Ginkgo Bioworks Awarded Grant for AI-enabled Forecasting of Measles Outbreaks

Posted on by Matthew McKnight

Ginkgo epidemiological modeling experts and Northeastern University researchers awarded new grant from the Bill & Melinda Gates Foundation

Today we’re thrilled to announce that we’ve been awarded a grant from the Bill & Melinda Gates Foundation to build an open-access, AI-enabled measles forecasting model to empower proactive public health measures, such as immunization campaigns, in partnership with Northeastern University researchers Alessandro Vespignani and Sam Scarpino.

Measles is a highly contagious and often severe disease that most commonly affects children.

While the widespread availability of measles vaccines has dramatically reduced the disease burden over the past several decades, cases are on the rise in the U.S. this year, and global outbreaks continue to cause significant illness and mortality, particularly in low- and middle-income countries. These consequences are largely preventable through early interventions, but getting ahead of major outbreaks is difficult when access to data is limited.

With support from the Gates Foundation, expert epidemiologists and modelers from Ginkgo Bioworks and Northeastern University will develop a measles forecasting model to assess the risk of outbreaks and inform decision-making for timely interventions. Because measles reporting is often sparse, especially in low-resource settings, the model will draw upon traditional and non-traditional data, including public health reports, travel patterns, economic activity, and other factors, and utilize AI approaches such as machine learning and deep learning to structure and analyze a multitude of data sources to produce actionable insights.

“With support from the Gates Foundation, our project with Ginkgo Bioworks sets a new standard for what can be achieved when academia, industry, and philanthropy come together to develop global health solutions. By bringing together the expertise of multiple sectors and modern AI capabilities, we can create powerful, innovative tools that will provide critical information for safeguarding communities worldwide against the threat of measles.”

Alessandro Vespignani, Director of the Network Science Institute and Sternberg Family Distinguished Professor at Northeastern University

The forecasting model will be available open-access to help the global health community understand how likely it is that measles will emerge and spread within a given area, with the intent of enabling them to better allocate scarce resources and reduce the global burden of measles.

If we wait until large pockets of measles show up in hospital systems to launch public health responses, we are missing a critical window to act and slow the spread of this debilitating and highly contagious disease. Modern data and AI tools can shift the biosecurity and public health paradigm from reactive to proactive by helping global health leaders make more timely, effective decisions to prevent outbreaks from happening in the first place.

We believe the technologies we’re developing will give us the ability to get ahead of the curve for measles and other biological threats.

Ginkgo Bioworks to Host 5th Annual Ferment Conference

Posted on by Ginkgo Bioworks

We’re hosting our annual conference, Ferment, on Thursday, April 11, 2024 in Boston, MA!

The conference brings together stakeholders from across the synthetic biology ecosystem and the Ginkgo community — from shareholders and customers to suppliers, academics, and many more.

Because we have reached in-person capacity, a video livestream of the event will be made available to the public, including on Ginkgo’s YouTube channel and on the company’s investor relations website at https://investors.ginkgobioworks.com/events.

Next-Gen Enzyme Development for Sustainable API Manufacturing with Prozomix

Posted on by Cindy Chang

We’re so excited to announce our new partnership with Prozomix, a UK-based biotech company focused on novel biocatalyst discovery and manufacturing!

Together, we aim to build out the production of next generation enzyme plates for active pharmaceutical ingredient (API) manufacturing. This collaboration aims to leverage Ginkgo’s Enzyme Services and industry-leading AI/ML models along with Prozomix’s existing enzyme libraries and deep experience manufacturing enzyme plates.

This agreement also marks Prozomix’s entry into the Ginkgo Technology Network!

Ginkgo’s Technology Network brings together a diverse array of partners, spanning AI, genetic medicines, biologics, and manufacturing, with the aim of integrating their capabilities to provide customers with robust end-to-end solutions for successful R&D outcomes. With Prozomix now in the Technology Network, Ginkgo customers will have access to Prozomix’s scalable contract manufacturing services, including enzyme samples from mg to kg scale.

For several decades, demands for both improved supply chain sustainability and reduction of costs of goods sold has driven the pharma industry towards the adoption of biocatalysts in commercial API manufacturing. Existing enzyme plates offer users an opportunity to rapidly screen potential candidates early in development to identify and de-risk the use of biocatalysts capable of supporting specific reactions in API manufacturing routes. As such, biocatalyst adoption largely depends on the diversity and performance of the enzymes available in these plates.

