Protein Expression Services Q&A

Sneha Srikrishnan, Director of Growth, Business Development at Ginkgo Bioworks, is here to answer your burning questions around our new offerings in protein expression!

This conversation was moderated by Annick Saralegui, Senior Marketing, Growth Specialist at Ginkgo.

To kick things off, tell me, what does Ginkgo have to offer for customers developing proteins?

Sneha Srikrishnan: This is super exciting! So we have four different modules of work that we would like to repeatedly use to help our customers in protein expression wherever they are in the R&D cycle. The 4 include:

  • Host evaluation: evaluate and compare your host strain with our suite of hosts
  • Strain optimization: optimize your strain with genome modifications for better quality, functionality, and titer
  • Classical strain improvement: use non-GM approaches to push titers higher 
  • Scale + fermentation: access our pilot and commercial scale fermentation facilities to increase production efficiency all in-house

For the first module, host evaluation, does this mean I can bring my own strain to Ginkgo? If I’ve spent a few long-and-hard years designing a host, can Ginkgo work with my strain?

Certainly! We can now engineer customer strains as much as we can engineer Ginkgo chassis strains. So that’s number one. 

And what that means is, if our customers have strains that they really like and they enjoy using, bring it to us! We can improve on it and help them get to higher titers, provide better functionality, and even improve on process media optimizations or process development for those strains.

In the early days at Ginkgo, we were more comfortable just working with Ginkgo strain backgrounds and now we’ve opened doors to customer strain backgrounds. And why? Because we recognize that our customers have put a lot of time and effort into their R&D and their strain backgrounds and have invested in CapEx to build processes that go along with their strains. So instead of backtracking and eliminating the body of work that’s already been invested in, we can add to it.

Let’s say I’m not too sure what strain I should use, mine or Ginkgo’s. Can Ginkgo help me make the right call to reach my goals? 

Yes. We can now perform host strain comparisons – early on. 

That means if anyone is starting early on and doesn’t know whether to invest in a fungal strain background which is filamentous in nature, like a Trichoderma or an Aspergillus, versus say a Pichia we have, we’ll run in a host evaluation body of work, which is very quick.

It can be run within six weeks, maximum eight weeks, to provide a high level feedback on whether Pichia or the others have better better titers and are able to be a good match for being a production organism. So it gives you quick feedback and this can help with early stage GRAS filing.

Let’s say I’m a prospective customer and I’d like early access to a protein sample. Is this something Ginkgo offers?

Yes, that’s very new!  If anybody wants protein samples to try and test for functionality during a strain engineering program, we’re willing to provide them with samples. These can be generated from ambr250 system fermentations or from 5L fermentations or even higher.  

What I’ll also mention is Ginkgo has invested in building out our scaling facilities so that we can even run strains at a commercial scale. Why is this important for the protein world? 

Under one roof, we have the ability of generating up to 10 grams of sample, if not at the kilogram scale when run at 3000 liters.

It can all be done in-house and this is very exciting because our partners can essentially receive samples, do some functionality testing, and if there’s anything to be changed from the same strain background to meet specs, we will now be able to fix the strain and not lose time in the process. So it’s time gained. 

What’s so special about Ginkgo’s strain assets especially for, as an example, alternative food protein production? 

I’m excited because we have developed cutting-edge strains for very special and complex, hard-to-engineer proteins such as iron-bound proteins. We’ve spent a lot of time determining how to modify the strains’ post-processing folding machinery in order to improve the titer and functionality of proteins.

So we’ve basically created a suite of strain backgrounds that can accommodate multi-copy integrations and codon optimization. We also have proprietary synthetic promoter systems that will allow for tunable and controllable expression which are not methanol-based. So methanol-free is based on simple carbon sources, which have very good COGS in terms of raw material usage.

We also have synthetic secretion signals for secreted protein. If you want to keep it intracellular, we can keep it intracellular and we’ve also developed a suite of strains which have unique helper genes or co-expression genes such as chaperones and protease knockouts.

Why is this important? Because we figured out ways in which the helper genes will help, post-translation, to package the proteins and help translate them across the ER, and then across the cell wall.

Essentially, we have identified unique ways to not just produce a protein but also to keep it stable once it’s secreted.

So all of this can be done in short spans of time. We have examples where we’ve run dairy-protein type projects. The first time we generated these strains, we invested close to 15 months worth of pre-work to generate the strains.

Because of the pre-work we invested, When we partnered with clients that needed iron-bound proteins, we were able to get from a single digit gram per liter, very quickly up to in the range of 5+ gram per liter scale for dairy protein within six months, which is significant time savings.

Can I test for functionality with Ginkgo?

We have some capability to test functionality within Ginkgo for a subset of samples. And if we are unable to run those functionality screens in-house, we have partnerships set up where we could be outsourcing to our partners for functionality screens for food proteins.

Assays such as iron binding can be done within Ginkgo.

