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Mottola A, Intermite C, Piredda R, Lorusso L, Ranieri L, Carpino S, Celano GV, Di Pinto A. DNA Metabarcoding Approach as a Potential Tool for Supporting Official Food Control Programs: A Case Study. Foods 2024; 13:2941. [PMID: 39335870 PMCID: PMC11430886 DOI: 10.3390/foods13182941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Revised: 09/14/2024] [Accepted: 09/16/2024] [Indexed: 09/30/2024] Open
Abstract
Food authentication significantly impacts consumer health and the credibility of Food Business Operators (FBOs). As European regulations mandate the verification of food authenticity and supply chain integrity, competent authorities require access to innovative analytical methods to identify and prevent food fraud. This study utilizes the DNA metabarcoding approach on meat preparations, sampled during an official control activity. It assesses animal and plant composition by amplifying DNA fragments of the 12S rRNA and trnL (UAA) genes, respectively. The results not only confirmed the declared species but also revealed undeclared and unexpected taxa in products labelled as containing a single animal species and various unspecified plant species. Notable findings such as the presence of Murinae, Sus scrofa, Ovis aries, and Pisum sativum could raise public health concerns, compromise consumer choices made for ethical or religious reasons, and reflect the hygienic conditions of the processing plant. This study demonstrates that the DNA metabarcoding approach looks to be a promising support tool for official control authorities to ensure food authenticity and safety, and to develop risk profiles along the supply chain.
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Affiliation(s)
- Anna Mottola
- Department of Veterinary Medicine, University of Bari Aldo Moro, Prov. le Casamassima 62, Km 3, Valenzano, 70010 Bari, Italy; (A.M.); (C.I.); (R.P.); (L.R.); (G.V.C.); (A.D.P.)
| | - Chiara Intermite
- Department of Veterinary Medicine, University of Bari Aldo Moro, Prov. le Casamassima 62, Km 3, Valenzano, 70010 Bari, Italy; (A.M.); (C.I.); (R.P.); (L.R.); (G.V.C.); (A.D.P.)
| | - Roberta Piredda
- Department of Veterinary Medicine, University of Bari Aldo Moro, Prov. le Casamassima 62, Km 3, Valenzano, 70010 Bari, Italy; (A.M.); (C.I.); (R.P.); (L.R.); (G.V.C.); (A.D.P.)
| | - Lucilia Lorusso
- Department of Veterinary Medicine, University of Bari Aldo Moro, Prov. le Casamassima 62, Km 3, Valenzano, 70010 Bari, Italy; (A.M.); (C.I.); (R.P.); (L.R.); (G.V.C.); (A.D.P.)
| | - Lucia Ranieri
- Department of Veterinary Medicine, University of Bari Aldo Moro, Prov. le Casamassima 62, Km 3, Valenzano, 70010 Bari, Italy; (A.M.); (C.I.); (R.P.); (L.R.); (G.V.C.); (A.D.P.)
| | - Stefania Carpino
- Department of Central Inspectorate for Fraud Repression and Quality Protection of the Agri-Food Products and Foodstuffs, Ministry of Agriculture, Food Sovereignty and Forests (ICQRF-MASAF), Via Quintino Sella 42, 00187 Rome, Italy;
| | - Gaetano Vitale Celano
- Department of Veterinary Medicine, University of Bari Aldo Moro, Prov. le Casamassima 62, Km 3, Valenzano, 70010 Bari, Italy; (A.M.); (C.I.); (R.P.); (L.R.); (G.V.C.); (A.D.P.)
| | - Angela Di Pinto
- Department of Veterinary Medicine, University of Bari Aldo Moro, Prov. le Casamassima 62, Km 3, Valenzano, 70010 Bari, Italy; (A.M.); (C.I.); (R.P.); (L.R.); (G.V.C.); (A.D.P.)
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Lee HT, Liao CH, Hsu TH. DNA metabarcoding unveils the hidden species composition in fish surimi: Implications for the management of unlabeled and mixed seafood products. Heliyon 2024; 10:e36287. [PMID: 39247285 PMCID: PMC11378893 DOI: 10.1016/j.heliyon.2024.e36287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 08/09/2024] [Accepted: 08/13/2024] [Indexed: 09/10/2024] Open
Abstract
Fish surimi products are traditional foods primarily made from fish meat and may contain a complex species composition. In Taiwan, the abundant fishery resources and diverse fish species lead to local catches being widely used as ingredients in fish surimi products. However, due to growing market demand and increasingly scarce resources, some surimi products contain sensitive species, such as sharks, posing potential threats to the ecological environment and biodiversity. In this study, by applying metabarcoding techniques, we analyzed 120 fish surimi product samples from different brands and types throughout the four seasons in Taiwan's market. The main fish species identified included milkfish (Chanos chanos), dolphinfish (Coryphaena hippurus), Pomfret (Taractes rubescens), swordfish (Istiophorus spp.) and cartilaginous. Moreover, at least 37 species of cartilaginous fish, including 26 endangered species, were found. Through comprehensive and accurate species identification of surimi product ingredients, we unveiled the usage of sensitive species in products on the market. This finding is important for the surimi industry's quality control and market supervision. Furthermore, it can promote the sustainable use of Taiwan's fishery resources and protect biodiversity.
