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DNA Bar Codes Added in Spores to Track Farm Products

Scanning electron microscope image of Saccharomyces cerevisiae, or baker’s yeast (Mogana Das Murtey and Patchamuthu Ramasamy, Wikimedia Commons)

5 June 2020. Synthetic microbe spores made with unique DNA identifiers are shown to be capable of safely tracking vegetable crops from the farm to retail stores. A team of systems biologists from Harvard Medical School describes its system and real-world tests in today’s issue of the journal Science (paid subscription required).

Researchers from the systems biology lab of Michael Springer are seeking practical solutions for tracing agricultural products through their supply chain, particularly to help determine the source of foodborne illnesses, affecting some 48 million people in the U.S. each year, leading to 3,000 deaths. Springer and colleagues study signaling and metabolic functions and interactions of cells with their environments, with much of their research centering on certain yeast species as models for higher-order organisms.

This work with yeast led to their genetic engineering of Saccharomyces cerevisiae, commonly known as Baker’s yeast, and a benign form of bacteria, Bacillus subtilis, which both form spores, reproductive cells emitted from these yeast and bacteria. The researchers’ changes in the two microbe genomes allow for adding sequences of DNA to produce spores that can uniquely identify objects to which they’re attached, much like bar codes in retail stores. At the same time, spores from the altered microbes are engineered not to reproduce, making them self-contained, inert in the wild, and safe to apply.

In addition, the system needs a simple way to read and identify the DNA sequences in the engineered spores. For that task, the researchers adapted a diagnostic gene-editing technique called Sherlock, short for Specific High Sensitivity Enzymatic Reporter Unlocking, developed at the Broad Institute, a genetics research center affiliated with Harvard and MIT. Sherlock is based on Crispr, but it edits RNA rather than DNA and uses a different editing enzyme than most Crispr applications. The process converts DNA to RNA, with the edits amplified to emit detectable signals identifying the RNA editing site.

Spores are already used in agriculture and can stay dormant for long periods. “Spores are in many ways an old-school solution,” says Springer in a university statement, “and have been safely sprayed onto agricultural goods as soil inoculants or biological pesticides for decades. We just added a small DNA sequence we can amplify and detect.”

The researchers tested their engineered spores on plants in the lab and found they can detect leaves sprayed with the spores, even when mixed with non-sprayed leaves. The team also tested their engineered spores on lawn grass growing on campus, as well as a variety of surfaces — sand, soil, carpet, and wood — showing the spores persist for months. In tests with fresh produce from grocery stores, the team simulated tagging items with indicators of bacterial pesticide, and found their DNA bar codes can distinguish between produce grown with or without the pesticide.

Another set of tests sprayed engineered spores with identifiers to mark different quadrants of a 100 square-meter indoor sand pit. The spores remained on the sand after simulated wind, rain, and physical disturbances. In addition, a remote-control robotic vehicle with a reader drove over the pit and accurately identified the quadrants.

The university filed a provisional patent on the technology. “We hope it can be used to help solve problems that have enormous public health and economic implications,” notes Springer.

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