Antimicrobial activity can be done within Ginkgo other more specific assays such as: melting temperatures, aggregation temperatures can also be done at Ginkgo. If there are more specific assays required, we can outsource to our partners.

I’m a prospective customer and have heard of EncapS and ALE.  EncapS for Encapsulation & Screening and ALE for Adaptive Laboratory Evolution. Can you explain that a bit more and how I can leverage those services for my project?

The EncapS strategy would normally work if you have a strain that’s already making something. If you have a strain that’s making a product of interest or a protein of interest, and it’s making a very small amount of the protein and you want to get to multifold improvements very quickly, then go with EncapS.  So with EncapS, what we can do is when you are already at reasonable titer in the gram per liter range, we can increase titers by 20, 30 percent or sometimes even reach 50 percent improvement.

We can run multiple rounds of classical mutagenesis or generate a library of semi-rational mutants. That semi-rational mutant library can then be quickly screened through encapsulated cells within nanoliter beads. And we can screen over 1 million clones in a single round.

Why is this useful? because when you screen for a million clones you can quickly get titer improvement jumps.

EncapS can also help you achieve better strain productivity.

We will essentially not just look for a high protein titer, but we’ll look for improved productivity.  So we’ll directly read out for secreted protein, as well as the biomass.

Why is this good? Because you not only want to have high titer, you also want to have decent microbial growth. Otherwise your fermentation will be challenging. So if you want to have good productivity, you look for both good biomass and good protein titer. The EncapS method can help you look for both.

Now, where does ALE come into picture, if you want to switch carbon sources?

So let’s say that you have a strain that is going to grow on waste material and you want to circularize the process. You want to do waste valorization and you want to pick up C5 sugars in addition to C6 sugars. Then ALE is a great way to change the carbon preference or to open out the carbon preference as an example for the organism that’s already making something of your interest.

If you’re looking for change or improvement in the growth rate specifically then it can be considered. That’s how I would use it.

Multi-Target RNA Discovery Collaboration with Pfizer

Today we’re thrilled to announce a collaboration with Pfizer focused on the discovery of RNA-based drug candidates.

Pfizer will leverage Ginkgo’s proprietary RNA technology to advance the discovery and development of novel RNA molecules across priority research areas. Ginkgo will receive an upfront payment and is eligible to receive research fees and development and commercial milestone payments, up to an aggregate total of $331 million across three programs. Ginkgo is entitled to potential further downstream value in the form of royalties on sales.

RNA therapeutics that encode proteins with the potential to treat or cure diseases represent an exciting new approach in medicine with the possibility of far-reaching application.

Our RNA technology combines high-throughput screening of the behavior of RNA constructs with a multi-parameter design framework to identify novel natural and synthetic elements optimal for a particular application. We will deploy these capabilities with the goal of achieving efficient production, circularization, improved stability, and enhanced translation of each RNA construct.

“RNA therapeutics are proving to be an important platform to advance the world of scientific innovation, and with progress in synthetic biology we have the potential to create new RNA treatments that may benefit patients worldwide. Access to Ginkgo’s proprietary platform will help enable Pfizer to search for novel and exciting RNA constructs with improved stability and expression that could lead to more effective treatments.”

Will Somers, PH.D., Head, Biomedicine Design, Pfizer

Billions of patients around the world have already benefited from advances in RNA-based technologies.

We’re thrilled to be able to help enable the discovery and development of novel drugs using this powerful modality by applying our platform technologies which are designed to program RNA for maximum therapeutic effect. Ginkgo’s approach enables and accelerates discovery across different disease areas and modalities for our partners, who bring deep expertise in drug development. We can’t wait to leverage our broad and deep RNA Codebase and deploy our Foundry to enable the era of programmable medicines with the Pfizer team.

To learn more about Ginkgo’s RNA Therapeutics offering, visit our webpage.

Ready to talk to our team about your RNA project? Get in touch here.

Find the full press release here along with all of the latest news from the Ginkgo team.

What will you grow with Ginkgo?

Enzyme Discovery and Engineering at Foundry Scale

Ginkgo Ferment 2023, Platform Presentation:

Ginkgo’s Head of Protein Engineering, Emily Wrenbeck, PhD, shares how our foundry makes it possible to generate valuable data that drives enzyme discovery and optimization.

Watch the full presentation here or read below for a summary.

At Ginkgo, we understand the value of data in biological engineering.

We source natural libraries of proteins through public and proprietary sequence databases. And we’ve built a broad computational protein design toolkit that includes classic methods like molecular dynamics and Rosetta. We also use the latest AI models for protein predictions, including AlphaFold and EVcouplings. Our Protein Production Services allow us to take a supervised machine learning approach to protein design, which means we train models directly on the experimental data that we generate in the process.

