Vanilla seed pods may be circumvented through synthetic biology (Image: Flickr/ted_major)
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Are Microbes the Taste-Makers of the Future?

On its journey from plant to ice cream cone, vanilla travels thousands of miles. Shady fields of waist-high vines in Madagascar, the South Pacific, or Latin America produce valuable fruit, which is cured, oxidized, and dried in an intensive sequence of events lasting several weeks. It’s then shipped to markets around the world, just as it has been for centuries.

The vast majority of the vanillin found in today’s products – from food to perfume – is derived from synthetic processes that convert guaiacol to vanillin in a three-step process. Both the natural and chemical methods are costly and environmentally burdensome, but a new approach using the advances of synthetic biology offers a promising third way. Starting with glucose, yeast is able to “ferment it just like beer,” explains Kevin Munnelly, CEO of the biotech company Gen9. “It’s the first flavor made by synthetic biology, and it’s entering commercial viability.”

To get to this point, genes for three enzymes from three different organisms – a dung mold, a bacterium, and humans – were inserted into the yeast cells. In Munnelly’s view, the construction of an engineered pathway to produce a high-value molecule such as vanillin is an important success story in the synthetic biology community. Given the multitude of biosynthetic and energy-procuring reactions taking place at any given time, the prospect of re-ordering metabolites and reaction steps in a rational manner is often over-optimistic. After all, a cell’s priority is to survive and replicate, not to produce tasty ice cream, but in the case of vanillin, the bioengineering team was able to accomplish both aims.

Predicting exactly how to achieve this tenuous balance between sustainable cell survival and product generation is challenging, but with reliable and affordable DNA synthesis, experimenters need not restrict themselves to a single attempt. “We can make a variety of different gene constructs, so you don’t have to pick just a few options to test,” says Munnelly. “And it’s an iterative process – we can do this quickly, so the results can feed back into the design.”

To achieve scale and speed in its DNA synthesis process, Gen9 adheres to an important mantra: avoid sequencing. Under the traditional gene production regime, oligos are stitched together, “and if you haven’t used error correction,” warns Munnelly, “you have a certain percentage of the population that is wrong. If you then have to put something into an organism and pick colonies and send them through a sequencing pipeline, it’s a really expensive process.” Gen9’s error evaluation approach uses the MutS enzyme to identify nucleotide bases that differ from the population’s consensus, and then repair the mismatches. “If the screening is cheap then you can make a lot of variants,” says Munnelly, which in turn allows researchers to query a wider range of products.

As synthetic pathways enter the industrial pipeline, Munnelly predicts that other products will join vanilla on the synthetic biology-produced shelf. Gen9 customers are actively developing fragrances, cosmetics, and other spices like saffron. “We have a much better understanding now of some of the complexities of how these processes work,” he says. “It’s getting more straightforward, and there will be many products to come.”

*This article is part of a special series on DNA synthesis that also appears on

Want to hear more? Devin Leake of Gen9 will be at SynBioBeta’s London event this April! Click here for more information!

Jeffrey Marlow is an author on WIRED

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