Growing anything (!!) with the bioeconomy

…and yet another piece of evidence that intersections and interdisciplinary problem solving is where the magic is at🧙🏽‍♀️

15 billion dollar valuation,

potentially solving the hunger crisis, curing cancer, and accelerating COVID-19 therapeutics,

revolutionizing what biology means, what it can enable, and subsequently enabling infinite possibilities of what the world can make by bridging software, hardware, wetware, design, engineering, art, and DNA together, I present to you…

Gingko Bioworks.

Okay okay okay that’s a lot. Taking a couple steps back

  1. Gingko Bioworks is a company.
  2. Gingko Bioworks is a biotech company.
  3. Gingko Bioworks is shifting use cases of biology from predominantly laboratory research for medicine to utilizing engineering and software principles to take full advantage of what it can be capable of.

This is fundamentally reliant upon their two-part system

Part 1: Foundries

  • Biological factories = foundries at Ginkgo Bioworks
  • automating and scaling the process of organism engineering, allowing engineers to prototype thousands of biological designs.
  • uses DNA synthesis, laboratory automation, analytics, and software tools to automate and scale organism engineering processes, enabling engineers to prototype thousands of biological designs.

Part 2: Codebase

  • acts as a biological portfolio which is used by organism engineers to start new projects leveraging the stored data on cells, enzymes, and genetic programs.
  • same way that software engineers use existing libraries of code to write new programs.

Putting “potential use-cases” into context…

Living Medicines

Art that signifies the collaboration between Synlogic and Gingko like “bacteria sensing and targeting various compounds, biofilm formation, and the gut living in the background.”

Challenge (/Opportunity)

The body cannot synthesize branched-chain amino acids such as leucine, isoleucine, and valine which are essential amino acids.

The pathways that exist for catabolizing branched-chain amino acids involve many highly regulated enzymes, and genetic defects that exist in those enzymes can result in severe metabolic disorders.

Solution

Synlogic is developing a platform that enables programming of probiotic bacteria to treat many different complex diseases using biology.

You see since, living cells unlike chemicals can sense and respond, deliver enzymes, and small molecules directly where they’re needed, and they can consume and break down potentially toxic molecules before they cause any harmful effects.

By genetically engineering microbes to deliver critical functions that are missing due to such diseases we can solve this problem.

So to combat this issue, Synlogic had been genetically engineering microbes to deliver the necessary functions missing in such diseases and had been prototyping an enzyme pathway to consume leucine within E. coli.

In order to optimize the pathway to increase the consumption of leucine, Gingko synthesized, and screened over 1,200 homologs of each enzyme, finding the best performing enzymes that had significantly more in vitro activity than the original enzymes used for the pathway.

350 operons (clusters of genes) were assembled into a library based on the top hits of each individual enzyme screening, and then this was screened with a high throughput leucine consumption assay.

This research paper published by researched from Ginkgo Bioworks and other partners, shares that ultimately the final optimized strain was SYN5941. In addition to being 7 times more effective in leucine consumption than the original strain, it was shown to be able to lower leucine consumption in other primates too.

For greater context on their overall work, Synlogic’s pipeline,

  • includes strains of E. coli which can consume phenylalanine or ammonia in diseases where patients’ bodies are unable to do that on their own. and so this is preventing toxicity and neurological damage from being left untreated in patients bodies.
  • is currently working on engineered bacteria that can send signals which alter the immune system to attack cancer sells after being injected directly into tumors.

Cultured Ingredients

Source

Challenge (/Opportunity)

Many treasured fragrances are extracted from botanical sources, which happen to be costly and resource intensive, increasing the pressure on natural biodiversity.

Additionally fluctuations in supply of such natural sources can be unpredictable given volatile weather changes and other such influences.

Solution

The actual process which is prized for bringing such fragrances to life is fermentation (from wine to cheese, to beer, to chocolate).

The creation of cultured ingredients can resolve the challenges explained previously, while still enabling the production of “delicious, renewable, and accessible products.”

The gene sequences which are used to produce the unique fragrances of plants and other organisms can be synthesized and then engineered into the genomes of yeasts.

Once the engineered yeasts grow and ferment sugars, they will then be able to produce flavor/fragrance compounds which can then be purified from yeast.

Oh AND…

“Cultured ingredients offer a third way for manufacturing valuable flavor and fragrance ingredients that is more renewable than chemical synthesis via petroleum and more stable and efficient than extraction from botanical sources.”

Future of Food

Source

Challenge (/Opportunity)

This should give you the gist…

“To feed a rapidly growing population on a warming planet, society needs to develop innovative new technologies to grow and distribute food. The cattle industry, which includes both beef and dairy products, represents a $1 trillion global market opportunity and contributes to 9% of global greenhouse gas emissions.”

Solution

Through their partnership with Motif and leveraging their Foundry + Codebase, Ginkgo is able to develop commercial yeast strains and processes for protein production at kilogram scale.

By screening 300+ proteins in order to identify candidates with the greatest benefits they can engineer (using novel expression systems) top performers to maximize protein expression. Wow.

Ps. Other awesome companies making moves in the alternative protein space are Aleph Farms and Perfect Day:)

Next up, I’m curious to understand

  • their experimentation and cataloging pipeline at a deeper level
  • the timeline for the production of a new (important) organism and the teams involved (bare minimum) to make it happen
  • if decision making on what new organisms should be created is predominantly dependent on economic incentive or a vision for where the world needs to go (categorizing priority based on problems that need to be solved)

Perhaps I’ll visit the headquarters in Boston to learn more👀

Finally, as a thank you for reading to the end of this article and being curious about the future of our world, here’s an interesting article you mind enjoy on #savingthebananas (?!) here.

Say hi🙋🏽‍♀️

What problem do you think is most important to be solved using Ginkgo Bioworks technology right now?

Feel free to share by commenting, or you can reach me via Twitter, LinkedIn, or Email (sriya.chintalapalli@gmail.com).

More of what I’m learning/building ~ YouTube and Personal Newsletter💖