What does all of this look like in practice? Here’s an example: 

  • A customer asked Ginkgo to optimize an enzyme that was critical to their project. The challenge? The enzyme was known to be difficult to engineer, due to its recalcitrant nature and unsolved reaction mechanism. In this case, traditional rational protein engineering approaches were not feasible.
  • To tackle this problem, Ginkgo opted for a data-driven approach to protein design. We engaged in four rounds of Design, Build, Test, and Learn. In the early rounds, we used a design toolkit with sequence-based, self-supervised model active sign mutagenesis and Rosetta docking to explore the sequence to activity relationship of the protein.
  • In the successive rounds, we fed all the data into our platform to train models and build designs. The library sizes in the final round were able to realize a big leap in performance with a rather small library. As the models are given more data, they get more predictive, enabling us to hit our goals in a much more focused way.
  • The outcome of this approach was a tenfold improvement over the starting enzyme. Our data-driven approach proved to be effective, even for a challenging enzyme that was not amenable to traditional protein engineering techniques.

This case study highlights the importance of how data enables breakthroughs in biological engineering. It also shows the power of a platform approach that combines state-of-the-art AI and computational tools with a data generation engine.

By investing in data generation and computational tools, we can push the boundaries of what is possible in protein design and engineering.

We’d love to add your enzyme to our growing list and help design and engineer it to fit your needs. Learn more about our Ginkgo Enzyme Services today!

What will you grow with Ginkgo?

Introducing: Bioworks7 Mammalian Screening at Scale

Our newest foundry increases our capacity to serve customers in biopharmaceuticals, biomanufacturing, and general mammalian programming for therapeutic applications

Today, we’re announcing the opening of Bioworks7, the latest expansion of our biological engineering foundry. With this new space, we’re increasing our capacity and capabilities to serve our partners in the spaces of cell and gene therapy, biomanufacturing and general mammalian programming for therapeutic applications and new biopharmaceutical modalities.

Ginkgo’s foundry automates and scales the process of organism engineering, allowing engineers to prototype thousands of biological designs. Our evolving platform equips companies and labs from startups to large pharmaceutical companies with access to robust technology, without the need for them to invest in costly lab and R&D infrastructure in-house, and aims to drive down the cost per biological design.

“Following our initial efforts in Bioworks4 in 2019, and expansion to our Cambridge facility, Ginkgo has created a strong foundation for culturing, engineering, and interrogating a variety of primary cells and cell lines to support both discovery and manufacturing efforts for cell and gene therapy, RNA therapeutics, and biologics including antibody and enzyme-based therapies,” said Narendra Maheshri, Head of Mammalian Foundry at Ginkgo Bioworks. “With Bioworks7, Ginkgo is able to further scale this work with dedicated capabilities for stem cell engineering, centralized mammalian cell operations services, and expanded capabilities in existing areas.”

This expansion of our R&D space will enable us to serve more strategic partners in applications across therapeutics and biomanufacturing.

In addition to the new foundry space, Ginkgo has also added expertise across our biopharma team, including the appointment of Dr. Behzad Mahdavi, senior vice president of biopharma manufacturing & life science tools. Ginkgo’s existing work in the biopharma space – such as partnerships with Aldevron, Biogen, Microba, Moderna, Novo Nordisk, Optimvia, Persephone, SaponiQx, Selecta Biosciences, Synlogic, Tantu, Totient, and Merck – span many therapeutic areas and approaches and contribute to the company’s growing expertise and Codebase. In addition, Ginkgo recently acquired Circularis, a biotechnology company with a proprietary circular RNA and promoter screening platform, to enable new solutions across bioproduction, RNA therapeutics, cell therapy, and gene therapy partnerships.

Since the opening of Bioworks4 when we formally kicked off our work in the mammalian space, we’ve experienced significant growth, creating new opportunities for us to advance our capabilities and contribute to our valued pharma partners. As the synthetic biology ecosystem rapidly evolves and the urgent need for biopharma options increases against the backdrop of the pandemic, we’re energized to expand our foundry to bring new capabilities to service the biopharma industry. With today’s opening, we look forward to enabling our partners to program mammalian cells at scale for more effective biomanufacturing workflows and new and improved biopharma products.

The Bioworks7 facility comprises 6,600 square feet of Biosafety Level 2 (BSL-2) lab space at Ginkgo’s headquarters in Boston’s Seaport District. It is co-located with Bioworks4, Ginkgo’s other mammalian foundry space, allowing for synergy with existing spaces within our headquarters. Notably, Bioworks7 houses a dedicated space for induced pluripotent stem cell (iPSC) work and advanced robotics to further scale and automate a variety of mammalian workflows.

By investing in the expansion of our mammalian foundry platform, Ginkgo expects to provide significant runway to support new programs in the pharmaceutical and biotech vertical.

Bioworks7 and Ginkgo’s advancement in the biopharma industry comes on the heels of our announcement of our foundry-enabled methods for large-scale, pooled combinatorial library screening of CAR domains for improved persistence. As our platform evolves to spearhead monumental work in the biopharma space, Ginkgo is equipping companies with the tools they need to innovate and shape therapeutics.