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Affiliation(s)
- Hung-Tai Lee
- Department of Environmental Biology and Fisheries Science, National Taiwan Ocean University, Keelung, 20224, Taiwan
| | - Cheng-Hsin Liao
- Department of Environmental Biology and Fisheries Science, National Taiwan Ocean University, Keelung, 20224, Taiwan
| | - Te-Hua Hsu
- Department of Aquaculture, National Taiwan Ocean University, 20224, Keelung, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, 20224, Keelung, Taiwan
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Mottola A, Piredda R, Lorusso L, Ranieri L, Intermite C, Barresi C, Galli C, Di Pinto A. Decoding Seafood: Multi-Marker Metabarcoding for Authenticating Processed Seafood. Foods 2024; 13:2382. [PMID: 39123573 PMCID: PMC11311639 DOI: 10.3390/foods13152382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 07/22/2024] [Accepted: 07/25/2024] [Indexed: 08/12/2024] Open
Abstract
Given the recognized nutritional value of fish and shifting consumer lifestyles, processed seafood has become increasingly prevalent, comprising a significant portion of global food production. Although current European Union labeling regulations do not require species declaration for these products, food business operators often voluntarily provide this information on ingredient lists. Next Generation Sequencing (NGS) approaches are currently the most effective methods for verifying the accuracy of species declarations on processed seafood labels. This study examined the species composition of 20 processed seafood products, each labeled as containing a single species, using two DNA metabarcoding markers targeting the mitochondrial cytochrome c oxidase I (COI) and 16S rRNA genes. The combined use of these markers revealed that the majority of the products contained multiple species. Furthermore, two products were found to be mislabeled, as the declared species were not detected. These findings underscore that NGS is a robust technique that could be adopted to support routine food industry activities and official control programs, thereby enhancing the 'From Boat to Plate' strategy and combating fraudulent practices in the complex fisheries supply chain.
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Affiliation(s)
- Anna Mottola
- Department of Veterinary Medicine, University of Bari Aldo Moro, Prov. le Casamassima 62, Km 3, 70010 Valenzano, Italy; (A.M.); (R.P.); (L.R.); (C.I.); (A.D.P.)
| | - Roberta Piredda
- Department of Veterinary Medicine, University of Bari Aldo Moro, Prov. le Casamassima 62, Km 3, 70010 Valenzano, Italy; (A.M.); (R.P.); (L.R.); (C.I.); (A.D.P.)
| | - Lucilia Lorusso
- Department of Veterinary Medicine, University of Bari Aldo Moro, Prov. le Casamassima 62, Km 3, 70010 Valenzano, Italy; (A.M.); (R.P.); (L.R.); (C.I.); (A.D.P.)
| | - Lucia Ranieri
- Department of Veterinary Medicine, University of Bari Aldo Moro, Prov. le Casamassima 62, Km 3, 70010 Valenzano, Italy; (A.M.); (R.P.); (L.R.); (C.I.); (A.D.P.)
| | - Chiara Intermite
- Department of Veterinary Medicine, University of Bari Aldo Moro, Prov. le Casamassima 62, Km 3, 70010 Valenzano, Italy; (A.M.); (R.P.); (L.R.); (C.I.); (A.D.P.)
| | - Concettina Barresi
- Laboratory of Modena, Department of Central Inspectorate for Fraud Repression and Quality Protection of the Agri-Food Products and Foodstuffs, Ministry of Agriculture, Food Sovereignty and Forests (ICQRF-MASAF), Via Domenico Cucchiari, 12, 41124 Modena, Italy;
| | - Carmela Galli
- Laboratory of Salerno, Department of Central Inspectorate for Fraud Repression and Quality Protection of the Agri-Food Products and Foodstuffs, Ministry of Agriculture, Food Sovereignty and Forests (ICQRF-MASAF), Via Frà Giacomo Acquaviva n. 1, 84135 Salerno, Italy;
| | - Angela Di Pinto
- Department of Veterinary Medicine, University of Bari Aldo Moro, Prov. le Casamassima 62, Km 3, 70010 Valenzano, Italy; (A.M.); (R.P.); (L.R.); (C.I.); (A.D.P.)
