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Barcoded Microbes Could Track Sources of Food Contamination

chart showing how produce can be barcoded using bacteria
Genetically barcoded spores could be used to tag produce and other objects with origin information. | Val Altounian/Science.

Spraying crops with microbes equipped with "barcodes" could make food safer by allowing the source of food poisoning to be rapidly identified, a new study says. The tagging approach, reported in the June 5 issue of Science, could also be used to track other products' origins, an increasingly difficult task in the complicated global supply chain.

"This could provide a solution to the object provenance problem," said Jason Qian, a researcher in the department of systems biology at Harvard Medical School.

Qian said that knowing the origin of a food product or other object can be critical ‐ as in cases of foodborne illness, for example. Current labeling technologies, which are labor-intensive and easy to subvert, make this challenging.

"By combining simple synthetic biology methods, we've developed a solution that is readily applicable," said Qian. "We've created an invisible microscopic label that can be mass produced and that works in real-world environments over long periods of time."

The World Health Organization estimates that almost 1 in 10 people worldwide get food poisoning and more than 400,000 die of it every year. Tracking the source of this contamination remains difficult and can take weeks.

Because objects gradually adopt the naturally occurring microbes present in their environments, some researchers have suggested microbial signatures as an alternative means to determine object provenance.

But this approach, too, is faced with a variety of challenges — including the need for extensive, expensive environmental mapping to survey the global distribution of microbe populations, nearly all of which are in constant states of change.

"Our approach bypasses these challenges by introducing the use of synthetic microbial spores harboring barcodes that can uniquely identify locations of interest, like food production areas," said Qian.

Qian and his team genetically engineered strains of Bacillus subtilis bacteria and Saccharomyces cerevisiae yeast — common microbes that form tough, long-lasting spores — to give them unique DNA barcode sequences. They then further manipulated the bacteria and yeast, so that their spores, which naturally persist for long periods without growth, would remain inert indefinitely. This was done to prevent any adverse effects once the spores were introduced in the environment.

"The main concern from the spores is disruption to the natural ecosystems," said author Michael Springer, associate professor of systems biology at Harvard Medical School. "The spores, if viable, could outcompete other microbes. They could then spread far beyond the site of release."

Yet another concern in designing the spores relates to horizontal transfer of genetic material that could confer antibiotic resistance. "If we had used genetic material that could make other organisms resistant to antibiotics, this could have many negative ramifications," Springer said. He and colleagues were careful to avoid this.

The team sprayed their engineered spores on various surfaces including sand, soil, carpet and wood. Three months later, they were able to detect them, even on surfaces that were vacuumed or subjected to wind or rain. In tests in which the spores were sprayed on plants growing in pots, the team was able to identify which pot a leaf came from a week later, they said.

They also tested the system in a simulated food supply chain in a laboratory setting, where the spores proved resilient to washing, boiling, frying and microwaving. Because spores like this are commonly used in agricultural chemicals approved by the U.S. Food and Drug Administration decades ago, in 1961, people are already eating them. "People have been eating Bacillus thuringiensis spores for much of their life," Springer said.

The approach could be used to provide a nearly infinite set of identification codes, tailored to individual locations (and thus objects) of interest. The barcodes can be decoded by a range of methods that involve detecting specific nucleic acids, the authors said.

"Our synthetic spores offer a sensitive, inexpensive and safe way to map object provenance," said Qian. He noted the spores are designed to be persistent in the environment, but they are not indestructible. "10% bleach [solution] can be used to destroy them. The system could be tampered with, but we envision this to be used on crops so it would be hard to imagine [bleach being added]."

He is even less concerned about the spores being counterfeited. "Even if someone were to take the significant effort to reproduce them by strain engineering, it's easy to add security by switching out barcodes to foil their attempt," he said.

Further testing with real-world environments needs to be conducted before this approach can be widely used, said Qian, but he envisions that one day, if unique spores were sprayed on crops at different farms before harvesting, authorities could rapidly find out where any specific produce came from.

This would not add significant extra cost to farmers, he explained, because many farmers, including organic farmers, already spray their crops with bacterial spores to kill pests.


Meagan Phelan

Science Press Package Executive Director

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