Find the full press release here along with all of the latest news from the Ginkgo team.

What will you grow with Ginkgo?

Ginkgo Acquires Zymergen

Ginkgo completes acquisition of Zymergen

Today, we’re pleased to announce our completed acquisition of Zymergen.

This is our largest acquisition to date! It’s expected to significantly enhance our platform by integrating strong automation and software capabilities as well as providing a wealth of experience across diverse biological engineering approaches.

It marks an important step in our long term growth, and we’re thrilled to welcome Zymergen’s world-class team to Ginkgo. We are excited to integrate Zymergen’s capabilities into our platform and explore new and expanded partnerships and opportunities for their diverse array of product concepts currently under development.

Under the terms of the merger agreement entered into on July 24, 2022, Zymergen stockholders received, for each share of Zymergen common stock, 0.9179 shares of Ginkgo Class A common stock. Zymergen shares will no longer be traded on Nasdaq. GinkgoClass A common stock will continue to trade on NYSE under the ticker symbol DNA.

Find the full press release here along with all of the latest news from the Ginkgo team.

What will you grow with Ginkgo?

Forward Looking Statements

This blog post contains forward-looking statements within the meaning of Section 27A of the Securities Act of 1933, as amended, and Section 21E of the Securities Exchange Act of 1934, as amended. You can generally identify forward-looking statements by the use of forward-looking terminology such as “anticipate,” “believe,” “continue,” “could,” “estimate,” “expect,” “explore,” “evaluate,” “intend,” “may,” “might,” “plan,” “potential,” “predict,” “project,” “seek,” “should,” or “will,” or the negative thereof or other variations thereon or comparable terminology. These forward-looking statements are only predictions and involve known and unknown risks and uncertainties, many of which are beyond Ginkgo’s and Zymergen’s control. Statements in this blog post that are forward-looking, including the expected benefits of Ginkgo’s acquisition of Zymergen, are based on management’s current estimates, assumptions and projections, and are subject to significant uncertainties and other factors, many of which are beyond Ginkgo’s and Zymergen’s control. These factors include, among other things, general economic and business conditions; changes in global, political, economic, business, competitive, market and regulatory forces; judicial decisions; changes in tax laws, regulations, rates and policies; future business acquisitions or disposals; litigation and the ability of the combined company to protect its intellectual property rights; and the timing and occurrence (or non-occurrence) of other events or circumstances that may be beyond Ginkgo’s and Zymergen’s control. Additional information concerning these risks, uncertainties and assumptions can be found in Ginkgo’s and Zymergen’s respective filings with the SEC, including the risk factors discussed in Ginkgo’s most recent Annual Report on Form 10-K, as updated by its Quarterly Reports on Form 10-Q, in Zymergen’s most recent Annual Report on Form 10-K, as updated by its Quarterly Reports on Form 10-Q, and in Ginkgo’s future filings with the SEC.  Important risk factors could cause actual future results and other future events to differ materially from those currently estimated by management, including, but not limited to, the risks that: Ginkgo is unable to achieve the synergies and value creation contemplated by the acquisition; Ginkgo is unable to promptly and effectively integrate Zymergen’s businesses, including retention of key personnel; Ginkgo management’s time and attention is diverted on transaction related issues; disruption from the transaction makes it more difficult to maintain business, contractual and operational relationships; or adverse developments or outcomes of legal proceedings that are pending or instituted against Zymergen, Ginkgo or the combined company. No assurances can be given that any of the events anticipated by the forward-looking statements will transpire or occur, or if any of them do occur, what impact they will have on the results of operations, financial condition or cash flows of Zymergen or Ginkgo. Should any risks and uncertainties develop into actual events, these developments could have a material adverse effect on Ginkgo’s ability to realize the expected benefits from the acquisition. You are cautioned not to rely on Ginkgo’s and Zymergen’s forward-looking statements. These forward-looking statements are applicable only as of the date of such statements. Neither Zymergen nor Ginkgo assumes any duty to update or revise forward-looking statements, whether as a result of new information, future events or otherwise, as of any future date.

Revolutionizing Enzyme Engineering: The Synergy of Big Data and AI at Ginkgo Bioworks


Enzyme Engineering and Artificial Intelligence

A new frontier

Enzymes are the heroes of biotechnology, serving as biological catalysts that make life’s complex reactions look easy. Inside of the cell, enzymes direct the flow of molecules through metabolic pathways, orchestrating biological functions. Outside of their cellular context, enzymes have been co-opted for specialized roles in manufacturing, speeding up processes that would otherwise be painstakingly slow. In pharmaceuticals, enzymes are custom-engineered to act as targeted therapeutics. Whether in life sciences or industrial applications, enzymes elevate our ability to engineer processes and enact chemistries by facilitating reactions with speed and specificity.

