A next-generation sequencing approach for the detection of mixed species in canned tuna

Klapper, Regina; Velasco, A. M.; Döring, Maik; Schröder, Ute; Sotelo, Carmen G.; Brinks, Erik; Muñoz-Colmenero, Marta

doi:10.1016/j.fochx.2023.100560

Cited by 12 publications

(11 citation statements)

References 56 publications

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“…. Among the included SPs, only three (13.0%) used this approach, all published in the last 2 analyzed years (Klapper et al., 2023; Mottola et al., 2022; Mottola et al., 2023), proving that the scientific community is becoming aware of the importance of the pipeline selection.…”

Section: Resultsmentioning

confidence: 99%

“…The maximum score of 5 was assigned only to the SP of Klapper et al. (2023) (4.3%). Note that the 92.3% of the SPs published in the first period 2017–2020 (12 out of 13) showed scores of 0 or 1, whereas 70% of the SPs published in the second period 2021–2023 (7 out of 10) showed scores in the range 2–5.…”

Section: Resultsmentioning

confidence: 99%

“…Note that the 92.3% of the SPs published in the first period 2017–2020 (12 out of 13) showed scores of 0 or 1, whereas 70% of the SPs published in the second period 2021–2023 (7 out of 10) showed scores in the range 2–5. Moreover, the maximum score of 5 was obtained by the SP published last in 2023 (Klapper et al., 2023). Based on this, an increasing trend with respect to the quality of the SPs—namely, greater attention of the authors in detecting and/or limiting the presence of false positives/negatives and thus ensuring the final data reliability and proper results interpretation—was highlighted over the years.…”

Section: Resultsmentioning

confidence: 99%

“…Specifically, the DNA targets of the taxa for which the primers present low binding efficiency are diluted in the amplification process, whereas the sequences with high binding efficiency increase content accordingly (Zhang et al, 2020). Basically, this is the reason why the metabarcoding cannot be considered a quantitative analysis but, at most, a "semi-quantitative" approach (Klapper et al, 2023;Zhang et al, 2020;Preckel et al, 2021). Despite the considerable development of DNA-based methods, the perfect barcode/s and primers for food authentication have not been found to date, especially considering that an increasing number of animal species originating from different areas of the world are now offered to consumers in processed products.…”

Section: Library Preparationmentioning

confidence: 99%

“…. Among the included SPs, only three (13.0%) used this approach, all published in the last 2 analyzed years (Klapper et al, 2023;Mottola et al, 2022;Mottola et al, 2023), proving that the scientific community is becoming aware of the importance of the pipeline selection. The remaining six SPs (26.1%) used Pip-2, including services provided by external companies that used inhouse developed pipelines, or trademark pipelines associated with the sequencing platform (viz., Ion Torrent and MinION-Oxford Nanopore).…”

Section: Final Data Analysismentioning

confidence: 99%

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Is the metabarcoding ripe enough to be applied to the authentication of foodstuff of animal origin? A systematic review

Giusti,

Malloggi,

Magagna

et al. 2023

Comp Rev Food Sci Food Safe

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Food authentication using molecular techniques is of great importance to fight food fraud. Metabarcoding, based on the next‐generation sequencing (NGS) technologies, allowing large‐scale taxonomic identification of complex samples via massive parallel sequencing of fragments (called DNA barcodes) simultaneously, has become increasingly popular in many scientific fields. A systematic review to answer the question “Is the metabarcoding ripe enough to be applied to the authentication of foodstuff of animal origin?” is presented. The inclusion criteria were focused on the selection of scientific papers (SPs) only applying metabarcoding to foodstuff of animal origin collected on the market. The 23 included SPs were first analyzed with respect to the metabarcoding phases: library preparation (target genes, primer pairs, and fragment length), sequencing (NGS platforms), and final data analysis (bioinformatic pipelines). Given the importance of primer selection, the taxonomic coverage of the used primers was also evaluated. In addition, the SPs were scored based on the use of quality control measures (procedural blanks, positive controls, replicates, curated databases, and thresholds to filter the data). A lack of standardized protocols, especially with respect to the target barcode/s and the universal primer/s, and the infrequent application of the quality control measures, leads to answer that metabarcoding is not ripe enough for authenticating foodstuff of animal origin. However, the observed trend of the SP quality improvement over the years is encouraging. Concluding, a proper protocol standardization would allow a wider use of metabarcoding by both official and private laboratories, enabling this method to become the primary for the authentication of foodstuffs of animal origin.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%