Zymergen Josh Hoffman Zymergen CEO and Co-founder Josh Hoffman.
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Zymergen Raises $44 Million Series A to Automate Microbial Engineering

Over the last two years, Zymergen has been working hard to develop better methods to optimize microbes for industrial fermentation. Their integrated approach, which combines robotic automation, large datasets, machine learning, and novel software algorithms to engineer industrial microbes dramatically accelerates the traditionally slow process of strain development. As a result, Zymergen’s technology seems poised to produce advanced materials, novel chemicals and pharmaceuticals at lower costs and higher speeds through this innovative process.

“We have developed algorithms for efficiently discovering the best paths for programming microbial DNA. The potential long-term applications are virtually limitless.” said Zymergen CEO Josh Hoffman, referring to the seemingly endless uses for biological manufacturing at an industrial scale.

Since it’s inception in 2013, today is the first time the company has revealed details about its internal growth and business development which includes a $44 million series A funding round led by the venture capital fund Data Collective (DCVC).

Founded by Josh Hoffman, who has a background in banking, and two ex-Amyris employees, Zach Serber and Jed Dean, in just two years the Emeryville-based company has grown to over 50 full-time employees, and their investors have taken note. Jenny Rooke of 5 Prime Ventures was an early fan:

In only a year, Zymergen’s top tier founding team has proven out all of the key elements of the original business strategy, exceeding the very high expectations I had for the company at the time of the Seed round (April 2014). Zymergen has a pole position in applying synthetic biology to the $3 trillion chemicals industry, and I’m thrilled to participate in their Series A.

So how does this company get so much done?

Scientists working at Zymergen’s laboratory.
Scientists working at Zymergen’s laboratory.

Applying Machine Learning and Automation to Microbial Engineering

High-throughput laboratory automation is transforming how we engineer biology and increasing the rate at which we discover new scientific knowledge. By reducing experimental error, lab automation platforms can reduce costs, increase productivity, and generate more reproducible and reliable experimental data. In addition, big data enables the storage of millions of genomic sequences and allows parallel searches to identify and create new metabolic pathways. Advances in automation make high-throughput genome assembly and testing a viable process, while machine learning guides future genomic exploration to ensure that the design, build, and test cycle continuously improves.

Zymergen’s work is performed in a high-throughput robotic lab, code-named “Helix”, that allows for the accelerated construction of microbial genomes and the automated collection and analysis of experiment-generated data. This platform uses modern machine learning techniques to recommend and prioritize genomic modifications that help scientists design and construct novel genomes at a much higher efficiency than manual techniques.


Zymergen is set up to produce microorganisms for a range of industries

With a seasoned leadership team, Zymergen is already bringing in revenue and is set up to mass produce microorganisms for a range of fields including the pharmaceutical, agricultural, and chemical industries. Having worked as the Director of Biology at Amyris before founding Zymergen, Chief Scientific Officer Zach Serber has extensive experience in creating advanced tools for synthetic biology. Meanwhile, Jed Dean was in charge of developing high-throughput laboratory automation at Amyris and the Stanford Genome Technology Center before becoming Zymergen’s VP of Operations and Engineering. To round-off the talents of Zymergen’s core group, CTO Aaron Kimball worked at several big data-oriented startups including Cloudera, while the CEO Joshua Hoffman was a Partner at Norcob Capital.

This dynamic team has attracted the attention and well-deserved support of many key tech investors including AME Cloud Ventures (Jerry Yang), Draper Fisher Jurvetson, HVF (Max Levchin), Innovation Endeavors (Eric Schmidt), Obvious Ventures, True Ventures and Two Sigma Ventures.

In an interview with SynBioBeta, Matt Ocko, co-founder of DataCollective, who led the round and has joined the Zymergen board, revealed:

The team has consistently under-promised and overdelivered on some of the hardest problems in biology today. They have never missed a deadline.

Andreas Stavropoulos, a partner at DFJ, who also participated in the round explained, “We believe that this platform [that hugely accelerates microbial strain optimization] combined with Zymergen’s team of renowned experts in both synthetic biology and computation, is the winning formula,” that they believe will revolutionize the notoriously slow process of wet-lab discovery. He is confident Zymergen’s massively parallel, computationally intensive approach will “produce keys to unlock significant improvements in some of the largest chemical markets globally.”

Matt Ocko, co-Managing Partner of Data Collective.
Matt Ocko, co-Managing Partner of Data Collective.

What Have Been the Biggest Challenges?

“Right now our biggest challenge is growth”, said CEO Josh Hoffman, emphasizing “all the challenges of scaling the business and hiring the right scientists, automation engineers, and data scientists.” The team is especially interested in improving the economics of novel products and applications that are not already on the market.

What’s different about Zymergen from other companies that have come before?

“Three key factors,” said Josh, “Automation, cutting edge computer science, and a platform that is truly organism agnostic. We have multiple contracts and a revenue similar to an enterprise software company.”

What Does the Future Hold for the Automation of Biological Design and Fabrication?

Zavain Dar, an investor at Lux Capital, who helped lead Zymergen’s investment while previously at Innovation Endeavors believes “Industrial biotech is almost by definition a vertical [market] ripe for technology driven disruption.” From what he has seen, “Existing incumbents are slow to innovate and haven’t figured out that tomorrow’s biologists will look more and more like today’s computer scientists,” which he believes sets Zymergen apart and has spurred him to also be an independent angel investor in Zymergen.

Zymergen joins two other strain platform companies Ginkgo Bioworks and Synthace who also announced investments earlier this year. Matt Ocko when asked about his dual stake in both Zymergen and Ginkgo explained, “This is more of a Qualcomm vs. Intel deal rather than an Uber vs. Lyft competition. Although both Qualcomm and Intel make chips, each enjoy healthy activity in  near-monopoly, orthogonal markets.” Besides he noted both of these companies are taking on “trillion dollar economic opportunities”, implying the market can accommodate multiple players, and Zymergen seems ready to make a powerful debut.

Thanks to Marianna Limas for contributing to this blog post. Please leave your comments or questions below!


Spencer R. Scott

I am a recent PhD graduate from the Bioengineering Department at UC San Diego, currently working as a Scientist in cancer immunotherapy at Cell Design Labs. I'm the project lead of the development team engineering our SynNotch technology for immunotherapy applications.

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