For years, scientists have used a variety of tools to design and optimize these crucial biological components. Traditional methods have often hinged on exploiting evolutionary pressures—letting nature do the heavy lifting over generations and then picking the winners. Structure-based prediction techniques, like Rosetta, also made a significant impact, allowing researchers to model how tweaks to an enzyme’s structure could influence its activity.

But we’re entering a new era–one in which we can train Artificial Intelligence (AI) models based on large biological data sets. This is where Ginkgo Bioworks comes in. Our expansive cell engineering platform is a data-generating powerhouse, churning out the kind of high-quality, voluminous data that AI algorithms thrive on. The marriage of this large-scale data generation with AI models allows us to transcend previous limitations, making Ginkgo an ideal environment to train and deploy machine learning tools for the complex art of enzyme engineering.

The AI Story

Big data, bigger breakthroughs

AI learns from large data sets. Ginkgo Bioworks generates these types of data: we make it possible for you to produce and learn from large data sets. Our extensive repositories of enzymes not only cover a wide range of protein sequences but are also complemented by highly targeted data, revealing precise sequence-function correlations. This dual-data approach is implemented through machine learning cycles in our enzyme engineering projects, enabling us to iteratively refine predictive models.

Ginkgo has developed an AI tool, Owl, to fine-tune enzymes for a specialized role. An expansive data set provides the foundational architecture. To construct the intricate details, however, we employ data that is calibrated to the specific enzyme and its intended function. This enables Owl, our machine learning tool, to not merely “learn” but to “apply” its learnings, writing the intricate, detailed novel enzyme that our scientists require. Owl can “see in the dark” and discern viable paths in complex enzyme design landscapes.

Ginkgo’s approach to enzyme design isn’t merely data accumulation; it’s strategic data deployment. Our Foundry is equipped to generate an extensive range of high-quality biological data at scale. From DNA design and synthesis to high-throughput screening, we create vast data sets corroborating structure-function relationships. Owl thrives in this environment, allowing us to design enzyme variants tailored to our partners’ unique specifications, whether that’s enzyme activity, specificity, or other parameters.

As we navigate the complexities of enzyme design and optimization, think of Owl as the expert navigator and our robust data sets and data-generating capabilities as the compass and map. Together, they form a symbiotic alliance that not only challenges but also redefines the boundaries of traditional R&D.

Tackling Enzymes in Central Carbon Metabolism

The power of iteration and integration

Enzymes that regulate flux through Central Carbon Metabolism (CCM) are biological masterpieces. These proteins have been shaped by billions of years of evolutionary refinement to execute their functions with unmatched precision and, in many cases, maintain high sequence and structure conservation throughout the tree of life.

In one example of Owl-guided enzyme optimization, we were asked to improve the reaction kinetics of an enzyme involved in CCM. While this enzyme had been studied for the past 50 years, the best improvement we found in the literature was a 2-fold increase in the kcat/KM–catalytic efficiency; our customer needed a 10-fold improvement in the efficiency of this enzyme in order to meet their economic targets.

Our approach to this project leveraged our Foundry’s ability to generate and test large libraries of strains. In our initial data-generation phase, we created a first-generation library featuring 2,000 distinct enzyme variants crafted using a structure-based design, as well as semi-rational methods like active-site mutagenesis for targeted alterations. This is an important step because it generated a data set for initial Owl training. With this information in hand, we designed a second generation library to give Owl more information: we maintained the library size of the first but incorporated insights from the previous round, resulting in an exciting 3.9-fold improvement—a leap that surpassed anything we had seen before.

But the real improvements were just beginning. The third generation of this program brought us to a pivotal point in our optimization journey. Leveraging Owl’s predictive analytics, we strategically developed a broad library of 4,000 enzyme variants, generating diversity where it mattered most. The result was an unprecedented 4.5-fold improvement in enzyme efficiency, serving as a testament to Owl’s growing mastery in predictive capability.

Data from these three consecutive generations positioned us to make our biggest improvements yet. Given the data that our scientists had generated, Owl continued to generate increasingly sophisticated models of enzyme function. The final iteration culminated in a fourth generation where only 100 enzyme variants needed to be tested. The result, which marked the successful completion of this customer program, was astonishing: a 10-fold improvement in enzyme function, verified through meticulous arrayed activity assays and detailed protein characterization. By integrating the large data sets generated by Ginkgo’s cell engineering platform with Owl’s predictive power, we surpassed the bounds of natural evolution and decades of research reported in the literature meet our customer’s targets.

The Future of Enzyme Engineering

Large data and machine learning at Ginkgo Bioworks

The confluence of big data and AI accelerates the pace of innovation to unprecedented speeds. Ginkgo’s cell engineering platform is an ecosystem designed for generating expansive, high-quality data sets customized for complex biological inquiries. This data, in turn, fuels the predictive power of AI models. Together, they form a symbiotic relationship that enables us to challenge the limitations of natural evolution and traditional research methods.