Prozomix and Ginkgo are partnering to usher in a new generation of biocatalysts built off of sequences and activity data from previous enzyme libraries.

Ginkgo will build class-specific AI models informed by enzyme sequences and data from its own massive metagenomic database as well as Prozomix’s enzyme libraries and associated screening data. These models can then be used to discover novel functional enzyme sequences. Prozomix intends to then use next-gen enzyme libraries, designed by these models, to manufacture novel enzyme plates.

Together, we expect these next-gen enzyme plates to have a diversity and performance that traditional plates lack, potentially unlocking biocatalytic opportunities where previous plates have failed. These plates will be freely available to all pharma process chemistry groups, provided that screening data is shared back with Ginkgo to drive further refinement of the Ginkgo AI/ML models.

“With a global reputation for de-risking early stage biocatalytic processes, we believe the Ginkgo partnership will keep Prozomix at the forefront of best in class biocatalyst provision throughout the AI revolution, enabling our customers to continue saving and improving more lives.”

Simon J. Charnock, CEO of Prozomix

API manufacturing is poised to greatly benefit from the latest in enzyme engineering and AI/ML enzyme models.

We are so excited to partner with Prozomix to get enzymes into as many API routes as possible and help partners meet both their COGs savings and sustainability goals.

To learn more about Ginkgo’s Enzyme Services, please visit https://www.ginkgobioworks.com/offerings/biopharma-enzyme-services/

Acquiring Modulus Therapeutics’ Cell Therapy Assets to Strengthen Next-Gen CAR Designs

Posted on by Jason Kelly

Today we’re excited to announce our acquisition of Modulus Therapeutics’ cell therapy platform assets, including their chimeric antigen receptor (CAR) and switch receptor libraries.

Modulus Therapeutics is a cell engineering company focused on the design of next-generation cell therapies for autoimmune diseases. In contrast to legacy cell therapy design, the company uses a combinatorial approach to build and screen cell therapy components that work in concert with one another to yield novel cell behaviors.

Modulus has used its platform to develop and screen libraries of novel NK-specific and T-cell specific CAR and switch receptor designs, which enable improved control and performance of immune cell-based therapies. This technology has the potential to improve the safety and efficacy of cell therapies by allowing for more precise control over activation and targeting. Modulus’ CAR-NK and CAR-T components are designed to enhance proliferation and cytotoxicity, even in inhospitable cellular environments, providing a deeper and more durable response against target cells.

Modulus’ assets complement Ginkgo’s extensive cell therapy capabilities.

With this addition, Ginkgo looks forward to supporting its customers who are improving the performance of T-cell and NK-cell based CAR therapies to treat solid tumors, autoimmune, and other diseases.

Modulus Therapeutics has built an array of incredible cell therapy assets that we are excited to add into the significant cell therapy capabilities Ginkgo has developed to date. Modulus’ CAR and switch receptor designs and libraries seamlessly integrate into our existing infrastructure and offerings. We are excited to put these new assets to work for our customers and contribute to the transformative advancements in CAR and cell therapies.

“At Modulus, we have always been motivated by enhancing access to cutting-edge cell therapy innovation. We’re very pleased that Ginkgo Bioworks shares this commitment and can leverage our technology to help transform oncology and autoimmune cell therapies. We are thrilled to contribute our innovative designs to the Ginkgo ecosystem, and look forward to seeing these tools deployed across a range of Ginkgo-partnered programs.”

Max Darnell, CEO and co-founder of Modulus Therapeutics

Ginkgo’s platform works to enable its partners to sample CAR domains with a variety of functional roles and structural positions, sourced from diverse immune cell types.

This approach to cell therapy discovery allows partners to thoroughly sample the breadth of therapeutic activities a CAR can produce.

Last year, Ginkgo entered a partnership with the Wisconsin Alumni Research Foundation (WARF) to discover and develop next-generation CAR-T cell therapies.

Ginkgo also presented new data on its high throughput pooled screening method to discover novel CAR-T designs for solid tumors at the 37th Annual Meeting of the Society for Immunotherapy of Cancer (SITC) in 2022, as well as data on its high-throughput screening platform for chimeric antigen receptor (CAR) libraries at the 26th American Society of Gene & Cell Therapy (ASGCT) Annual Meeting in 2023. The poster highlighted Ginkgo’s Foundry-enabled methods for large-scale, combinatorial library design and screening of CAR domains for improved persistence.

