What is precision fermentation? Trade associations nail down definition

The Precision Fermentation Alliance (PFA) and Food Fermentation Europe (FFE)— two trade associations formed in the past year—have come up with a definition of ‘precision fermentation’ to help industry stakeholders, regulators and consumers understand how it differs from other forms of fermentation.

According to the new definition: “Precision fermentation combines the process of traditional fermentation with the latest advances in biotechnology to efficiently produce a compound of interest, such as a protein, flavor molecule, vitamin, pigment, or fat.”

How does it work?

• A specific molecular sequence is inserted into a microorganism to give it instructions to produce the desired molecule when fermented. These molecular sequences are derived from digitized databases rather than taken directly from the relevant animals or plants. 
• At the end of the fermentation process, the resulting compounds are filtered out, separating them from the microorganisms that produced them.
• Precision fermentation has been in use globally for over 30 years to make medicines (like insulin) and countless common food ingredients (such as human milk oligosaccharides or rennet).”

While the term ‘precision fermentation’ is relatively new (coined by RethinkX in 2019) the technology has been used for many years to make insulin and enzymes such as chymosin, a process aid used in cheese making that was historically sourced from calf stomachs but is now routinely made by genetically engineered microbes, note the trade associations.

However, advances in synthetic biology enabling the rapid reading (sequencing) and writing (synthesizing) of DNA have fueled a flurry of startups in recent years producing everything from sweeteners, flavors and colors; to dairy, egg, and collagen proteins; and high-value components found in human breastmilk to enhance the nutrition of infant formula.

Biomass fermentation, ‘wild’ fermentation, precision fermentation…

The new definition “draws clear boundaries between precision fermentation and other fermentation-based technologies,” PFA spokesperson Irina Gerry told AgFunderNews.

In ‘biomass fermentation,’ firms such as Quorn, Nature’s Fynd and Superbrewed Food grow Non GMO microbes such as fungi and bacteria and harvest the whole ‘biomass’ at the end of the fermentation.

In ‘precision fermentation,’ by contrast, firms such as Perfect Day and The EVERY Company use genetically engineered fungi or yeast strains as mini factories to produce their target ingredients, which are then separated from the host microbe at the end of the fermentation during downstream processing and purification.

Although some microbes naturally produce food ingredients used by the food industry (eg the fungus Blakeslea trispora makes beta-carotene and some microalgae strains naturally make omega-3s), precision fermentation is distinct from this sort of ‘wild’ microbial fermentation in that it uses microbes that have been genetically engineered to produce ingredients that would not normally be produced by these microbes, explained Gerry.

Multiple ways to make Reb M

According to Gerry: “We have biomass fermentation, microbial fermentation, precision fermentation, molecular farming [eg. growing dairy proteins in soybeans or growth factors in barley], and plant cell culture [growing target molecules in plant cells in culture rather than fully grown plants] and these are all different technologies.

“People who are in this industry get the distinctions, but it’s hard for other stakeholders including food retailers, consumers, regulators, and the media to get the nuance.

“Take stevia,” she added. “You can extract the molecule [a sweet-tasting steviol glycoside such as Reb M] from the leaf [some firms also use enzymes to convert the lower value Reb A in some leaf extracts into Reb M]. You can do plant cell culture [growing plant cells in culture to produce specific molecules], and you can do precision fermentation [genetically engineering yeast to produce steviol glycosides], so it can get very confusing for the consumer.”

She added: “And then you’ve got techniques such as mutagenesis that are used in traditional plant breeding to develop microbial strains that might produce a higher amount of a target substance [which is not considered genetic engineering for regulatory purposes]. What do we call that? It’s getting a lot more nuanced.”

She added: “And that’s why honestly, we as an industry group, started to say, ‘You know what, let’s refine and draw some of these distinctions.’ So we specifically drew a distinction around whether bioengineering is used or not used, which is important when it comes to different regulatory frameworks in different markets.

“It also matters for regulatory purposes if the ingredient is bio-identical versus just similar in function, especially when the issue of allergenicity comes up [if your microbe is making something bio-identical to a milk or egg protein, for example, this will trigger allergen labeling in many markets].”

Synthesizing DNA

The other thing the associations wanted to stress was the fact that while an original DNA sequence for something like a dairy or egg protein was identified in an animal, precision fermentation firms do not use animal DNA (hence the use of the term ‘animal-free’).

Once the genetic sequence to produce a target protein or substance has been identified in an animal, this is kept in a digital database and serves as a production blueprint.

The next step is to physically create the DNA that carries this sequence. Synthesized DNA is made from the same basic building blocks as natural DNA: chemical compounds called nucleotides. In the lab, these nucleotides (A – adenine, T-thymine, C-cytosine, and G- guanine) are chemically synthesized and then assembled in a specific order to create a strand of DNA that matches the desired sequence.

According to Gerry: “This is important for some people in the vegan community because we now have a massive databank of all kinds of molecules and proteins that have been sequenced, so you don’t have to go back to the animal. No animals are involved in the production of dairy or egg proteins from precision fermentation.”

Vegan dairy?

Whether ‘animal-free’ dairy or egg proteins should be marketed as vegan is a more complex question, however, said Gerry. First, the term ‘vegan’ is not legally defined in key markets such as the US for food labeling purposes, and second, not all vegans feel exactly the same about it.

‘Ethical’ vegans who avoid animal products because they don’t want to harm animals or the environment, or are against factory farming, might embrace whey, egg, or myoglobin proteins made in fermentation tanks, she said. But other vegans will want to steer well clear of any proteins that are found in animals, regardless of whether they were made in a fermentation tank without animals.

Putting the term ‘vegan’ on product labels for dairy proteins made via fermentation may also be risky given that some consumers with milk protein allergies may see the term ‘vegan’ as a proxy for allergen-free, even if there’s a milk allergen warning on the label, said Gerry.

The term ‘animal-free,’ meanwhile, is still being discussed within the industry, with some stakeholders moving away from it because they fear shoppers might erroneously see it as a proxy for ‘plant-based’ or ‘allergen-friendly,’ while others believe it has strong consumer appeal.

The refined definition of precision fermentation highlights key distinctions, including:

• Leveraging bioengineering: Precision Fermentation (PF) stands apart from traditional/wild fermentation and natural breeding techniques by leveraging the latest bioengineering techniques.
• Producing specific compounds: Unlike cell cultivation, PF focuses on using microorganisms to produce specific compounds of interest, rather than growing an entire cell or biomass.
• Sourcing from digital databases: Molecular sequences used in PF are sourced from digitized databases, eliminating the need for animal involvement in any part of the process.
• Filtered compounds: At the end of the fermentation process, the targeted molecules are isolated and filtered out from the fermentation broth, which is different from biomass fermentation, where the entire biomass (including the cells) is the product.
• Established technology: While new molecules are now being produced using PF, the process itself has been safely utilized in food and medicine for decades.