On a sunny June afternoon, I visited Dr. Christina Agapakis at the Ginkgo Bioworks offices in Boston’s Innovation and Design Building (also the future home of America’s Test Kitchen!). Ginkgo Bioworks, the “The Organism Company,” engineers custom microbes by genetically modifying organisms like yeast to produce particular flavor and aroma compounds during the fermentation process. During my visit, Agapakis talked about the cutting-edge field of synthetic biology, and how it might impact the future of industries from flavors and foods to cosmetics and perfumes.
Cook’s Illustrated: Synthetic biology is a not a field most people are familiar with. Can you explain, in a nutshell, what you and your colleagues do here at Ginkgo Bioworks?
Christina Agapakis: We’re interested in how to build and make stuff with biology. And it grows in this way that’s inherently sustainable and part of ecosystems. We see biology as a better way to make stuff and we see it impacting a lot of different industries as a result. At Ginkgo, the focus of the company has been on making biology easier to design, easier to engineer, and building a platform on which biological engineers can use biology to build something new.
A lot of our business today is in cultured ingredients, which is the idea that you can genetically engineer yeast to produce [specific molecules or compounds] during the process of fermentation. These are often flavors or fragrances, specialty ingredients, or even nutritional ingredients.
CI: Our team at Cook’s Illustrated and much of the general public, is familiar with yeast and with using bacteria to ferment pickles, beets, sauerkraut, etc. How does that sort of fermentation relate to the fermentation you’re doing at Ginkgo Bioworks?
CA: It’s the same biochemical process . . . the same transformation of sugar into something else by the yeast cells. When you’re talking about beer, that’s yeast taking the sugars from barley or other grains and transforming them into alcohol, carbon dioxide, and all the flavors you get along with the beer. What we do [at Ginkgo Bioworks] is start with that process and say: What enzymes can we take from other plants or other organisms and add them to the yeast [by modifying the yeast’s DNA] so that during fermentation, some of the energy from the sugar is going to create another product as well as the alcohol and carbon dioxide.
One product that’s been made using fermentation for a long time is amino acids, especially amino acids used in animal feed. Those are produced in huge vats on a huge scale; a scale that would not have been possible if you were trying to purify amino acids from proteins from another food source. But there are other kinds of products [made using fermentation], especially in fragrances and cosmetics. There are a lot of compounds present in very small quantities in plants and extracting them has led to a situation where [companies] have farmed or harvested those plants to near-extinction, so now the resource is constrained. Now, [with synthetic biology] there’s the opportunity to be able to synthetically make these compounds at a scale that wouldn’t otherwise be possible.
CI: What are some industries or companies you’ve designed microbes for?
CA: We work with companies like Robertet, which is a flavor and fragrance company, on different ingredients. [Editor’s Note: For example, Ginkgo and Robertet are currently working to insert DNA sequences into yeast so they will produce rose scent compounds during fermentation.] During development here in the lab, we do fermentation in about 250-milliliter containers, about the size of a soda can. When a product eventually goes to full, commercial-scale fermentation, it can grow to 50,000 liters in just a couple of days, which shows you what biology can do when the yeast itself acts like the factory that makes these molecules or compounds.