As stakeholders in the biotechnology industry, navigating complex R&D challenges requires more than just robust tools; it requires effective partnerships. Ginkgo Bioworks offers the specialized machine learning models and data-generation capabilities necessary to advance your research and overcome bottlenecks. Our suite of resources is designed to integrate seamlessly with your objectives, providing actionable insights and solutions tailored to your specific challenges.

Ginkgo is investing in the future of AI for biotech: see our recent announcement with Google about developing foundation generative AI models for DNA and protein. Leverage our expertise and technology for your next project, and to join us in pushing the boundaries of what is possible in synthetic biology.

Acquiring Altar and Circularis to Strengthen Our Capabilities

Ginkgo strengthens technical capabilities through acquisitions of Altar and Circularis to provide further capabilities to customers in adaptive laboratory evolution, circular RNA, and promoter screening

We are excited to announce two new acquisitions today: Altar, a French biotechnology company that has developed a proprietary adaptive evolution platform, and Circularis, a biotechnology company with a proprietary circular RNA and promoter screening platform. Through these acquisitions, we expect to offer new solutions to customers across multiple industries and further bolster our capabilities across the full stack of biological engineering.

At Ginkgo, we are constantly searching for technologies and capabilities that will make biology easier to engineer and help our customers achieve their goals. Altar will help us achieve this mission through the integration of a fleet of its automated adaptive laboratory evolution (ALE) instruments into Ginkgo’s Foundry to serve our customers in industries including the food and beverage, biofuels, biomaterials, cosmetics, animal health, and human health sectors. The Circularis platform will enhance our capabilities in circular RNA and ultra-high-throughput screening of promoters, enabling us to develop new solutions for customers across bioproduction, RNA therapeutics, cell therapy, and gene therapy applications.

Incorporating Altar’s adaptive laboratory evolution platform

We’ve come a long way in rational genome editing and high-throughput testing over the last decade. But it still often remains challenging to engineer microorganisms that meet target specifications under harsh, industrially-relevant conditions. That’s due in part to the complexity and unknowns of the underlying genetics of organisms that grow in these unfavorable conditions and settings. ALE can be a powerful approach to address this challenge.

By incorporating Altar’s ALE platform into our existing strain engineering and screening capabilities, we expect to be able to routinely engineer and identify phenotypes that meet our customers’ specifications. Selected strains from ALE will be characterized and further validated by our existing suite of test workflows. We’ve had success collaborating with Altar in the past on customer programs and are thrilled to welcome them to the team.

“As the range of programs we work on continues to expand, it is imperative that we have the best tools in rational design as well as the ability to leverage the inherent diversity and creativity that emerges from evolutionary processes,” said Nikos Reppas, our senior director of Foundry Technology. “We’re excited to welcome the Altar team to Ginkgo and look forward to integrating the Altar technology into Ginkgo’s suite of offerings so we can better serve existing and future customers.”

“We founded Altar to increase the feasibility and reduce time-to-market for bio-manufactured products,” said Simon Trancart, CEO of Altar. “We’ve been working with Ginkgo for a few years now, and are thrilled to join the Ginkgo platform as we work to accomplish our mission at an even greater scale by collectively using biology to drive innovation across industries.”

Incorporating Circularis’ proprietary circular RNA and promoter screening platform

The Circularis platform will strengthen our ability to assist customers in their cell and gene therapy development. The acquisition will improve our capability to rapidly identify novel promoters with appropriate strength and tissue-specificity designed into customer-specific delivery modalities. Leveraging Ginkgo’s ability to explore large numbers of genetic designs, these promoter libraries can be explored in combination with modified therapeutic payloads and capsids. This will provide our customer who are gene therapy developers with a solution that works across any range of cell or organism models. Similarly, the Circularis platform will give us the ability to rapidly identify context-specific promoters for cell therapy applications, such as those that modulate gene expression in the tumor microenvironment.

“Circularis has built an exceptional platform to screen gene expression regulatory elements, a need across the cell and gene therapy space,” said Narendra Maheshri, our head of Mammalian Foundry. “We are excited to leverage the strong expertise of the Circularis team to further develop circular RNA methods for therapeutic use, and can’t wait to incorporate this technology into existing and upcoming cell programs across therapeutic applications as well as more broadly.”

“Circularis was founded because we saw a need for better tools to control gene regulation in a range of species. Our team is incredibly proud of what we’ve built, and the opportunity to scale it on the Ginkgo platform means we’re a major step closer to realizing this technology’s potential,” said Mat Falkowski, Chief Executive Officer at Circularis. “We are excited to bring the power of the Ginkgo platform to both Circularis’ already existing customer base and future partners.”

Find the full press release here along with all of the latest news from the Ginkgo team.

What will you grow with Ginkgo?

Exciting M&A Update: Scaling our Platform Capabilities

Our mission is to make biology easier to engineer. At Ginkgo, we’ve always strived to bring the best technologies—including biological tools, automation, and software—together onto one platform to better serve our customers. 