We expect Modulus’ cell therapy assets to help us continue to strengthen our CAR-T research & development offerings!

Learn more about Ginkgo Cell Therapy Services here.

Producing Novel Proteins to Control Ice in Extreme Cold Weather Environments with DARPA

Posted on by Jason Kelly

Ginkgo has been awarded a contract for up to $6 million from the Defense Advanced Research Projects Agency (DARPA) to achieve DARPA’s objectives under its new Ice Control for cold Environments (ICE) program.

DARPA’s ICE program aims to develop new materials that control the physical properties of ice crystals to facilitate operations in extreme cold weather environments, which can pose a variety of risks to both personnel health and critical equipment. To meet this goal, Ginkgo, in collaboration with Netrias, Cambium, and consultant Dr. Ran Drori, aims to develop novel biologically-sourced and inspired materials that leverage biological adaptations to cold environments.

The Ginkgo team will work to enable the sustainable production of novel de-icing proteins with ice-modulating behaviors to improve operational efficacy in extreme cold weather environments.

These materials will be designed with the goal of meeting U.S. Department of Defense specifications and could potentially be used in solutions with broad commercial applications. One such application could be a lens coating to prevent frost formation for a range of optics applications from satellites and high altitude imaging instruments to security and wildlife cameras. The aviation and automobile industries could also benefit from de-icing products that facilitate safe operations in icy conditions. Furthermore, a topical frostbite prevention product could be developed for outdoor enthusiasts. If successful, these solutions could impact high value and consumer markets and facilitate replacement of current environmentally harmful de-icing agents.

The team plans to leverage Ginkgo Protein Services to design, screen, and optimize a library of novel proteins that demonstrate ice-modulating behaviors.

Ginkgo will design a library of proteins using metagenomic discovery and de novo computational design to source known, naturally occurring ice-modulating behavior proteins. During the discovery phase, predictive models will be used to iterate Design–Build–Test–Optimize loops, maximizing discovery of proteins with ice inhibition, induction, and low-adhesion properties. Throughout the process, Ginkgo will selectively screen promising proteins with further high-performance, application-specific characterization to inform the final down selection.

We are honored to be selected by DARPA to work on this program to facilitate sustained cold weather operations.

Building high-throughput libraries of candidate proteins is possible thanks to Ginkgo’s unique and differentiated data assets. Biology offers us a myriad of ways to adapt to our environment, and synthetic biology allows us to tap into nature’s capabilities and apply them to our own needs. We look forward to the products that the ICE program generates, which may enable enhanced safety and proficiency across various use cases.

To learn more about Ginkgo Protein Services, please visit https://www.ginkgobioworks.com/offerings/protein-services/.

If you are interested in working with Ginkgo for the public sector, check out our Offerings for Governments page.

Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the Defense Advanced Research Projects Agency.

Optimizing Alt-Seafood Production with AQUA Cultured Foods

Posted on by Mervyn de Souza

Today we’re thrilled to announce our new partnership with AQUA Cultured Foods!

AQUA has chosen Ginkgo to help optimize its innovative fermentation technology to elevate the quality of its fish-free seafood products that authentically replicate the look, feel, and taste of fresh-caught seafood. Leveraging Ginkgo’s microbial characterization and analytics, along with AQUA’s proprietary strains and processes, the partners aim to transform the future of alt-seafood production.

AQUA is a leader in the alternative seafood industry, delivering products with the texture, taste, and appearance of fresh-caught seafood filets, without using any fish or animal inputs.

  • Their debut offerings, tuna, and scallops, maintain freshness and tenderness for six weeks.
  • Powered by a patent-pending fermentation process, which can be scaled on a global level, AQUA’s fish-free seafood is made from microbes and fibers combined with plant-derived flavors that replicate the buttery texture and umami notes found in fresh-caught seafood.
  • Unlike traditional seafood, AQUA’s products contain no contaminants, antibiotics, allergens, cholesterol or saturated fats, and can be consumed and enjoyed by those with diverse dietary needs, including pregnant people and those with shellfish allergies.

The AQUA team uses a consortium of microbes that work synergistically to make its appetizing and affordable products.

