How Sequencing Foods’ DNA Could Help Us Prevent Diseases

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What’s almost as important to life as food? Food safety.

Last year, in the US, according to the CDC, one in six people were affected by food-borne diseases, resulting in 128,000 hospitalizations, 3,000 deaths, and an economic burden totaling $80 billion.

We need to do better. But ensuring that every piece of food pushed through the supply chain is safe enough to eat is no small task. Yes, some food companies test their ingredients before cooking and shipping, but there’s no way to test for unknown pathogens or impurities that may cause contamination. And as the supply chain expands, the difficulties will only increase.

Enter a new project from IBM Research and Mars Incorporated. Today, scientists from the two organizations announced the Sequencing the Food Supply Chain Consortium, a collaborative food safety organization that aims to leverage advances in genomics and analytics to further our understanding of what makes food safe.

The researchers will conduct the largest-ever metagenomics study of our foods, sequencing the DNA and RNA of popular foods in an effort to identify what traits keep food safe and these can be effected by outside microorganisms and other factors. Eventually, the researchers will extend the project “from farm to fork,” examining materials across the length and breadth of the supply chain.

In this way, IBM Research and Mars are joining many others, including the San Francisco-based startup Hampton Creek, who hope to supercharge food R&D using data analysis. After reinventing Google and Facebook and so many other online operations, the big data movement is now moving into other industries, ranging from medicine and healthcare to the development of new industrial materials.

The Baseline

“We want to get a baseline for safe food ingredients, all the way up and down the food supply chain, including what makes healthy biochemistry,” says James Kaufman, public health manager for IBM Research. “If you can understand what a normal, healthy microbiome looks like, you can figure some things out about how that microbiome will respond to the unknown.”

Courtesy IBM

Essentially, the scientists are hoping to uncover what combination of microbes that makes food ingredients safe, and what factors affect the structure of these microbial communities, including exposure to new pathogenic organisms and other impurities that may not have ever come up yet. It is these unknowns, Kaufman explains, that can eventually make food unsafe—whether that’s the evolution of new organisms, a misguided attempt at innovating food, or even because of an intentional act of terrorism.

In order to reach their lofty goal, the scientists are embarking on a massive experiment to sequence both the DNA and RNA of major food ingredients in various environments. To start with, they are examining things like poultry meal, fish meal, egg powder, and ground corn and will track them in the factory ecosystem, as they ship out, and even through different weather conditions.

The Muscle

Leveraging the computing muscle at IBM’s Accelerated Discovery THINKLab—which puts over 500 computing nodes at their disposal and can be scaled up as needed—the researchers will be running sequencers for weeks at a time to determine the necessary depth of coverage. As Kaufman tells it, though the researchers already know which ingredients they’re sequencing, they don’t yet know what the diversity will be.

Apart from sequencing the food as deeply as possible, researchers plan to deliberately expose some ingredients to impurities along the way in a controlled study. Then they’ll see if their system will catch it.

Everyone’s Interest

The tasks is bigger than you might think. By 2050, according to the Food and Agricultural Organization of the United Nations, we’ll have to increase the food supply by 70 percent to accommodate an additional 2.3 billion people. In other words, we’ll have a third more mouths to feed. And that will mean that Kaufman and crew will have to analyze a far more complex food chain.

Kaufman acknowledges the size of the challenge. And that makes it all the more attractive. As he says: “It’s in everybody’s interest to make food—and the food supply—safer.”