Today we’re excited to announce that we’ve signed definitive agreements to acquire two teams and technologies that will help us achieve this important mission, one from Bayer and Joyn that builds our vertical capabilities in agricultural biologicals and the other, Zymergen, that brings in-house core hardware and software to accelerate our horizontal Foundry capabilities.

We are building this platform for our customers, who come to us with their biological design challenges and product ideas. We reiterate this point a lot, because it is unusual in the biotech industry: we aren’t interested in building our own products, we’re interested in building a platform that will allow the rest of the world to deploy biology as a solution for our hardest challenges, from food security to pandemic response, from supply chain resilience to climate change.

We previously announced our plans for this agreement with Bayer, to acquire Bayer’s 175,000-square-foot West Sacramento Biologics Research & Development facility, team, and internal discovery and lead optimization platform, as well as integrate the R&D platform assets from Joyn Bio, our joint-venture with Leaps by Bayer formed in 2017. 

We share a common vision with the teams at Joyn and Bayer that will be joining our team to develop and deploy the best that biology has to offer in agriculture. To ensure sustainable food security for an ever growing population, we need to invest in biological solutions and work with the best teams around the world to bring these solutions to market. We are excited to be able to make this platform accessible to innovative companies and teams who may otherwise not have the resources or expertise to develop these capabilities in house. We look forward to engaging with other customers in supporting the development of their agricultural biological programs in addition to Bayer on our new agriculture biologics platform.

We also share a common vision with Zymergen—that biology can transform a wide range of industries including manufacturing, agriculture, and medicine. Through the transaction announced today and expected to close in the first quarter of 2023, we plan to integrate Zymergen’s core automation and software technologies for scaling strain engineering capacity into our Foundry, including Zymergen’s machine learning and data science tools for exploring known and unknown genetic design space. 

We expect this acquisition to significantly enhance the strength of our platform to better serve our customers, both through the expansion of our Codebase of biological assets and the automation, software, and data tools of our Foundry. We will as always remain a horizontal platform, enabling customers across industries rather than producing our own products, and will support Zymergen’s plans to evaluate strategic alternatives for their Advanced Materials and Drug Discovery businesses. 

We have always had incredible respect for the Zymergen team and the strength of the technologies that they have built for cell programming. We are beyond thrilled to integrate Zymergen’s capabilities into our Foundry, which we expect to accelerate the growth of our platform as we continue to deliver on our mission to make biology easier to engineer for our customers, helping us drive down the costs of cell programming as we invest in scale. We can’t wait to welcome Zymergen technical teams, who will support our scaling objectives.

We’re so excited to work with the amazing teams from Bayer, Joyn, and Zymergen to continue to grow our offerings and our capabilities to support the essential work happening across industries to grow the bioeconomy. See key legal info here and read more about these exciting transactions in our press releases today on Bayer and Zymergen, or watch the recording of our conference call this morning here.

Ginkgo Publishes Inaugural Sustainability Report

Today, we are happy to share Ginkgo’s inaugural sustainability report, Caring at Ginkgo.

At Ginkgo, we believe our platform can play an important role in addressing some of the major societal and environmental challenges that we face today.

Further “caring how our platform is used” has always been a key lens through which we consider the choices we make as we grow our business, and, since 2020, has been an explicit part of our company-wide goal-setting framework. When we went public last year, we declared that “ESG is in our DNA.”

Accordingly, over the past year, the Ginkgo ESG Working Group has worked across the Ginkgo ecosystem and with key external stakeholders to produce this first report and to position ourselves for routine reporting moving forward.

Our inaugural sustainability report is organized across three themes:

  • The Impact of Cell Programming (“Environmental”)
  • Technology Isn’t Neutral (“Social”)
  • Ownership Is the First Step in Caring (“Governance”)

Read the full report here.

We all know that today’s ‘ESG’ reporting systems are far from perfect. Nonetheless, we are proud to have built out a first-class team that has strived to maintain an authentic, “first principles” approach to ESG reporting. Our inaugural report is guided by key ESG frameworks and standards (e.g., the Global Reporting Initiative and Stakeholder Capitalism Metrics), as well as a third-party led materiality assessment.

We look forward to sharing our progress and continuing the conversation about the impacts and implications of synthetic biology.

If you have comments on our report, or if you would like to chat more, please email [email protected]. In the meantime, thank you for being a part of this ongoing conversation, because a future where we can grow everything requires care, transparency, and many voices.

Find our full press release here along with all of the latest news from the Ginkgo team.

What will you grow with Ginkgo?