Ginkgo will leverage its high throughput next-generation sequencing and advanced analytics services to help optimize and tune AQUA’s strains to aid in the scale-up of their novel manufacturing process. With Ginkgo, AQUA hopes to amplify its R&D capabilities and further optimize its consortium to establish consistent, high-quality products.

Through this, AQUA envisions a future where its proprietary microbe consortium can be used to produce not just whole-cut and ground alt-seafood products, but also introduce unique flavors and textures to the broader food industry.

This inaugural partnership paves the way for future projects leveraging Ginkgo’s strain engineering capabilities as well.

AQUA’s fermentation process provides an alternative to fishing and fish farming.

Research shows that there are serious health risks associated with eating both wild-caught seafood from the ocean and farmed fish. The U.S. Environmental Protection Agency states that contaminated fish are a persistent source of toxic polychlorinated biphenyls (PCBs) and mercury in the human diet. Eating farmed fish comes with the added risk of consuming antibiotics and pesticides.

Both the fishing and fish farming industries cause detrimental environmental damage. Wild fisheries have been depleted worldwide, causing scientists to fear their impending collapse. Industrial fishing practices, such as bottom trawling and long-lining, affect endangered animals such as sea turtles, dolphins, and whales. Untreated waste from farmed fish — including excess feed, decomposing fish, excrement, and chemical residue — can pollute waterways and create toxic algal blooms that kill wild aquatic life. AQUA is confident that its products deliver the experience of eating seafood without the health or environmental risks associated with traditional seafood.

“Today marks a significant step towards revolutionizing alternative seafood production. AQUA’s commitment to sustainable seafood aligns with Ginkgo’s dedication to innovation. Our partnership aims to accelerate our technology, bringing our delicious products to market faster. With Ginkgo’s expertise in working with microbes, we are confident in optimizing and applying our technology to create the most delicious seafood products possible. Beyond sequencing, we envision engineering our proprietary consortium for next-gen products, pushing alt-seafood boundaries with unique textures and building the nutrition beyond a good source of fiber. We look forward to how our sustainable approach can revolutionize the fishing industry and contribute to the regeneration of our oceans.”

Stefan Baier, PhD, Chief Science Officer of AQUA Cultured Foods

We couldn’t be happier to partner with AQUA and get to work with their cutting-edge technology.

This collaboration aligns beautifully with our commitment to work on projects that embody innovation and sustainability. AQUA’s groundbreaking fermentation technology is reshaping the future of alt-seafood, and we at Ginkgo are thrilled to contribute to this transformative journey. Together, we’re paving the way for a more sustainable and responsible approach to meeting the world’s growing food demands.

AQUA will also be at Ginkgo’s annual Ferment conference this year on April 11th.

Baier will be presenting at the conference, and AQUA products will be available for conference attendees to taste.

Producing Animal-Free Non-Whey Dairy Proteins with Imagindairy

Posted on by Jennifer Wipf

 

Today we’re thrilled to announce our new partnership with Imagindairy!

Together, we aim to deliver a global solution for animal-free non-whey dairy protein production in a highly cost-effective manner.

  • This collaboration will leverage Ginkgo Protein Expression Services and Imagindairy’s process development and scale-up expertise to accelerate the development of functional non-whey dairy proteins.
  • This is a multi-year program, funded in part by a joint grant from the Board of Governors of the Israel-U.S. Binational Industrial Research and Development (BIRD) Foundation.

Imagindairy envisions a cutting-edge transition in the dairy industry that preserves the flavor, functionality and experience of dairy without relying on cows. Imagindairy combines its proprietary AI platform with the age-old art of precision fermentation and uses microorganisms to create sustainable, scalable dairy proteins, without sacrificing quality, flavor, or nutritional value. With access to its own fully operational production lines, a first in the industry, Imagindairy is able to produce cost-effective dairy proteins at scale.

Imagindairy and Ginkgo have partnered to design an optimized organism capable of cost-effectively producing non-whey dairy proteins. This will allow Imagindairy to remain focused on whey protein production and commercialization while accelerating time to market of non-whey proteins. In tandem, Ginkgo will utilize its AI and high throughput Foundry capabilities to engineer biological systems for improved production economics and functionality. Imagindairy will then develop the production process and perform scale-up and manufacturing of these proteins, marking a significant milestone in their mission to provide a full range of high-quality, animal-free dairy proteins to food producers.

