DNA barcoding revealing mislabeling of seafood in European mass caterings

Fish species authentication in commercial fish products using mass spectrometry and spectral library matching approach

Seafood fraud has become a global issue, threatening food security and safety. Adulteration, substitution, dilution, and incorrect labeling of seafood products are fraudulent practices that violate consumer safety. In this context, developing sensitive, robust, and high-throughput molecular tools for food and feed authentication is becoming crucial for regulatory purposes. Analytical approaches such as proteomics mass spectrometry have shown promise in detecting incorrectly labeled products. For the application of these tools, genome information is crucial, but currently, for many marine species of commercial importance, such information is unavailable. However, when combining proteomic analysis with spectral library matching, commercially important fish species were successfully identified, differentiated, and quantified in pure muscle samples and mixtures, even when genome information was scarce. This study further tested the previously developed spectral library matching approach to differentiate between 29 fish species from the North Sea and examined samples including individual fish, laboratory-prepared mixtures and commercial products. For authenticating libraries generated from 29 fish species, fresh muscle samples from the fish samples were matched against the reference spectral libraries. Species of the fresh fish samples were correctly authenticated using the spectral library approach. The same result was obtained when evaluating the laboratory-prepared mixtures. Furthermore, processed commercial products containing mixtures of two or three fish species were matched against these reference spectral libraries to test the accuracy and robustness of this method for authentication of fish species. The results indicated that the method is suitable for the authentication of fish species from highly processed samples such as fish cakes and burgers. The study shows that current and future challenges in food and feed authentication can efficiently be tackled by reference spectral libraries method when prospecting new resources in the Arctic.

Can consumers avoid mislabelling? Genetic species identification provides recommendations for shrimp/prawn products

BACKGROUND

Crustaceans of the superfamily Penaeoidea (e.g., shrimps and prawns) are among the most commercially available aquatic products worldwide. However, there are few studies regarding not only the presence but also the characteristics of mislabelling in these food products. Such information would be helpful for consumers in order to avoid the typical problems associated with mislabelling (e.g., health and economic issues). For this reason, this work considers Penaeoidea mislabelling by comparing different products (frozen, fresh, boiled), and sources (hypermarkets, supermarkets and fishmongers) from Spain (Europe).

RESULTS

A total of 94 samples from 55 different products were collected, representing 19 different species from 13 genera. Mitochondrial DNA (COI gene) was amplified, revealing mislabelling in almost 30% of supermarket products and almost exclusively found in frozen samples (95% of the total) regardless of its price. In addition, products from the Pacific Ocean seem to be particularly susceptible to mislabelling.

CONCLUSIONS

All in all, recommendations for the consumer in order to avoid mislabelling of prawns include purchasing them fresh from fishmongers; aquaculture products must not be avoided. This study represents, to our knowledge, the first attempt to provide recommendations to consumers based on DNA analyses in order to avoid mislabelling in food products. Further research is therefore required to provide such recommendations in different food products, particularly those that are processed, packaged and/or frozen. © 2024 The Author(s). Journal of the Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Food fraud threats in UK post-harvest seafood supply chains; an assessment of current vulnerabilities

Seafood fraud is commonly reported on food fraud databases and deceptive practices are highlighted by numerous studies, with impacts on the economy, health and marine conservation. Food fraud assessments are a widely accepted fraud mitigation and prevention activity undertaken to identify possible points of deception within a supply chain. This study aims to understand the food fraud vulnerability of post-harvest seafood supply chains in the UK and determine if there are differences according to commodity, supply chain node, business size and certification status. The SSAFE food fraud vulnerability assessment tool was used to assess 48 fraud factors relating to opportunities, motivations and controls. The analysis found seafood supply chains to have a medium vulnerability to food fraud, with the highest perceived vulnerability in technical opportunities. Certification status was a stronger determinant of vulnerability than any other factor, particularly in the level of controls, a factor that also indicated a higher perceived level of vulnerability in smaller companies and the food service industry. This paper also reviews historic food fraud trends in the sector to provide additional insights and the analysis indicates that certain areas of the supply chain, including uncertified prawn supply chains, salmon supply chains and food service companies, may be at higher risk of food fraud. This study conducts an in-depth examination of food fraud vulnerability relating to the UK and for seafood supply chains and contributes to a growing body of literature identifying areas of vulnerability and resilience to food related criminality within the global food system.

