Inside South Boston's new organism factory | Crain's Boston

Inside South Boston's new organism factory

  • Ginkgo Bioworks calls the new Bioworks2 space "the next generation of their foundry for designing and prototyping organisms." (courtesy Ginkgo Bioworks)

    Ginkgo Bioworks calls the new Bioworks2 space "the next generation of their foundry for designing and prototyping organisms." (courtesy Ginkgo Bioworks)

The wharves and industrial spaces along the South Boston Waterfront have housed all kinds of manufacturers since the 19th century, from WWII weapons makers to seafood processors and furniture designers. Today it’s where Harpoon makes beer and, as of Sept. 29, where one ascendant Boston biotech has planted their “foundry” for designing and manufacturing living organisms.

Just a year and half after their first round of venture capital netted $9 million, Ginkgo Bioworks has increased its capacity six-fold with a new 18,000-square-foot facility in the historic Innovation and Design Building complex on Drydock Avenue. They’ve grown to 115 employees from just 25 in March of last year, and reported raising more than $150 million in funding since then.

The self-proclaimed "organism design company" actually has a lot in common with its neighbors at Harpoon a few blocks away: both toy with yeast to brew interesting and aromatic compounds for mass consumption. But for Ginkgo Bioworks it’s not beer, it’s custom ingredients and chemical compounds for industrial inputs—things like rose and peach flavors for perfumers, special enzymes for cheese-makers, or engineered microbes for agricultural conglomerates including Cargill.

While beer itself isn’t a focus, Ginkgo Bioworks employees did homebrew a batch for their opening party. It featured yeast engineered in their labs to have an orange flavor, thanks to a compound called valencene they swabbed off an apple at a local orchard.

That kind of biological odyssey is typical of the larger-scale fermentation work done at Ginkgo Bioworks, a spin-off from the Massachusetts Institute of Technology.

“I often end up talking with our customers who are perfumers about what might activate their creativity,” says the company’s creative director, Christina Agapakis. "It's really exciting when we can help fill in those gaps.”

With the massively expanded footprint, Agapakis says there’s more room for experimentation that could yield novel solutions. Much of that is cooked up at the lab benches of the company’s synthetic biologists, who hold PhDs from institutions including MIT and Harvard, but some of it is just identifying and relying on features that have evolved naturally.

“We can’t guess a totally novel [DNA] sequence and know what it’s going to do. We don’t know enough about proteins,” says Agapakis. “But we know a sequence that has evolved is going to work, at least.”

From there it’s a matter of tinkering, or genetically engineering, DNA sequences to produce new flavors and functions, or to manufacture commonly used compounds with less environmental impact. Cheese-makers use an enzyme called rennet that’s traditionally extracted from the stomach lining of baby cows, for example, but synthetic biology companies like Ginkgo can engineer plants, microbes or fungi to make it instead.

Ginkgo finalized a partnership with California-based Amyris in September to scale up that manufacturing.

“For the Boston area what’s most exciting is that the real edge for how to engineer organisms is actually being built there," says Amyris CEO John Melo. “Ginkgo has the ability to quickly engineer an organism, and then we scale it, produce it and deliver it to market.”

Melo sees two major growth areas for that supply chain: biopharma, or manufacturing chemical compounds for drugs, and natural flavors for food companies.

That partnership will produce 600 million base pairs of DNA next year, Agapakis says, or roughly half of the market for synthetic DNA. According to Allied Market Research, the global synthetic biology market, which includes making DNA, could reach $38.7 billion by 2020.

Ginkgo isn’t the only “engineered organism factory” out there. Novamont, an Italian company, recently announced the grand opening of the world's first commercial plant for bio-production of a widely used industrial chemical called 1,4-butanediol, to be produced at a $100 million facility in Bottrighe, Italy.

In addition to growing in their hometown and teaming up with Amyris, Ginkgo is forming partnerships with other big players in the market, including Genomatica, which also has deals with Novamont. Twist Bioscience, a San Francisco-based customer of Ginkgo’s, said in a statement that Ginkgo’s new production capacity bodes well for the industry.

“The rapid scalability of our high throughput silicon platform will enable our customers to work with unparalleled quantities of synthetic DNA, driving new applications and innovative scientific developments,” said CEO Emily M. Leproust.

In Ginkgo Bioworks’ “engineered organism factory,” rows of robots on carts serve a giant glass box of gleaming white lab space. Robotic arms shuffle liquids and plates of cells around inside, while mass spectrometers peek at what’s going inside the cells they’ve cooked up. Though their new space is just a week old, the company already has room in the building that could be used for a future expansion. Melo says he's looking forward to Bioworks3.

For Agapakis, too, it’s an exciting time.

“When I was a student I was really satisfied with what I could do with my hand, my pipette,” she says. “But I wasn’t able to think yet at the scale that we need to make things happen. Now we can really start thinking at this bigger scale.”

October 10, 2016 - 7:48pm