“Ginkgo has firmly established itself in the alternative dairy and food proteins industry, showcasing our leadership in protein and organism engineering. We have many successful collaborations in this space, and we’re thrilled to get to work with Imagindairy on this innovative and market relevant project. We’re also honored to be recognized by the BIRD Foundation. Being awarded this highly competitive grant is a testament to our technical expertise and ability to accomplish this project with Imagindairy. I can speak for the entire team when I say that the samples that Imagindairy have shared are absolutely next-level. If the rest of their pipeline is anything like what we’ve tasted, we can’t wait to try what’s next.”

Jennifer Wipf, Chief Commercial Officer at Ginkgo Bioworks

“We’re proud of this acknowledgment by the BIRD Foundation, as it highlights the importance of further innovation in the alternative proteins field, and our capability to successfully execute this project. Our process development capabilities and industrial-scale precision fermentation lines will allow us to rapidly scale the optimized strains created with Ginkgo and bring innovative non-whey proteins to the market faster. We’re deeply impressed by Ginkgo’s work in the foodtech industry and look forward to collaborating with them on the project. We’re confident this collaboration will unlock further product offerings, providing consumers with additional animal-free dairy delights that match the cost and taste of traditional dairy, making significant contributions to the industry, consumers, and the world.”

Eyal Afergan, Co-Founder & CEO at Imagindairy

To learn more about Ginkgo Protein Expression Services, please visit https://www.ginkgobioworks.com/offerings/protein-services/

Low Viscosity Aspergillus niger: Your Key to Enhanced Productivity

Posted on by Ginkgo Bioworks

Enhance Your Commercial Enzyme and Protein Production

If you’re interested in fermentation-based production of enzymes and proteins, chances are you have heard of the filamentous fungus, Aspergillus niger. It is an efficient factory for making everything from citric acid to a variety of industrially relevant enzymes and proteins. But if you know A. niger, you’re likely aware of the challenges in engineering and fermentation scale-up that limit its potential applications for commercial production. Addressing these challenges requires hefty investment into developing suitable host strains. This is where Ginkgo can help. Our solution is a scalable, low viscosity best-in-class production host of A. niger designed to help you achieve your commercial production goals.

The Challenge

A. niger has long been valued for commercial-scale enzyme and protein production for a variety of factors:

  • High native production of industrially relevant enzymes and proteins
  • “Generally recognized as safe” (GRAS) by the FDA making an easier path towards commercialization
  • High-level protein secretion systems that reduce recombinant protein degradation by intracellular proteases and make downstream processing easier and cheaper

High Viscosity Fermentation
A major challenge of working with A. niger is its high viscosity fermentation, caused by long filamentous structures known as hyphae, which make production and purification difficult. Thick cell culture presents challenges in oxygenation, reactor mixing and nutrient feeding in scaling, which reduces enzyme and protein expression as well as making product recovery almost impossible. These factors may lead to increased time, cost, and resources required for commercial production.

Low-Throughput Strain Engineering
Beyond these challenges in manufacturing, strain improvement in A. niger is complicated by low transformation efficiency, difficulty in isolating correct edits from multinucleated cells, difficulty in automating HTP workflows because of filamentous growth, and secretion of many native proteases which can degrade the product. This can lead to longer, more expensive, and less predictable R&D programs to develop new products using A. niger as an expression host.

Our Solution: A Low Viscosity A. niger Expression Platform
We are pioneering new innovation in filamentous fungi-based manufacturing. We have applied our platform to create a new proprietary low viscosity A. niger production chassis, which we believe is a major advance against all of these challenges, and shows great promise for the development of other host strain expression platforms. By decreasing viscosity of our host strain, we unlock the ability to increase feed rate, oxygen transfer, and ultimately achieve higher expression rates for enzymes and proteins. The result? Increased titers at significantly reduced time and cost compared to conventional high viscosity strains.

 

Video (7 seconds): Fermentation process in a 10L reactor demonstrating Ginkgo’s low viscosity Aspergillus technology. The opaque broth contains a high cell density critical to industrial fermentation, yet low viscosity of the Ginkgo technology enables smooth continuous mixing with standard, scalable CapEx.

Solutions For You

Value of Low Viscosity Fermentation

  • Reduced Energy Consumption: Lower viscosity requires less energy for stirring at the same biomass levels therefore contributing to lower COGS.
  • Enhanced Biomass Yield: With a low viscosity phenotype maintained at a constant stirring rate, higher biomass levels can be achieved as we can unlock increased feed rate and oxygen transfer. This increased biomass can be attributed to increased production, improving protein titers and decreasing cycle time per batch, therefore lowering manufactured COGS.
  • Streamlined Downstream Processing: The lower viscosity phenotype facilitates potentially easier downstream processing and purification, simplifying the overall production workflow.