Seafood label quality and mislabelling rates hamper consumer choices for sustainability in Australia

Seafood mislabelling and species substitution, compounded by a convoluted seafood supply chain with significant traceability challenges, hinder efforts towards more sustainable, responsible, and ethical fishing and business practices. We conducted the largest evaluation of the quality and accuracy of labels for 672 seafood products sold in Australia, assessing six seafood groups (i.e., hoki, prawns, sharks and rays, snapper, squid and cuttlefish, and tuna) from fishmongers, restaurants, and supermarkets, including domestically caught and imported products. DNA barcoding revealed 11.8% of seafood tested did not match their label with sharks and rays, and snappers, having the highest mislabelling rate. Moreover, only 25.5% of products were labelled at a species-level, while most labels used vague common names or umbrella terms such as 'flake' and 'snapper'. These poor-quality labels had higher rates of mislabelling than species-specific labels and concealed the sale of threatened or overfished taxa, as well as products with lower nutritional quality, reduced economic value, or potential health risks. Our results highlight Australia's weak seafood labelling regulations and ambiguous non-mandatory naming conventions, which impede consumer choice for accurately represented, sustainable, and responsibly sourced seafood. We recommend strengthening labelling regulations to mitigate seafood mislabelling and substitution, ultimately improving consumer confidence when purchasing seafood.

Conservation tools: the next generation of engineering-biology collaborations

The recent increase in public and academic interest in preserving biodiversity has led to the growth of the field of conservation technology. This field involves designing and constructing tools that use technology to aid in the conservation of wildlife. In this review, we present five case studies and infer a framework for designing conservation tools (CT) based on human-wildlife interaction. Successful CT range in complexity from cat collars to machine learning and game theory methodologies and do not require technological expertise to contribute to conservation tool creation. Our goal is to introduce researchers to the field of conservation technology and provide references for guiding the next generation of conservation technologists. Conservation technology not only has the potential to benefit biodiversity but also has broader impacts on fields such as sustainability and environmental protection. By using innovative technologies to address conservation challenges, we can find more effective and efficient solutions to protect and preserve our planet's resources.

Molecular Barcoding: A Tool to Guarantee Correct Seafood Labelling and Quality and Preserve the Conservation of Endangered Species

The recent increase in international fish trade leads to the need for improving the traceability of fishery products. In relation to this, consistent monitoring of the production chain focusing on technological developments, handling, processing and distribution via global networks is necessary. Molecular barcoding has therefore been suggested as the gold standard in seafood species traceability and labelling. This review describes the DNA barcoding methodology for preventing food fraud and adulteration in fish. In particular, attention has been focused on the application of molecular techniques to determine the identity and authenticity of fish products, to discriminate the presence of different species in processed seafood and to characterize raw materials undergoing food industry processes. In this regard, we herein present a large number of studies performed in different countries, showing the most reliable DNA barcodes for species identification based on both mitochondrial (COI, cytb, 16S rDNA and 12S rDNA) and nuclear genes. Results are discussed considering the advantages and disadvantages of the different techniques in relation to different scientific issues. Special regard has been dedicated to a dual approach referring to both the consumer's health and the conservation of threatened species, with a special focus on the feasibility of the different genetic and genomic approaches in relation to both scientific objectives and permissible costs to obtain reliable traceability.

A case study on DNA barcoding for pet food mislabeling in South Korea

Due to the close relationship between pets and humans, pet owners are highly invested in proper diets for their pets. Even though pet food mislabeling is concerning, there are few studies on this topic. This study investigated pet food mislabeling in South Korea’s market based on DNA barcoding. In total, 10 pet food products were purchased, and 200 sequences of the partial Cytochrome c oxidase subunit 1 (COI) gene were generated from clones of the samples. The obtained sequences were compared to available public databases to identify species present in the ingredients. The data analyses showed that the labeled species were consistent with species detected by COI sequences in 6 of the products. However, the expected species were not detected in 4 products, revealing possible mislabeling in these samples. Our findings indicated that DNA barcoding might represent a promising tool to detect pet food mislabeling.

An Authentication Survey on Retail Seafood Products Sold on the Bulgarian Market Underlines the Need for Upgrading the Traceability System

Economically motivated or accidental species substitutions lead to economic and potential health damage to consumers with a loss of confidence in the fishery supply chain. In the present study, a three-year survey on 199 retail seafood products sold on the Bulgarian market was addressed to assess: (1) product authenticity by molecular identification; (2) trade name compliance to the list of official trade names accepted in the territory; (3) adherence of the list in force to the market supply. DNA barcoding on mitochondrial and nuclear genes was applied for the identification of whitefish (WF), crustaceans (C) and mollusks (cephalopods-MC; gastropods-MG; bivalves-MB) except for Mytilus sp. products for which the analysis was conducted with a previously validated RFLP PCR protocol. Identification at the species level was obtained for 94.5% of the products. Failures in species allocation were reconducted due to low resolution and reliability or the absence of reference sequences. The study highlighted an overall mislabeling rate of 11%. WF showed the highest mislabeling rate (14%), followed by MB (12.5%), MC (10%) and C (7.9%). This evidence emphasized the use of DNA-based methods as tools for seafood authentication. The presence of non-compliant trade names and the ineffectiveness of the list to describe the market species varieties attested to the need to improve seafood labeling and traceability at the national level.

