Probiotic 'bar-code' could boost strain identification
The technique, licensed by Maryland-based Opgen from New York University and the Wisconsin Alumni Research Foundation (WARF), has implications throughout the food chain, said Noel Doheny from Opgen, from probiotic producers to consumers.
“Optical mapping provides a new level of information about bacterial genomes (content and arrangement),” Doheny told NutraIngredients.com. “For IP submissions, research comparisons or production verification, the high intensity data output provides never before available details,” he added.
The technique works by using a specific enzyme called a restriction endonuclease to cut DNA in fragments at so-called restriction sites, which are specific repeating sequences of nucleotides in the DNA. These cuts then produce restriction fragments which are imaged using photography, and then combined into an overall map to produce a consensus map, which resembles the bar-code system used in retailing.
And since the bar-code is specific for each strain, researchers can use the technique to detect for insertions, deletions, and translocations responsible for most of the variations in microorganisms.
“Optical mapping is a true representation of the bacteria in the product,” said Doheny.
“For the food industry where probiotics are rapidly growing, the optical mapping technology provides component producers, product producers, distributors and consumers a new level of confidence about the organisms used in production,” he said.
Gilbert Skorski from Phylogene, a French company with a cooperation agreement with Opgen to offer optical mapping in Europe, told NutraIngredients.com that optical maps can be compared to publicly available sequenced reference strains, thereby allowing identification of unknown genes in the strains. This leads to cost savings against traditional sequencing, he said.
Every DNA molecule is taken into account, added Skorski, and so the technique could be used to identify strains in a mixture of bacteria.
Skorski noted that the technique can also have applications in food safety, allowing for the identification of unknown organisms from strain culture mixes, which may include both process strains and food pathogens.
A demonstration of this was published in the journal Microbiology in 2007 (Vol. 153, pp. 1720-1733) showing the tracking of the origin of E coli O157H7 in food contamination, said Skorski.
This study, by researchers at the US Food and Drug Administration, concluded: “The resolution and detail that optical maps provide underscore their usefulness for molecular epidemiological studies.
“The method should also prove useful for microbial forensics investigations, which require technologies that discriminate between closely related strains or that detect insertions in engineered strains. In this respect, optical mapping offers a tractable solution for triaging microbial strains for complete genome sequencing.”