Generating a scalable low-viscosity A. niger manufacturing platform means an easier path to commercialization. We achieved this phenotype by integrating base strain screening with rigorous fermentation process optimization. Our novel base strain shows reduced filamentation in culture, and our optimized process – achieved through strategic changes to media composition, pH and feed rates – promotes enhanced growth of our strain without needing improved aeration strategies. We can promote high efficiency sporulation on agar plates for starting cultures and aiding recombinant gene transfer, and also prevent sporulation in liquid media that causes batch-to-batch variations in bioreactors and other processing issues. Through these methods, we have generated a base production strain optimized for low viscosity growth in scale-up fermentation.

The improved process created by our low viscosity strain and the strain’s genetic make-up which included multiple copies of the target enzyme, allowed us to improve production of a native secreted enzyme to 120 g/L, five times higher than our initial titers. With further strain engineering, there is potential to achieve even higher performance for this protein. These successes present opportunities for manufacturing other native products of A. niger to achieve similar titers. With the development of a fully validated fermentation process from 250 mL to large-scale industrial bioreactors we have helped reduce risk and associated R&D costs for future programs.

Chassis Strain Development
We can offer solutions for customers interested in developing their own chassis strain. We have identified several genomic mutations that confer the low-viscosity phenotype, and have confirmed that the equivalent edits replicate the phenotype in other fungal species. We see potential to engineer other filamentous fungi, including existing production strains, with similar phenotypes to generate multiple low viscosity expression platforms.

Development of a Clean Background
Using multiple gene editing approaches – a combination of classical split marker homologous recombination and CRISPR – we made significant improvements to our strain background. We performed targeted knockouts of multi-copy genes for secreted proteins that would compete with heterologous products, and for major protease genes and those related to protease regulation that can result in degrading your targets. Through these modifications of the host strain, we have generated a clean background strain with diverse project applications.

Strain Engineering Standardization
In parallel to developing a scalable fermentation process, we made fungal strain engineering more efficient and predictable. While filamentous fungi are notoriously difficult to engineer, we have developed efficient transformation protocols. We made the strain compatible with our platform by creating high-throughput transformation protocols that can leverage our in-house liquid handling robots and other clonal separation technologies, streamlining the process further. These improvements can give you confidence in our ability to express a variety of heterologous enzymes and proteins.

Conclusion

Expanding the scope of products that can be manufactured in filamentous fungi like A. niger offers immense industry value. Our breakthrough low viscosity expression platform stands as a key innovation, enhancing oxygenation and feed to maximize titer output of industrial enzymes and proteins. By combining our low viscosity strain with extensive R&D efforts, we’ve not only pushed titer limits but also simplified scale-up fermentation and optimized strain engineering processes. We’ve taken on the heavy lifting for you, streamlining production and reducing fixed manufacturing costs. With our proprietary high-productivity, low viscosity strain of A. niger, we’ve eliminated the complexities of strain development. This means you can feasibly achieve faster, more cost-effective commercial-scale production with reduced risk.

We’re equipped to engineer your strains and any enzyme or protein of interest in our production host. Stay engaged with us as we continue to push boundaries and uncover the full potential of A. niger.

Learn more about Viscosity in our Foundry Theory Video!

Hard Biology: Viscosity

In Summary

Our ready-to-use proprietary Aspergillus niger strain delivers:

  • Low viscosity – also in your own preferred production strain
  • High production of native enzymes and proteins
  • High-level enzyme secretion system
  • Clean background – Minimal native secreted protein / protease activity

Work With Us

Partner with us to unlock the potential of Aspergillus niger today!

Contact our technical consultants to learn more: Peter Punt & Kenneth Bruno

Engineering Biology: Advancing the Bioproduction at Ginkgo’s Cell Engineering Platform

Posted on by Sudeep Agarwala

Ginkgo Bioworks’ cell engineering platform lowers the bar for entry into developing products through metabolic engineering.

High-throughput strain design and testing on industry-leading chassis strains, paired with AI-enhanced enzyme engineering tools provides Ginkgo’s partners rapid prototyping and development. Nádia Parachin, Senior Director of Business Development at Ginkgo discusses how this streamlined process enables quicker market entry, fostering a lower barrier to bringing new products to market.

