Advances in the analysis of complex food matrices: Species identification in surimi-based products using Next Generation Sequencing technologies

Abstract

The Next Generation Sequencing (NGS) technologies represent a turning point in the food inspection field, particularly for species identification in matrices composed of a blend of two or more species. In this study NGS technologies were applied by testing the usefulness of the Ion Torrent Personal Genome Machine (PGM) in seafood traceability. Sixteen commercial surimi samples produced both in EU and non-EU countries were analysed. Libraries were prepared using a universal primer pair able to amplify a short 16SrRNA fragment from a wide range of fish and cephalopod species. The mislabelling rate of the samples was also evaluated. Overall, DNA from 13 families, 19 genera and 16 species of fish, and from 3 families, 3 genera and 3 species of cephalopods was found with the analysis. Samples produced in non-EU countries exhibited a higher variability in their composition. 37.5% of the surimi products were found to be mislabelled. Among them, 25% voluntary declared a species different from those identified and 25% (all produced in non-EU countries) did not report the presence of molluscs on the label, posing a potential health threat for allergic consumers. The use of vulnerable species was also proved. Although the protocol should be further optimized, PGM platform proved to be a useful tool for the analysis of complex, highly processed products.

MinION sequencing of seafood in Singapore reveals creatively labelled flatfishes, confused roe, pig DNA in squid balls, and phantom crustaceans

“…Fortunately, these problems can be overcome by using new sequencing methods that are often collectively referred to as Next-Generation sequencing (NGS) or High Throughput Sequencing technologies (HTS). DNA barcodes obtained on platforms such as Illumina, Ion Torrent, and PacBio have been used for food authentication (Carvalho et al, 2017;Giusti et al, 2017;Xing et al, 2019), but they have several disadvantages. The equipment and maintenance cost for Illumina and PacBio instruments are so high that these sequencers are mostly found in sequencing centres that have fairly long turnaround times for submitted samples.…”

Using genetic methods for analysis of fish meals and feeds employed in Greek mariculture

“…For this reason, specific primers for the amplification and detection and a QC‐PCR methodology for a more accurate quantification of plant species in fish feeds are needed. Additionally, advanced technologies like NGS sequencing can increase the resolution of fish meal analysis since they are faster and even more informative than cloning, since they can detect also low‐represented species in mixtures as well as plants and they can lead to relative quantification of detected species (Giusti, Armani, & Sotelo, ; Ribani et al, ). However, they are still costly and they cannot yet be considered enough mature to be applied as routine method.…”

MiFish metabarcoding: a high-throughput approach for simultaneous detection of multiple fish species from environmental DNA and other samples

“…The results from these two case studies indicate that MiFish primers are useful as supplementary to barcoding when amplification fails or sub-optimal reads are obtained with the full COI fish-barcoding primer cocktail (Calosso et al 2020). In the case of processed foods (e.g., surimi-based products or fish cakes), where multiple raw materials may be used, a metabarcoding approach would be useful for identification of the source materials (Giusti et al 2017). Similarly, MiFish metabarcoding can be applied to fish silage used for animal feed or fish-oil production, which consists of minced fish from multiple species dissolved in acid upon capture (Hansen et al 2018).…”