Expanding Our Platform Capabilities in Agricultural Biologicals and Launching Flagship Partnership with Bayer

Announcement Highlights:

  • Planned transaction expands Ginkgo’s horizontal platform capabilities to support agricultural biologicals R&D from discovery through formulation and early field trials and will offer services to allow access to customers of all sizes in the agriculture industry
  • Under the proposed transaction, Ginkgo to acquire Bayer’s West Sacramento agricultural biologicals site and team, adding a 175,000 square-foot R&D facility with pilot scale fermentation, formulation, and greenhouse facilities, along with access to Bayer’s large agricultural strain collection
  • Joyn Bio, the joint-venture between Ginkgo and Leaps by Bayer formed in 2017, to be integrated into the parent companies, with the core technology platform becoming part of Ginkgo’s platform and key products being advanced by Bayer in a new collaboration
  • Bayer to be an anchor customer of Ginkgo’s agricultural biologicals offering, signing a follow-on multi-year platform collaboration deal to enable continued development of Joyn Bio’s flagship nitrogen fixation program and launching new programs in fields including next-generation crop protection and carbon sequestration

We’re excited to announce plans to significantly expand our platform capabilities in agricultural biologicals from discovery to field. These capabilities will be built through a series of transactions; Ginkgo will acquire Bayer’s 175,000 square-foot West Sacramento Biologics Research & Development site, team, and internal discovery and lead optimization platform. Ginkgo will also integrate the R&D platform assets from Joyn Bio, a joint-venture between Ginkgo and Leaps by Bayer formed in 2017. Bayer will be the anchor agricultural customer of Ginkgo’s expanded platform, entering into a significant new multi-year collaboration which will focus on the advancement of Joyn’s marquee nitrogen fixation program as well as new programs in areas such as crop protection and carbon sequestration.

While Ginkgo will continue to evaluate the operating expenditures required to launch and scale its expanded agricultural capabilities following these transactions, it is expected that the cash proceeds from this multi-year collaboration with Bayer may significantly offset such anticipated expenditures. The proposed transactions are projected to close before the end of 2022, pending the finalization of definitive agreements and subject to regulatory approvals.

Agricultural biologicals are a rapidly growing category of solutions that offer tremendous sustainability and performance benefits. Against the backdrop of rising fertilizer costs and novel pest and disease threats, growers are calling for new agriculture solutions that can increase yields while decreasing their environmental footprint. While chemical and plant trait solutions have long been the dominant solutions on the market, demand for biologicals has increased dramatically.

Bayer, Ginkgo, and Joyn share a common vision, which is to enable biological products to be a critical part of the solution to the world’s greatest agricultural and environmental challenges. We are incredibly impressed by the success of the Joyn team and the deep expertise of Bayer’s West Sacramento R&D team and are thrilled to have them join Ginkgo as we build deep end-to-end capabilities in ag biologicals on top of our large scale horizontal platform. We believe we’re bringing together the most innovative minds in agriculture with the experience of a team that has brought several effective biological products to market for Bayer — opening this platform up to the world has the potential to truly revolutionize the field.

Bayer has long been committed to expanding its product offerings to benefit growers around the world. In recent years, the company has made a strategic decision to focus on becoming the preferred research, development, and commercial partner in the biologicals segment, while leveraging an “open innovation” model to be able to partner broadly with disruptive discovery companies.

Through this agreement, Bayer is committing to a significant multi-year collaboration, advancing multiple programs including a marquee nitrogen fixation program as well as a suite of other programs in areas such as next-generation crop protection and carbon sequestration.

“Biological solutions will play a critical role in the agricultural innovation ecosystem, and we see tremendous opportunity for biologicals to add even more value for agriculture in the future because they are effective and offer environmental benefits that producers want,” said Bob Reiter, Head of R&D for Bayer Crop Science. “Bayer is moving to strengthen its product development and commercial positioning through strategic research partnerships for new product development, and we are excited to deepen our relationship with Ginkgo, which we expect to be a key partner for many years to come.”

Over the last five years, Joyn has developed a new class of microbial solutions in partnership with Bayer and Ginkgo. Through this transaction, Joyn’s product concepts will be advanced by Bayer, with a particular focus on its nitrogen fixation program, while the platform assets and supporting team members will be integrated into Ginkgo as the company expands its support for agricultural biologicals.

Ginkgo will offer these new platform capabilities to a wide variety of customers in the agriculture space.

Ginkgo expects to provide a full stack of services in this field. This extension of our platform will allow companies of all sizes to access best-in-class lab-to-field translation expertise, greenhouse capacity, formulation capabilities, and pilot fermentation.

“With support from Ginkgo and Bayer, Joyn Bio has made groundbreaking discoveries across a number of programs that will be foundational for future work in biologicals,” said Michael Miille, CEO of Joyn Bio. “We are excited to take this platform to the next stage, with Bayer advancing key programs to the next level and working with Ginkgo to open our capabilities up to a broader set of commercial partners.”

The parties expect to sign a definitive agreement and proceed toward an efficient close, supported by ongoing integration planning efforts. More details and updates will be provided when available.

Find the full press release here along with all of the latest news from the Ginkgo team.