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Singh M, Young RG, Hellberg RS, Hanner RH, Corradini MG, Farber JM. Twenty-three years of PCR-based seafood authentication assay development: What have we learned? Compr Rev Food Sci Food Saf 2024; 23:e13401. [PMID: 39073284 DOI: 10.1111/1541-4337.13401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/27/2024] [Accepted: 06/14/2024] [Indexed: 07/30/2024]
Abstract
Seafood is a prime target for fraudulent activities due to the complexity of its supply chain, high demand, and difficult discrimination among species once morphological characteristics are removed. Instances of seafood fraud are expected to increase due to growing demand. This manuscript reviews the application of DNA-based methods for commercial fish authentication and identification from 2000 to 2023. It explores (1) the most common types of commercial fish used in assay development, (2) the type of method used, (3) the gene region most often targeted, (4) provides a case study of currently published assays or primer-probe pairs used for DNA amplification, for specificity, and (5) makes recommendations for ensuring standardized assay-based reporting for future studies. A total of 313 original assays for the detection and authentication of commercial fish species from 191 primary articles published over the last 23 years were examined. The most explored DNA-based method was real-time polymerase chain reaction (qPCR), followed by DNA sequencing. The most targeted gene regions were cytb (cytochrome b) and COI (cytochrome c oxidase 1). Tuna was the most targeted commercial fish species. A case study of published tuna assays (n = 19) targeting the cytb region found that most assays were not species-specific through in silico testing. This was conducted by examining the primer mismatch for each assay using multiple sequence alignment. Therefore, there is need for more standardized DNA-based assay reporting in the literature to ensure specificity, reproducibility, and reliability of results. Factors, such as cost, sensitivity, quality of the DNA, and species, should be considered when designing assays.
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Affiliation(s)
- Maleeka Singh
- Department of Food Science, University of Guelph, Guelph, Ontario, Canada
| | - Robert G Young
- Biodiversity Institute of Ontario, Centre for Biodiversity Genomics, Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Rosalee S Hellberg
- Schmid College of Science and Technology, Food Science Program, Chapman University, Orange, California, USA
| | - Robert H Hanner
- Biodiversity Institute of Ontario, Centre for Biodiversity Genomics, Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Maria G Corradini
- Department of Food Science, University of Guelph, Guelph, Ontario, Canada
- Arrell Food Institute, University of Guelph, Guelph, Ontario, Canada
| | - Jeffrey M Farber
- Canadian Research Institute for Food Safety, University of Guelph, Guelph, Ontario, Canada
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Spatola G, Giusti A, Armani A. The "Dry-Lab" Side of Food Authentication: Benchmark of Bioinformatic Pipelines for the Analysis of Metabarcoding Data. Foods 2024; 13:2102. [PMID: 38998608 PMCID: PMC11241536 DOI: 10.3390/foods13132102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 06/25/2024] [Accepted: 06/29/2024] [Indexed: 07/14/2024] Open
Abstract
Next Generation Sequencing Technologies (NGS), particularly metabarcoding, are valuable tools for authenticating foodstuffs and detecting eventual fraudulent practices such as species substitution. This technique, mostly used for the analysis of prokaryotes in several environments (including food), is in fact increasingly applied to identify eukaryotes (e.g., fish, mammals, avian, etc.) in multispecies food products. Besides the "wet-lab" procedures (e.g., DNA extraction, PCR, amplicon purification, etc.), the metabarcoding workflow includes a final "dry-lab" phase in which sequencing data are analyzed using a bioinformatic pipeline (BP). BPs play a crucial role in the accuracy, reliability, and interpretability of the metabarcoding results. Choosing the most suitable BP for the analysis of metabarcoding data could be challenging because it might require greater informatics skills than those needed in standard molecular analysis. To date, studies comparing BPs for metabarcoding data analysis in foodstuff authentication are scarce. In this study, we compared the data obtained from two previous studies in which fish burgers and insect-based products were authenticated using a customizable, ASV-based, and command-line interface BP (BP1) by analyzing the same data with a customizable but OTU-based and graphical user interface BP (BP2). The final sample compositions were compared statistically. No significant difference in sample compositions was highlighted by applying BP1 and BP2. However, BP1 was considered as more user-friendly than BP2 with respect to data analysis streamlining, cost of analysis, and computational time consumption. This study can provide useful information for researchers approaching the bioinformatic analysis of metabarcoding data for the first time. In the field of food authentication, an effective and efficient use of BPs could be especially useful in the context of official controls performed by the Competent Authorities and companies' self-control in order to detect species substitution and counterfeit frauds.
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Affiliation(s)
- Gabriele Spatola
- Department of Veterinary Sciences, University of Pisa, 56124 Pisa, Italy
| | - Alice Giusti
- Department of Veterinary Sciences, University of Pisa, 56124 Pisa, Italy
| | - Andrea Armani
- Department of Veterinary Sciences, University of Pisa, 56124 Pisa, Italy
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Giusti A, Malloggi C, Magagna G, Filipello V, Armani A. Is the metabarcoding ripe enough to be applied to the authentication of foodstuff of animal origin? A systematic review. Compr Rev Food Sci Food Saf 2024; 23:e13256. [PMID: 38284609 DOI: 10.1111/1541-4337.13256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 09/25/2023] [Accepted: 10/02/2023] [Indexed: 01/30/2024]
Abstract
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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Affiliation(s)
- Alice Giusti
- FishLab, Department of Veterinary Sciences, University of Pisa, Pisa, Italy
| | - Chiara Malloggi
- FishLab, Department of Veterinary Sciences, University of Pisa, Pisa, Italy
| | - Giulia Magagna
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Brescia, Italy
| | - Virginia Filipello
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Brescia, Italy
| | - Andrea Armani
- FishLab, Department of Veterinary Sciences, University of Pisa, Pisa, Italy
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