Humans of Ginkgo Bioworks is an interview series featuring Sudeep Agarwala interviewing some of the brilliant folks at Ginkgo to learn more about the technology that makes our work possible.

Sudeep Agarwala: You’ve run projects for quite some time at Ginkgo, but before that, were spanning both academia and industry, correct?

Nádia Parachin: Well I’ve been at Ginkgo for almost four years now, but you’re right–I came to Ginkgo from Brazil. In Brazil, I was a professor at Universidade de Brasilia and at the same time, I was the Co-Founder and CEO of Integra Bioprocessors. Integra used metabolic engineering to convert agro-residues (glycerol, for example) into high-value chemicals. And in fact, two of the technologies that we co-developed at Integra and UnB was a microbial strain producing PLA from glycerol and another strain producing Hyaluronic acid from sugar.

But that also naturally led to this position at Ginkgo. Since 2020, I have run quite a few projects at Ginkgo through the Foundry in yeast–Saccharomyces cerevisiae. What can I say? It’s my favorite yeast.

SA: Recently you’ve made an interesting shift–you’ve moved over to the commercial side, thinking about how Ginkgo’s platform can be applied widely to different companies?

NP: What is most impressive to see at Ginkgo during these years is not only once but–to my knowledge–at least a few times, the production of molecules that have never been made in a microbial host before. I’ve seen the same for enzymatic reactions. At Ginkgo, we demonstrated reactions not found in nature, truly contributing to the company’s mission of making biology easier to engineer. 

The reason for these success stories is the combination of our physical platform–automated, high-throughput strain design, construction, and testing– paired with our digital assets– incredible database of enzyme engineering experimental results and now AI-enabled engineering tools.  An equal player in this is the expertise of the people who run these workflows and design the experiments at Ginkgo. We have a collection of people who have deep knowledge of the different microbial hosts and have been working for years on critical pathways and developing tools to make this engineering possible.

What I find exciting about being on the commercial team is that my team’s technical expertise can be teamed up with people who have a real understanding of the market, resulting in tailor-made offers for what the market demands. It has been a fun journey, and I’m thrilled to be part of this team.

SA: Maybe to go into more detail here, what exactly does Ginkgo provide to its partners?

NP: Ginkgo provides our partners with a head start–partially because of the platform and our knowledge-base–technical assets we’ve collected over the years. So if a partner comes to us and wants to make an innovation in their field, they don’t have to invest in their own lab space, expensive specialized equipment, etc. They can get started very quickly by leveraging Ginkgo’s R&D capabilities and running experiments for a fraction of the cost of building a lab from scratch. This means they have a lower barrier to explore which  product has the potential to make a real difference in the market. 

We’re also providing value to the companies already in the field, who are already doing synthetic biology and fermentation. These companies know what they are doing in terms of their technology, their market. They have a good understanding of their processes for commercialization. But with our expertise, we can take on newer, earlier-stage projects instead of these companies having to rearrange their internal R&D: let us do your innovation, and when the technology is mature, you can incorporate it into your pipeline–you do the manufacturing and the commercialization.

SA: I’m curious about the difference between Ginkgo and CROs. When does it make sense to come to Ginkgo vs. say, going to a CRO?

NP: We see this question come up all the time. The most important difference is that besides our platform and a proprietary database, Ginkgo has developed and owns what we call “chassis” strains: microbial hosts that have been modified for increasing flux throughout key metabolic pathways.

Take the shikimate pathway, for example. This pathway can produce multiple molecules, ranging from building blocks for polymer production to flavors, fragrances, and nutraceuticals.

When you go to a CRO to engineer a product off the shikimate pathway, you have to start from scratch to develop dedicated enzymes for your target’s pathway. In parallel, you also have to develop a strain that will have a high flux through the shikimate pathway to get your product to your target titers.

But when you’re working with Ginkgo, our starting point is lightyears ahead. We’ve already developed the base assets, our ‘chassis’ strains that have flux through the shikimate pathway at very high levels. So now we dedicate our work to the specific part of our customer’s pathway that converts this flux into their target molecule. And because it’s only this part, we can deliver both prototyping and strain development faster than any other CRO. 

