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July 6, 2017

Engineering Microbes for Manufacturing

For a group of former MIT graduate students-turned-entrepreneurs, the future of programming has little to do with silicon. Instead, they are focused on engineering biology; specifically, manipulating the DNA of various organisms like yeast to become micro-manufacturers of products ranging from perfumes to nutritional supplements.

Alice McCarthy



Austin Che
Startup Founder
Ginkgo Bioworks

For a group of former MIT graduate students-turned-entrepreneurs, the future of programming has little to do with silicon. Instead, they are focused on engineering biology; specifically, manipulating the DNA of various organisms like yeast to become micro-manufacturers of products ranging from perfumes to nutritional supplements. Together, they founded Ginkgo Bioworks in 2008 to commercialize their synthetic biology technology and ideas.

Starting with a five-person team of MIT grad students and their advisor, Tom Knight, formerly of the MIT Computer Science and Artificial Intelligence Laboratory, Ginkgo’s mission is to radically scale up engineered organisms to make an extensive variety of products.

“When we started the company synthetic biology was a pretty new field and we wanted to take it to the next level to see if we could commercialize some of the ideas that we had,” says Austin Che, PhD, Ginkgo co-founder, who was convinced by Knight that the next big technology era involved programming biology instead of silicon. The team did not have a specific technology they planned to use in 2008 but after several years of exploring the field, the company has found its technical feet and opened its doors – and vats of simmering designer organisms—to customers in 2014 when it simultaneously received its first funding. Now, Ginkgo is enjoying explosive growth and interest in the company.





DNA as Code
Ginkgo uses DNA as its programming code instead of typical programming language and silicon. Che acknowledges that while silicon has been great at processing information it fails when interacting with the physical world. By comparison, biology is great at manipulating atoms.

By writing specific DNA code into the genetics of its manufacturing organisms, Ginkgo programmers can precisely direct them to produce the compounds of interest. “We just have to learn which letters to put into the organism,” Che says, adding that figuring out what DNA combinations to use – the string of A, T,G, C bases that pair up to make DNA—is the essential first step of any project. The second step is to add that DNA into the organisms which, in the third step, hopefully make the compounds the company is interested in for a given client.

Ginkgo claims to be the world’s largest writer of DNA. In one year, the company generates 500 million base pairs of DNA.

Biological Foundry
Their two main production facilities, called foundries or Bioworks, house the engineered organisms to churn out the goods. The company recently demonstrated scale-up capacity of 50,000 liters. A third foundry is in the building phase now.

Che explains the Bioworks concept is to use the microbes as a systematic platform that makes it easy to make many different molecules. “When I was in grad school, this kind of synthetic biology was done by highly-trained scientists at the bench pipetting. A lot of manual labor,” he says. “We don’t think that’s a very good use of a scientist’s time.”

Instead, within each Bioworks, robotics and equipment automate each step of engineering an organism through to manufacturing and product testing. “We try to batch things together and take advantage of cost, scale and automation so that the PhD scientist can spend their time thinking about how to design new organisms rather than pipetting,” Che adds. “The way we put them together is kind of our secret sauce for how to design each foundry.”

Ginkgo is currently working with about 20 different customers producing approximately 40 different products. Most are in the chemical industry involving flavors and fragrances. Other partners produce cosmetics and nutritional supplements but Ginkgo sees its manufacturing platform can be used in many areas – some not so obvious. One of its projects involves reviving extinct scents by examining the genomes of extinct flowers and bringing them back to see what scents they could have made.

“We hope to find partners we can work with in pharma, agriculture, or others where we can apply our biological tools for manufacturing or organism engineering to bring value to new partners,” Che adds. “We view biology as a manufacturing platform for making a wide variety of molecules; so anything that you can imagine – anything chemical or physical – we think that biology should be able to do it.”




About STEX25 and MIT’s Industrial Liaison Program (ILP)
STEX25 is a startup accelerator focused on fostering collaboration between MIT-connected startups and member companies of MIT’s Industrial Liaison Program (ILP). STEX25 is managed by MIT Startup Exchange, and its parent, the ILP. The ILP is a key player in making industrial connections for MIT, with over 220 of the world’s leading companies using their ILP memberships to advance research agendas at MIT.