Scientists develop a "passport" for fruit

The microbes in your apple will soon be able to identify the source down to the meter.

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Food crisscrosses the world to reach people in a globalized economy, but how safely do apples, tomatoes, grapes and so much more make this journey? It's hard to track.

Thanks to synthetic biologists from Harvard, MIT and Boston University, this crucial process in food safety is about to get a lot easier.

Scientists have now designed genetically engineered microbes with unique DNA "barcodes" that can track these items across the world. Decoding these barcodes takes less than an hour and these microbes can last on surfaces for months and even though food preparation. It's a passport of sorts for the food you eat.

But, while this technology represents a promising solution to tracking foodborne illnesses, it also has the potential to be used by law enforcement as a form of invisible identity tracking on people as well.

Microbes are everywhere -- in your bed, on your food, and even in your body. But, like any misunderstood anti-hero, they're not all bad. Previous research has shown that objects can take on environmental microbes around them and that different locations may have different unique sets of microbiotic life. But, these environmental microbes are too easily prone to mixing or changing over time to be useful as a tracker.

At least, not without some genetic alterations.

"It blurs the lines between if they're still alive or if they're just a sack of DNA."

In a new study published Thursday in the journal Science, a team of synthetic biologists from Boston describes how they genetically altered microbes to withstand environmental damage and survive on food -- and people -- much longer than microbes in the natural environment.

Jeff Nivala, a synthetic biologist from the University of Washington who was not involved in the study but wrote an accompanying analysis, also published Thursday in Science, tells Inverse that the reason these microbes are so much heartier than their natural counterpart is that they've been put into a kind of vegetative state.

"What makes them different than a normal, living, sort of microbe is that these are in spore form," Nivala says. "It's sort of like a vegetative state that the cell can go into... it's kind of blurring the lines between if they're still alive or if they're just a sack of DNA."

By injecting unique combinations of DNA sequence into genetically engineered microbes and spraying those on food, scientists are track where food was harvested even months later.

Jeff Nivala/Science

To ensure the unique trackability of these microbes the researchers designed a dozen unique DNA sequences to inject into the genomes of the bacterium Bacillus subtilis and the yeast Saccharomyces cerevisiae. This unique DNA sequence became these microbes' barcodes. Through mixing and matching how these codes were injected, the researchers were able to design a nearly infinite number of unique barcodes.

In a number of tests in different environments, including sand, wood, carpet, and grass, the researchers explored how long these microbes could remain traceable in a simulated natural environment. The team found that even in dynamic environments (like simulated windstorms, sweeping, and evening boiling and microwaving) the microbes could still be identified and decoded in less than an hour even after being left on the surfaces for up to five months.

Through simply spraying these engineered microbes on plants through the growing process, researchers found they could still be traced back to their places of origin even months later.

Qian et al. / Science

Researchers write that this technology could be used to trace food production all the way from the farm to the plate (and even the sewer afterwards...) to trace the spread of food-borne illnesses -- such as the ever-recurring scourage of E. coli on romaine lettuce. Nivala tells Inverse that this could help save time and money because farmers could pinpoint specific fields to investigate instead of shutting down production altogether.

But, the authors also write that this technology could be adapted to be used for law enforcement surveillance as well.

As part of their study, the team found that microbes sprayed on a surface and picked up by shoes could still be decoded and traced up to four hours later. The authors write that this could be used to trace the movement of people across "locations of interest" (for example, country borders) as a complement to video and fingerprint surveillance.

While this technology has great potential for tracking food borne illnesses through food supply chains, it can also be used to track people across borders.


"I think the invisibility of the whole system certainly makes it on one hand powerful, but [also] hard to enforce how it's being used and where it's being used," says Nivala.

The Inverse Analysis

This technology offers a cheap and easily scaled solution to tracking foodborne illnesses as they spread across the world, for example, the spread of E. coli through tainted romaine lettuce. This could be used to improve global public health and ensure better food safety regulations at agriculture sites and processing plants. However, just as important is the role this innovation could play in the tracking of people. As this technology matures it will be important to look equally at how it interacts with people through these different applications and who is being helped -- or harmed -- the most.

Abstract: Determining where an object has been is a fundamental challenge for human health, commerce, and food safety. Location-specific microbes in principle offer a cheap and sensitive way to determine object provenance. We created a synthetic, scalable microbial spore system that identifies object provenance in under 1 hour at meter-scale resolution and near single-spore sensitivity and can be safely introduced into and recovered from the environment. This system solves the key challenges in object provenance: persistence in the environment, scalability, rapid and facile decoding, and biocontainment. Our system is compatible with SHERLOCK, a Cas13a RNA-guided nucleic acid detection assay, facilitating its implementation in a wide range of applications.

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