I’m talking about the shikimate pathway here, but it also applies towards fatty acid metabolism, terpenes, any range of pathways that you’re engineering off of. You’re not starting from scratch–you have the starting strain, the platform, the enzyme engineering capabilities, and that gives you a head start towards commercialization. 

SA: So this is a compelling reason for leveraging Ginkgo’s platform, but I’m curious what happens if too many people start to do that. Like you’ve acknowledged, there’s a big market in metabolic engineering for small molecules. How does Ginkgo think about protecting information between different companies who are coming to Ginkgo?

NP: This has come up a few times as a major concern from people who are talking to us. We’ve had partners who have said “Look, I know you guys have a project with my competition. Can you guarantee that there’s not going to be any sharing of my information?”

And one of my arguments for the companies in industrial biology has been that we aren’t just doing small molecules: we have pharmaceutical companies on the platform–that’s the standard that we’re working with to ensure that there’s no sharing of information between different projects for different companies. We have that capability and we take it very seriously. We’ve developed systems internally that flag information so that it cannot be shared and that data that results from one customer’s project cannot be shared.

The entire point is that Ginkgo prepared itself over the years to be positioned at the cutting-edge of synthetic biology technology, and we’re working towards utilizing the platform to enable the sustainable production of biomolecules applied to several industrial sectors. It’s not just about engineering strains, it’s also about creating a bioeconomy and seeing it thrive. And we’ve made it possible so people can develop their strains and bring their products to market with confidence that they’ll be competitive.

Work with Us

Nádia Skorupa Parachin, Ph.D., is Senior Director of business Development at Ginkgo Bioworks, leading the Industrial Biotechnology sales team for the production of small molecules. Nádia brings over 15 years of experience in synthetic biology, metabolic engineering, and project management. She has previously served on the technical team at Ginkgo as a Senior Program Lead, engineering and delivering custom strains for Ginkgo’s partners. Before joining Ginkgo Bioworks, she was CEO of Integra Bioprocessors and a professor of biotechnology at Universidade de Brasilia (UnB).

Welcome Dr. Mitch Wolfe!

Posted on by Ginkgo Bioworks

Welcome Dr. Mitch Wolfe!

Dr. Wolfe brings over 20 years of experience in developing public health infrastructure in the U.S. and internationally

We are excited to welcome Mitch Wolfe, MD, MPH, RDML (ret.), USPHS, as Vice President of Global Engagement and Governance in biosecurity. In this new role, Dr. Wolfe will bolster partnerships, both in the U.S. and internationally, to advance the development of effective, sustainable, and equitable infrastructure for biosecurity and pathogen monitoring. Dr. Wolfe, a medical epidemiologist, has guided strategies for national and global public health systems for over 25 years.

Throughout his career, Dr. Wolfe has defined critical public health strategies and bolstered multilateral and multisectoral collaboration to combat transboundary biosecurity threats. Dr. Wolfe joins Ginkgo’s biosecurity and public health unit, Concentric by Ginkgo, which is building global infrastructure for biosecurity to empower governments, communities, and public health leaders to prevent, detect and respond to a wide variety of biological threats. Dr. Wolfe will grow and catalyze collaboration across our global biosecurity network, which currently includes 14 countries and several multilateral organizations with active programs, pilots, or memoranda of understanding.

“Every country in the world needs strengthened biosecurity to enable better detection and response to pandemic threats,” said Dr. Wolfe. “Early detection is a critical element, and innovation, flexibility, and collaboration are critical for success. I joined Ginkgo because I believe we can add tremendous value to these efforts as a systems integrator and strategic partner, helping to build country-level and global health security infrastructure. I am excited to work with Ginkgo’s biosecurity team to grow innovation and collaboration among public and private partners, to collectively tackle the rising risks from known and novel pathogens.”

Dr. Wolfe most recently served as global public health consultant for multiple organizations, and previous to that was the Chief Medical Officer for the U.S. Centers for Disease Control and Prevention (CDC), where he led global strategy for the agency. He has previously served in critical global health leadership roles, including as the Deputy Assistant Secretary for Global Affairs at the U.S. Department of Health and Human Services, and CDC Country Director in Thailand and Vietnam. In 2020, he retired from the Commissioned Corps of the United States Public Health Service at the rank of Rear Admiral. Dr. Wolfe holds a Medical Doctorate from the University of Vermont College of Medicine and his Master of Public Health degree from University of California, Berkeley.

Learn more about our global biosecurity programs and tools here.