DNA barcoding of fresh seafood in Australian markets reveals misleading labelling and sale of endangered species

Flake and shark samples were purchased from outlets in several coastal Australian regions and genetically barcoded using the cytochrome oxidase subunit 1 (CO1) gene to investigate labelling reliability and species-specific sources of ambiguously labelled fillets. Of the 41 shark fillet samples obtained, 23 yielded high-quality CO1 sequences, out of which 57% (n = 13) were labelled ambiguously (misleading) and 35% (n = 8) incorrectly. In contrast, barramundi fillets, which are widely available and sought after in Australian markets, were shown to be accurately labelled. Species identified from shark samples, including the shortfin mako (n = 3) and the scalloped hammerhead (n = 1), are assessed by the IUCN as endangered and critically endangered, respectively, with several others classified as vulnerable and near threatened.

Mezcal worm in a bottle: DNA evidence suggests a single moth species

Mezcals are distilled Mexican alcoholic beverages consumed by many people across the globe. One of the most popular mezcals is tequila, but there are other forms of mezcal whose production has been part of Mexican culture since the 17th century. It was not until the 1940-50s when the mezcal worm, also known as the "tequila worm", was placed inside bottles of non-tequila mezcal before distribution. These bottled larvae increased public attention for mezcal, especially in Asia, Europe, and the United States. Despite these larvae gaining global interest, their identity has largely remained uncertain other than that they are larvae of one of three distantly related holometabolous insects. We sequenced the COI gene from larvae in different kinds of commercially available mezcals. All larval DNA that amplified was identified as the agave redworm moth, Comadia redtenbacheri. Those that did not amplify were also confirmed morphologically to be the larva of this species.

COIBar-RFLP Molecular Strategy Discriminates Species and Unveils Commercial Frauds in Fishery Products

The DNA analysis is the best approach to authenticate species in seafood products and to unveil frauds based on species substitution. In this study, a molecular strategy coupling Cytochrome Oxidase I (COI) DNA barcoding with the consolidated methodology of Restriction Fragment Length Polymorphisms (RFLPs), named COIBar-RFLP, was applied for searching pattern of restriction enzyme digestion, useful to discriminate seven different fish species (juveniles of Engraulis encrasicolus and Sardina pilchardus sold in Italy as “bianchetto” and Aphia minuta sold as “rossetto”; icefish Neosalanx tangkahkeii; European perch, Perca fluviatilis and the Nile Perch, Lates niloticus; striped catfish, Pangasianodon hypophthalmus). A total of 30 fresh and frozen samples were processed for DNA barcoding, analyzed against a barcode library of COI sequences retrieved from GenBank, and validated for COIBar–RFLP analysis. Cases of misdescription were detected: 3 samples labeled as “bianchetto” were substituted by N. tangkahkeii (2 samples) and A. minuta (1 sample); 3 samples labeled as “persico reale” (P. fluviatilis) were substituted by L. niloticus and P. hypophthalmus. All species were simultaneously discriminated through the restriction pattern obtained with MspI enzyme. The results highlighted that the COIBar-RFLP could be an effective tool to authenticate fish in seafood products by responding to the emerging interest in molecular identification technologies.

Detection and identification of marine fish mislabeling in Guangzhou's supermarkets and sushi restaurants using DNA barcoding

In this study, DNA barcoding was applied to identify the distinct species of fish products in Guangzhou supermarkets and sushi restaurants in order to confirm whether products were correctly labeled. Samples were analyzed using mitochondrial cytochrome C oxidase subunit I (CO I) gene as the target. Our results showed that the CO I gene of all 139 samples examined was successfully amplified by PCR. When sequenced, 30 samples (21.58%) were mislabeled as the wrong species, 11 samples had insufficient information provided on the label to determine if the labeling was correct (7.91%), and four samples failed sequencing (2.88%). We also found that the use of proper labels for fish products in sushi restaurants was higher than that in supermarkets. As a simple, rapid, and efficient technology, DNA barcoding can be widely used for species identification of fish products. Our work shows that regulation of the labeling of fish products, as we evaluated in Guangzhou and other markets in China, is needed on a global scale.

