Using genetically engineered, barcoded microbes to track food contamination and more

June 04, 2020

Synthetic spores programmed with DNA barcodes provide a highly flexible, high-resolution system for tagging and tracking the provenance of an object. In a new report, researchers present their novel approach - the barcoded microbial spores (BMS) system - which could be particularly useful in tracing supply chains following detection of foodborne pathogens. The ability to quickly and accurately determine the provenance of an object can be critical in applications spanning tracing vegetables to their agricultural source or identifying the manufacture of counterfeit goods. Current labeling technologies are often labor-intensive and easy to subvert, particularly in light of complex global supply chains. Given the ubiquity of naturally occurring microbes, their distinct populations and the ability for physical objects to adopt the unique microbial composition of their environment, it's been suggested that the use of an object's microbial signature to determine its provenance could offer an alternative to standard labeling approaches. But it, too, is faced by a variety of challenges, including the need for extensive and expensive environmental mapping. Here, Jason Qian and colleagues present a new approach that uses genetically engineered microbes as durable molecular labels. Qian et al. created synthetic, non-viable strains of Bacillus subtilis bacteria and Saccharomyces cerevisiae yeast that harbor unique DNA "barcode" sequences, which can be quickly identified using a variety of tools, including SHERLOCK, a new field-portable, CRISPR-based DNA detection device. When dispersed on objects or in the environment, BMS can persist on a variety of surfaces for months and marked spores can be transferred to other objects that come in contact with them. Qian et al. demonstrate the system's particular applicability to determining food provenance and in rapidly tracing food contamination to its source. DNA-barcoded B. subtilis remained detectable on tagged produce even after washing and cooking. In a related Perspective, Jeff Nivala discusses the approach in more detail.

American Association for the Advancement of Science

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