SAN FRANCISCO — When a Chicago couple grew dangerously ill two years ago after eating a home-cooked fish dinner, Canadian scientists figured out what had sickened them by using a new genetic test.
The test is designed to identify animal species based on subtle variations in a single gene. Dubbed the “barcode of life,” it provides a fast, cheap alternative to sequencing the entire genome.
By applying this technique to a remnant of the dinner, scientists at the University of Guelph in Ontario discovered that the Chicago couple — who recovered — had dined on poisonous puffer fish that had been mistakenly labeled as a safe monkfish, according to a report in a scientific journal.
“The incident showed regulatory authorities, especially the U.S. Food & Drug Administration, that DNA barcoding could be useful in food safety investigations,” said Robert Hanner, a biology professor at the Biodiversity Institute of Ontario at the University of Guelph, where the test was performed. “Now we are trying to make barcoding easier to use in the field, so fish inspectors and buyers can catch such errors in advance,” Hanner said.
Guelph has been a leader in the Consortium for the Barcodes of Life, an international effort to develop this quick, precise way to differentiate species. Formed in 2004, the consortium includes hundreds of scientists from 43 nations.
The barcoding technique targets a single gene located in the mitochondria, the energy-producing region of the cell. This gene appears to be active in all living things and consists of 648 base pairs of DNA. Each species arranges that short snippet of DNA differently, which makes it a useful genetic marker to identify “birds, butterflies, fish, flies and many other animal groups,” as scientists explain on a website about DNA barcoding.
The consortium has been gathering tissue samples and doing the laboratory work to isolate and sequence this barcode gene and match it to various animal species. So far, genetic tags for more than 60,000 species have been deposited in the Barcodes of Life database that serves as the consortium's global repository.
Though barcoding is primarily a research tool, Hanner said it has started to find real-world applications such as helping air safety investigators identify birds that collide with jets during take offs and landings.
“Once a bird gets sucked through a fuselage it's pretty hard to tell what it was,” Hanner said. The barcoding technique can identify the type of bird from tissue samples retrieved after the accident. “When you know which species was involved you can change the vegetation around the air field to minimize the chance of future strikes,” he said.
Hanner said the first big commercial application for barcoding is likely to be making sure that fish are correctly labeled — and not just for safety reasons.
“Fish comprise the largest component of protein in the human diet globally, and fish stocks are under great pressure,” he said, adding that studies have shown that fish are often mislabeled for reasons that range from error to fraud.
Last year, for instance, when the United Kingdom's Food Standards Agency used DNA barcoding to test fish sold at catering houses throughout the country, it found that 10 percent was mislabeled. In its report, the agency said the declining availability of popular cod and haddock due to overfishing had increased “the potential for economic gain by substituting more expensive fish species with less expensive ones.”
Biotech scientist Mary McBride with California-based Agilent Technologies worked with U.K. officials on that barcoding project. “Once the head and the fins are removed it becomes very difficult to do a species identification of fish,” she said.
McBride said the goal is to develop devices to automate DNA barcoding so the technique can be performed outside of the academic laboratories in which it evolved. Ideally a food inspector or fish buyer would take a tiny fish sample and drop it into a testing kit rugged enough to be brought into the field, yet sophisticated enough to perform the many steps involved in extracting the barcode gene and using it to identify the species.
“We're not yet in the marketplace,” McBride said.
But Hanner said barcoding technology is evolving rapidly as academic and biotech scientists work to simplify the process.
“Right now we can do the test for a few dollars a sample,” he said. “To be used by industry we have to get it down to pennies,” which he estimated could take another few years.