Ginkgo and Synlogic partner to develop 9 new microbe therapies

The Boston-based cell engineering company Ginkgo Bioworks is gearing up to make engineered bacteria the next big thing in medicine. The private firm, known for designer microbes that produce cannabinoids and fragrances, is expanding a collaboration with microbe therapy-maker Synlogic and planning to launch 9 drug programs over the next 12 months.

Synlogic is already testing two of its own engineered microbes in humans, both designed to help people with metabolic diseases break down toxic molecules that their bodies can’t process. Ginkgo thinks it can make the process of engineering and optimizing these microbes faster and easier, thanks to its automated labs and genomic databases.

Ginkgo has purchased $80 million worth of Synlogic’s shares. In return, Synlogic will pay Ginkgo $30 million for access to Ginkgo’s labs for five years. “We are in the business of programming cells,” Ginkgo CEO Jason Kelly says. “So if living cells that are genetically engineered become a new modality—a new type of drug—that’s a great thing for Ginkgo.”

The two companies have been working together since 2017. At the time, Synlogic was working on a rare genetic condition called maple syrup urine disease, in which mutations in a metabolic pathway prevent the proper breakdown of three amino acids. Accumulation of the molecules can cause brain damage and make urine smell similar to maple syrup. Synlogic had developed a prototype microbe that was genetically engineered with genes for three enzymes needed to break down the amino acids, but the firm wanted to see if it could make the microbe better.

Synlogic shared the prototype with Ginkgo, which proceeded to look for variants of the three enzymes that worked better than the human versions. “We scanned a thousand different versions of each of those enzymes,” Kelly says. Ginkgo tested the best ones in about 500 combinations until it found the trio that worked best together.

The optimized microbe was tested in a monkey. Both companies were impressed with the results—due to be presented at a conference this summer—and the firms agreed to scale up their therapeutic efforts.

In addition to optimizing microbe efficacy, Ginkgo is working on improving the production of microbe therapies. Synlogic’s first clinical trials used liquid formulations of its engineered bacteria, but the firm has since developed methods to lyophilize—or freeze dry—the microbes into a powder, which will make the medicine easier to store and use. Kelly says Ginkgo is also engineering the microbes to make them more amenable to lyophilization and subsequent resuscitation in a pill.

The two companies’ expanded collaboration may also benefit from Ginkgo’s recent acquisition of Warp Drive Bio’s genome mining platform. Warp Drive had amassed the genomes of more than 135,000 bacterial strains to search them for genetic instructions for producing new antibiotics. Ginkgo plans to use the database to continue searching for antibiotics, but Kelly notes that genes lurking in the database could also be helpful for optimizing future therapies it makes with Synlogic.

This kind of “compounding”—where seemingly different projects and partnerships play off each other—is something that makes Ginkgo unique, Kelly says. “Every time we add another one of these things, they all get better.”