgo Bioworks lists more than 20 different “cultured ingredients” that are coming to market soon (including six from Ginkgo).

However, let’s step back a second. The idea that some companies are messing around with the DNA of microbes, storing vast quantities of designer organisms in a factory, and having robots mix together product samples understandably makes some people nervous.

Obviously, there are a number of concerns about synthetic biology, especially in an era when even the mention of genetically modified organisms (GMOs) tends to freak people out. But these concerns are largely overwrought. Synthetic ingredients are actually more “natural” than the artificial ingredients found in stores. There are no genetically modified organisms in the final food product — the “engineered organisms” are only used in the fermentation process as a raw material to help make the final product.

The really interesting part is how the synthetic biology work at Ginkgo has been inspired by the early days of computer programming. Ginkgo is essentially programming organisms, getting them to behave the same way as one might a piece of computer code. Tom Knight, who started in MIT’s artificial intelligence and computer science program, has suggested that learning how to program organisms is more fascinating than the ability to program computers.

The idea of programming microbes to create stunning new tastes is not as outlandish as it might seem. A highly-acclaimed upscale restaurant in Manhattan – Eleven Madison Park – offers a 13-course, $225 tasting menu that features a “pre-dessert” inspired by a flavor of grapes infected by the grey fungus botrytis. Now imagine pairing this dish with a dessert wine such as a Sauternes, which also relies on fermentation for its complex taste. That could be paired, perhaps, with a uniquely fermented chocolate. You get the idea – microbes everywhere.

In many ways, says Boyle, Ginkgo’s goal is “partnering with creative people to bring biology to them.” Ginkgo is a technology company and is run by technologists – but it could also become a new creative platform to empower tech-savvy bakers, chefs and brewers to isolate and use interesting new flavor profiles. Five or maybe ten years from now, when you arrive at a restaurant, check the menu. You might find the term “engineered organism” next to foodie epithets such as “farm-raised” or “cage-free” or “wild-caught.” The humble microbe – so often blamed for the spoiling of food – might actually be praised for unlocking the hidden potential of food.