InnovatioN Economy

Researchers making microbes that can do the dirty work

 Ginkgo BioWorks has engineered bacteria to produce fuel using electricity and CO2.
Ginkgo BioWorks
Ginkgo BioWorks has engineered bacteria to produce fuel using electricity and CO2.

On the edge of Boston Harbor, just a short walk from where Harpoon Brewery harnesses the power of yeast to produce tasty beverages, researchers are designing new kinds of micro-organisms that might one day scrub waste water clean, crank out fuel for our cars, or keep hospital equipment perfectly sterile. While making beer can be traced back to ancient Mesopotamia, this new field - often called synthetic biology or engineered biology - belongs to the 21st century.

With government grants, and in some cases venture capital funding, this cluster of companies is trying to “build new microbes that can do things,” in the words of Jason Kelly, a cofounder of one of the start-ups, Ginkgo BioWorks. He notes that tools for reading and writing in DNA - understanding how organisms work and custom-crafting new ones - are getting cheaper and more powerful by the month.

”In the 1980s and 1990s, it took biotech companies 10 or 15 years to develop a new biological drug,” says Christopher Pirie, cofounder of Manus Biosynthesis, an MIT spin-out. “The tools we have now are enabling the designers of new microorganisms to work at a much more accelerated pace.”


Three of the companies, including Cambrian Innovation, are neighbors in the Marine Industrial Park, a hulking collection of buildings on the harbor, originally built for Army and Navy logistics and ship repair.

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Cambrian is cultivating colonies of bacteria found in nature that, when charged with electricity, can serve as “living catalysts” in a chemical reaction. “These kind of electrically active microbes were only discovered in 1999,” says chief executive Matthew Silver.

Packed together into modules, the microbes can convert carbon dioxide into methane gas - useful if you want to keep the CO2 from escaping into the atmosphere - or extract pollutants from waste water while generating electricity.

One Cambrian project, called Exogen, has received about $2 million in funding from the National Science Foundation and private investors, Silver says. It seeks to use bacteria for waste-water treatment. This is already done in places like the giant egg-shaped “digesters” on Deer Island, but Cambrian says its process would require much less energy.

Next door, a start-up called Novophage is working with bacteriophages, a kind of virus that is a natural predator of bacteria. Explains chief executive Micah Rosenbloom, “We’re engineering phages that find a specific kind of bacteria” - like the kind you wouldn’t want hanging around a hospital or food-processing plant - “and can degrade it, or just find it and detect it and let you know that it’s there,” perhaps by changing color or emitting a faint radio signal. The phages might also be useful in combating bacteria that can gum up machinery used in oil production or papermaking, Rosenbloom says.


Novophage raised $5.75 million last year - some of it from the Kraft family, owners of paper and cardboard businesses as well as the New England Patriots.

The company is sequencing the genome of different species of bacteria, like E. coli or listeria, then building phages to detect or destroy them. Novophage takes phages found in nature and attaches custom-made DNA to give them new instructions. The company plans to start pilot tests this year to see how its phages perform in the real world.

The plan at Ginkgo is essentially to be a bacterial job shop, “building organisms and licensing them to other companies, in the pharmaceutical industry and energy and chemicals,” says Kelly. Like Cambrian, Ginkgo is working on the Department of Energy’s electrofuels program, designing bacteria that can make a fuel to replace gasoline using only electricity and carbon dioxide as inputs.

The company is preparing to move into an 11,000-square-foot office and lab space next month. Lots of technology has been designed into the space to enable the company to speedily produce new strains of organisms. “It looks more like a chip fabrication factory, with robotic automation and bar-coding, than a bench-top biology lab,” Kelly says. “About a quarter of our team are software developers,” writing the programs that will control all the new machinery. Ginkgo has 20 employees.

Pirie, the Manus Biosynthesis cofounder, says his start-up has not yet received any grants or funding and it’s still hunting for office space. But the company is talking to executives in different industries, including fragrances and cosmetics, about using microbes to produce “clean replacements for the chemicals they currently use,” many of which come from petroleum. “Sometimes the issue is the price, and there are other examples where there’s just scarcity,” he says.


Any time you talk about genetic modification, of course, some people are going to have concerns. At Novophage, they’re sensitive to not making phages sound “scary.” (They don’t infect humans, only bacteria.) Kelly at Ginkgo acknowledges that “people have a visceral response to living organisms. But historically, we’ve done a lot of organism engineering in the past. If you have a dog, you have a genetically modified wolf living in your house, and while you didn’t do the genetic engineering yourself, you still trust it around your kids.”

The biotech industry, which uses genetically modified cells from hamster ovaries to produce protein-based drugs, may serve as a positive poster child for synthetic biology companies. “Biotech has been a clean and safe industry, especially when you compare it to the chemical or oil industries,” Kelly says.

In the 1980s, young people who wanted to be in the center of the action learned to build spreadsheets. In the 1990s, they crafted websites. Today, they’re designing and customizing microorganisms and phages, with an eye toward solving unsolved problems. In the labs of these new companies, it feels like the future.

Scott Kirsner can be reached at Follow him on Twitter @ScottKirsner.