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How genetic modification of microbes that help make foods can contribute to a more stable (and delicious) food chain

Genetic modification (GM) has been an exciting tool in food production for decades. While it sometimes gets a bad rap, the reality is that it has significantly helped feed and nourish the fast-growing global population, and will continue to support its growth, which is expected to top 9.6 billion in the next 30 years. We mostly hear about GM in crops, but more and more, scientists are learning that modifying the organisms that help ferment the foods we love—cheese, yogurt, beer, and chocolate—could also produce more sustainable, and better-tasting, foods.

Today, most corn and soy crops are genetically modified to resist both pests and herbicides. Modifying crops has also helped produce more food with less acreage—some estimates suggest that the increased yield in corn, wheat, and soy may be 20% or more. Researchers have been creating GM crops that can withstand the higher temperatures and changing atmospheric conditions that are expected in the coming decades.

Genetically modified crops have also played an important role in addressing vitamin deficiencies—for instance, vitamin A deficiency is a huge problem across the world and can result in irreversible blindness and death in children. To address this, scientists engineered rice to produce beta-carotene, a building block for vitamin A. Similar work has been done in bananas, corn, and other vegetables to address iron and folate deficiencies, among others, and has a lot of promise for tackling these issues on a global level.

But there’s another area of food production that’s been using GM, which people may be less familiar with—microorganisms. As most people know, many of the foods we love depend on microbes—yogurt, cheese, and beer use fermentation, as do wines, chocolate, sauerkraut, sourdough bread, kimchi, and tempeh, to name a few. Almost every culture across the globe has made use of fermentation, for the flavors and textures it can produce, as well as for preservation, since it allows foods to remain edible for much longer—cheese is stable far longer than milk, and vegetables can be preserved for months after fermentation.

A huge variety of organisms—bacteria, yeasts and fungi—are used in the different fermentation processes. For some foods, multiple microbes contribute to the final product, each performing different intermediate steps—this is true for kombucha, sour beers, and everyone’s favorite pandemic pastime, sourdough bread. Chocolate also requires yeasts and a variety of bacteria to carry out a number of chemical conversions over several days, which ferment the sugars, break down the pulp, kill the cacao bean, and begin to produce the flavor.


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In many cases, the type of organism is known and added intentionally—lactic acid bacteria in yoghurt and yeast in bread or beer making—but in other cases, the makeup of the organisms is still being mapped out. For instance, my earlier research looked at how cabbage turns into sauerkraut when just salt is added. We determined that the lactic acid bacteria that perform the fermentation came from the soil and water in low levels, but once in the anaerobic environment of the fermentation jar, they overpower everything else and proliferate. What was especially interesting was that the bacterial makeup was different in different parts of the country, which impacted the taste of the final product.

Cheese is another great example of how different combinations of bacteria, yeasts, and fungi, interacting with the cheese for different lengths of time (aging) and in different environmental conditions (terroir) will affect the finished product’s color, taste and texture. Another earlier study of mine found that the strain of bacteria present can affect the finished product, which may be why the look and taste of cheese varies from region to region.

The next logical step in all of this is using GM in microbes, and in fact, this is becoming an area of high interest to food researchers interested in reducing food waste and costs, while improving quality and safety. For instance, the popular genetic engineering tool, CRISPR, has been valuable to yogurt makers for years—this is logical, since CRISPR is the mechanism by which bacteria naturally fight off viruses known as bacteriophages. Since infection is common to the lactic acid bacteria used in yogurt making, and can destroy entire batches, using CRISPR intentionally in yogurt production has been key in reducing food waste, and ultimately contributes to a more stable food chain.

Similar methods could be applied to other foods, like salami, which can be ruined by the mold that’s added to enhance the drying process and flavor. Sometimes the organisms that are essential to the process can overtake it, so figuring out how to engineer communities to be more resistant to intruders will be an important area of future study.

Cheese making has already been improved greatly by GM. Researchers engineered E. coli to produce chymosin, the active compound in rennet, which is used to break down protein in cheese production—and, for many thousands of years, came from calf stomachs. In the future, GM might also be used to reduce the number of steps (and time and cost) involved in cheese making, perhaps by modifying bacteria or yeast to perform multiple steps in the process rather than just one.  Like the grain crops, GM might also be used to boost the nutritional composition of dairy products.


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Finally, GM might also help reduce the number of ingredients required: A team at the University of California made news a few years ago for producing GM yeast that created a “hoppy” flavor. Though craft beer makers might be skeptical, reducing the amount of hops required could be great for the environment. Brewers might be more eager about the idea that GM can also be used to produce yeast that yield more ethanol or those that produce lactic acid, which would eliminate the addition of bacteria to the brewing process for sour beers, which are increasingly popular.

In this vein, human preferences change all the time, and GM can help accommodate that—for instance, yogurt trends have gone from Greek to Icelandic to French in a matter of years. Rather than overhauling the process with each new trend, yogurt makers could mimic the textures and flavors using GM bacteria. The same is likely true for bringing out different notes or flavors in chocolates, or any fermented food.

Beckman Coulter Life Sciences, where I’m a Commercial Product Manager, has been producing tools used at the forefront of genetic engineering for years. Our Echo Acoustic Liquid Handler is an ideal tool for researchers developing new strains of bacteria or yeast, as it enables highly efficient, high-throughput cloning workflows that save time while reducing costs and waste. And since interchanging modular pieces of DNA is the preferred method for many DNA construction workflows due to decreased synthesis cost, the ability of the Echo to transfer these in any volume from any source to any destination well allows for faster progression along the design, build, test, and learn cycle.

Though genetic engineering and our tools were originally developed for use in research, they clearly have huge relevance in food production, a critical area in itself. Close partnerships between life sciences companies, food makers, and public health organizations are going to be increasingly important moving forward. In the meantime, next time you’re enjoying your favorite yogurt, take a second to thank not only the makers, but all the engineering that went into keeping it disease-free—or in the case of cheese, no longer dependent upon calf stomachs.


Brittany Niccum

Commercial Product Manager at Beckman Coulter Life Sciences

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