Precision Fermentation Perfected: Strain Engineering

How did you become interested in precision fermentation?

_Dr. Amanda Fischer: In an undergraduate microbiology class I was excited to learn how precision fermentation can use microbes to make industrial enzymes like the ones found in the Tide detergent I used. As a graduate student, I engineered a protein that glowed due to its pigment._

_Nina Jorgensen: As a kid, I played a lot of Pokemon and really, really wanted to make a Pokemon in real life. As I learned more about genetic engineering as an undergraduate student, it became apparent that making a Pokemon through genetic engineering isn’t possible just yet. Despite this, I still appreciate precision fermentation because of its ability to contribute to safe and sustainable agricultural practices._

What’s your favorite part of your job?

_Dr. Shannon Ceballos: I love to solve problems and there are plenty of problems to solve in this job. Science never works in real life as easily as it does on paper. We are constantly making experiments to try to solve problems, but then complications come up that need to be worked through. When you finally do make that breakthrough, though, it’s a great feeling!_

_AF: In the long run: using biotechnology to bring sustainable products to the world.  On the daily: working with people who are passionate, engaged, and excited to try the next thing._

What’s your favorite piece of lab equipment or lab method to use?

_AF: I like to use any modular robot or lab automation tool that can remove the manual aspects from my work._

_SC: Streaking strains to plates.  So much of my work feels like moving clear liquid from one tube to another that it’s very satisfying to actually see the results._

What are you most likely to be listening to while working in the lab?

_AF: Last year it was Jane’s Addiction, this year it’s Dirty Heads. I get a lot of Spotify listening awards._

_NJ: Peach Pit!_

_SC: Anything upbeat that I can move to._

Now that you’ve been introduced, read on as our strain engineering scientists break down the basics of strain engineering, the first step in the precision fermentation process.

What is strain engineering in microbiology and how does it relate to genetic engineering?

Genetic engineering is the broad field of modifying an organism’s DNA. Theoretically, any organism could undergo genetic modification to produce new versions of that organism through genetic engineering.

Genetic engineering has been applied to plants and crops to create genetically modified food like apples that don’t brown when cut or crops that are resistant to bacterial infection.

A few have made genetically modified (GM) animals, like AquaBounty’s GM salmon that’s engineered to grow faster than traditional salmon.

Microorganisms too can be genetically engineered and in most cases they are engineered to optimize a strain for fermentation.

A strain is defined as “a group of organisms that belong to the same species but share certain genetic characteristics not found in other members of the species”. When strains are genetically modified to increase their usefulness in microbiology and fermentation, we call this strain engineering. Strain engineering and precision fermentation go hand in hand.

Without strain engineering, only traditional fermentation can occur: the process that creates beer or wine. With strain engineering, precision fermentation can create new products from modified microorganisms.

Strain engineering\* is an incredible tool that allows scientists to improve a strain’s overall usefulness for industrial fermentation applications. Various improvements can be made to any strain: from encouraging faster growth, to making growth more efficient at a certain temperature or pH, to reducing the amount of native protein that’s produced.

In precision fermentation, strain engineering is used to make organisms produce new outputs that they wouldn’t naturally make, such as using a microbe to produce dairy proteins.

In our previous post, we explained how strain engineering is the first of the three major steps of precision fermentation.

In its simplest explanation, strain engineering allows scientists to give genetic instructions to the organism on how to produce the product of interest.

\*A note from our very own Dr. Amanda Fischer about terminology: While “genetic engineering” and “strain engineering” are common terminology in the field, “engineering” is really a misnomer here.

These technologies more squarely fall under biology than engineering. Engineering is static in the sense that established, well-understood, models are applied to various systems and are expected to work. As a field, biology is the complete opposite of engineering. B

iology is a cycle of constant discovery, followed by evolving ones practices to accommodate new understanding. Strain engineering is a tool of synthetic biology, and like many biotechnological innovations, requires constant trial and error to arrive at the best possible version of the strain.

Rather than following a comprehensive road map, instead scientists make educated guesses on what to do next based on institutional knowledge or academic literature.

The difference between strain engineering and genetic engineering

The biggest difference between strain engineering and other genetically engineered products, like a GM barley crop, for example, is what exactly receives genetic modification. In strain engineering, the _strain_ is GM, but not the final product.

The compounds that the strain produces, which become the commercialized product, are not genetically modified.

For example, TurtleTree’s LF+ is _not_ genetically modified. Only our strain is. On the flipside, genetic modification of a barley crop creates a genetically modified barley crop (a “GMO” barley).

Another difference between genetically engineering a barley crop and engineering a strain: the modified barley plant produces an _entire_ barley plant.

Strain engineering can produce new strains of microbes, but when used with precision fermentation, those strains produce _single compounds or ingredients_.

Take TurtleTree for example, we use microbes to produce a single protein of cow milk – not a whole cow or even whole milk. This is in line with our broader, long term goal of bringing cell-based milk to the world.

While genetic modification (whether to a microbe or a food crop) might feel futuristic and scary, it’s actually a process as old as the earth itself, having happened since the origin of life via evolution and adaptation. Genetic engineering is a new biotechnology only in its ability to accelerate the natural genetic modification process and its ability to make very specific, intended, changes instead of global, random changes.

Remember Gregor Mendel’s pea plant experiment you learned about in high school biology class? You might call this “V1” of genetic modification.

Mendel succeeded in altering the pea plants’ genetics, but crossbreeding could only lead to modifications inherent to pea plants.

Moreover, the pea plant offspring could only carry a combination of the genes of the parent plants, not some entirely new DNA.

Genetic engineering, on the other hand, is a much more advanced version of genetic modification because genes from one species can be introduced into genes of another species.

For instance, with genetic engineering, Mendel might have been able to produce a pea plant that could glow in the dark like an underwater fish! Had Gregor Mendel been alive in the era of strain engineering, he might have used this technology to create a new strain of yeast that produces an enzyme typically produced by pea plants!

So now that we’ve delineated the differences between strain engineering and genetic engineering, let’s delve further into strain engineering and how it can be used to improve our food system when coupled with precision fermentation.

The evolution of precision fermentation and the addition of strain engineering

As we’ve covered in our FAQ, fermentation technology has been used for centuries to make alcohol and preserve foods.

In the last half-century, precision fermentation has combined fermentation and strain engineering techniques to make pharmaceuticals,  industrial enzymes, and more recently, food ingredients.

But this change from traditional fermentation to precision fermentation didn’t come about overnight as a radically new method. Instead, across fermentation’s long history in making food, techniques have evolved to improve the final product.

At first, these modifications were simply improvements to traditional fermentation.

However, starting in the 1980s, strain engineering was implemented to improve starter cultures.

Since then, the marriage of strain engineering and fermentation techniques has drastically changed the power of fermentation and created the precision fermentation technology we know today.

The evolution of fermentation and the addition of strain engineering can be broken down into 5 stages: