DNA and Next Generation Sequencing for Food Authenticity, Traceability and Safety
Knowing exactly what is in complex food samples has long been a highly-pursued aim.
Hence, the use of DNA-based methodologies has become a powerful tool for food analysis, the detection of potential adulteration, and as a deterrent to economically motivated adulteration.
However, most methods are based on polymerase chain reaction (PCR) amplification and usually target either one or a small number of ingredients. This requires knowledge about which organism to search for and can be limited to a restricted number of targets because of the narrow range of commercially available test kits. Therefore, the results obtained by direct PCR detection only produce presence/absence results for the targeted species. No additional information is obtained, such as whether any other species is present in the sample.
Next Generation Sequencing
In recent years, DNA-based approaches have been greatly improved by the recent application of Next Generation Sequencing (NGS) techniques.
At the end of an NGS analysis, millions of individual sequences are obtained making it possible to identify species in complex foods containing multiple ingredients. This is because each ingredient will produce a single and unique DNA sequence. The sequences obtained are compared with databases (containing several thousands of species) resulting in a complete list of all the species present in the sample, including the scientific name of the species identified.
This technique is recognized as the most reliable method for species detection and identification. NGS therefore allows untargeted detection of thousands of organisms with no requirement for previous knowledge of the supply chain, or about the species to search for.This means that today the question is simply, which animal species are in this sample?
Likewise, are there any other plants in my dried oregano, or can I defend a claim that is made on the food label? As a result, NGS is becoming an increasingly useful and powerful way to check the robustness of controls for a large number of steps in a process, or to reduce the risk of undiscovered fraud when the number and variability of suppliers impacts the supply chain.
NGS is presently the only test method that ensures the correct identification of species in complex foods due to the untargeted nature of the method, and even exotic species can be identified. Therefore, the use of this method is increasing and it is routinely being applied in food authenticity analysis. SGS leads a working group that is involved in the aim of publishing an officially accepted test method.
Dealing With Damaged DNA
One of the challenges in the analysis of highly processed food products using PCR was the fragmentation of DNA caused by many manufacturing processes, like the high temperatures and/or pressures used for sterilization. These damage DNA and produce very short DNA fragments. Therefore, to avoid false negative results it is essential to use a NGS approach optimized to work with those short fragments, bearing in mind that the DNA sequences must still be informative enough to discriminate among closely related species. The DNA sequence analysis takes advantage of the uniqueness of DNA sequences for each organism. Each different species has its own DNA sequence that can be used as a unique identifier, and is commonly designated as a ‘DNA barcode’.
SGS has developed a unique workflow combining a broad range of short DNA fragments with PCR amplification to guarantee the detection of thousands of species together with specific in-house software for NGS data analysis. By using this workflow, food products can be analyzed for almost all types of organisms including meat, fish, seafood, plants and microbes. This workflow is so broad that virtually any kind of food product can be analyzed as long as it still contains DNA.
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