DNA Barcode Identification of Fish Products from Guiyang Markets in Southwestern People's Republic of China

ABSTRACT

Global fish consumption is increasing in tandem with population growth, resulting in the dilemma of overfishing. Overfished high-value fish are often replaced with other fish in markets. Therefore, the accurate identification of fish products in the market is important. In this study, full-DNA and mini-DNA barcoding were used to detect fish product fraud in Guiyang, Guizhou Province, People's Republic of China. The molecular results revealed that 39 (20.42%) of the 191 samples were inconsistent with the labels. The percentages of mislabeling of fresh, frozen, cooked, and canned fish products were 11.70, 20.00, 34.09, and 50.00%, respectively. The average Kimura two-parameter distances of mini-DNA barcoding within species and within genera were 0.56 and 6.42%, respectively, and those of full-DNA barcoding were 0.53 and 7.25%, respectively. Commercial fraud was evident in this study; most high-priced fish were replaced with low-priced fish with similar features. Our findings indicate that DNA barcoding is an effective tool for identifying fish products and could be used to enhance transparency and fair trade in domestic fisheries.

HIGHLIGHTS

Molecular tools for assuring human health and environment-friendly frozen shellfish products in the United Arab Emirates markets

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Frozen UAE shellfish samples were identified using 16S rDNA barcoding.

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Significant substitutions were identified for calamari by peanut worm, cattle, and rat.

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Although labelled as UAE in origin most shrimps were non-native species.

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Analyzed shellfish barcodes showed most species belong to low diversity populations.

Shellfish consumption in the United Arab Emirates (UAE) exceeds local supply and frozen fish and seafood products are imported to fill the gap. To determine the species in frozen shellfish brands on the UAE markets, 95 frozen samples were subjected to PCR amplification and sequencing of the hypervariable region of the 16S rDNA. This identified 11 different shrimp species and two squid species in the frozen shellfish packs. About 40% of calamari brands contained peanut worm, cattle, and rat 16S rDNA. Also, most shellfish species analyzed had low nucleotide diversity, including two shrimp species (Litopenaeus vannamei and Metapenopsis barbata), which had very limited genetic diversity, low raggedness, and an absence of population expansion. Species misnaming, substitution, overexploitation, origin misreporting, and low genetic diversity were found across frozen UAE shellfish samples analyzed, suggesting inspection and monitoring of frozen seafood sold in UAE markets would be appropriate.

A Multiplex PCR Assay Combined with Capillary Electrophoresis for the Simultaneous Identification of Atlantic Cod, Pacific Cod, Blue Whiting, Haddock, and Alaska Pollock

With an increased consumption of seafood products, food fraud with fish resources has been continuously reported. In particular, codfish has been exploited worldwide as a processed product in fresh, frozen, smoked, canned, or ready-to-eat dish forms. However, it is challenging to identify processed fish products after processing because of their similar morphological characteristics. Substitution and mislabeling of codfish among different species are also happening deliberately or unintentionally. Thus, it is necessary to distinguish cod species to prevent fish adulteration and food fraud. In this study, we developed a multiplex PCR for simultaneously identifying five cod species within Gadidae using capillary electrophoresis. Then, their species-specific primer sets were designed by targeting the mitochondrial cytochrome b gene. Subsequently, the amplicon sizes obtained were 237 bp, 204 bp, 164 bp, 138 bp, and 98 bp for Atlantic cod, Pacific cod, blue whiting, haddock, and Alaska pollock, respectively. The specificity of each primer was further tested using 19 fish species, and no cross-reactivity was observed. The limit of detection of this multiplex PCR assay was 1 pg. The developed multiplex PCR assay can be applied to 40 commercial food products successfully. This detection method will be efficient for managing seafood authentication by simultaneously analyzing multiple cod species.

DNA Analysis Detects Different Mislabeling Trend by Country in European Cod Fillets

Atlantic cod, Gadus morhua, is a highly appreciated fish in European seafood markets and is one of the most substituted fish species in the world. Fraud have been detected in European markets in the last decade, finding different substitute species sold as G. morhua or Atlantic cod on the label. In this study, we analyzed 252 samples of fresh and frozen cod fillets sold in Germany, the Netherlands, and France using DNA barcoding. Different trends were found in different countries: while the level of mislabeling found in Germany and the Netherlands remained at zero in the last years, a significant increase was found in the French markets comparing the current results with previous studies on fillets in France. On the one hand, this mislabeling proves the need to encourage European efforts to control seafood authenticity; on the other, zero mislabeling in two countries shows the success of current European regulations.

Efficiency of DNA Mini-Barcoding to Assess Mislabeling in Commercial Fish Products in Italy: An Overview of the Last Decade

The problem of fish traceability in processed products is still an important issue in food safety. Major attention is nowadays dedicated to consumer health and prevention of possible frauds regulated by national and international laws. For this reason, a technical approach is fundamental in revealing mislabeling at different levels. In particular, the use of genetic markers has been standardized and DNA barcoding is considered the gold-standard strategy to examine and prevent species substitution. Considering the richness of available DNA databases, it is nowadays possible to rapidly reach a reliable taxonomy at the species level. Among different approaches, an innovative method based on DNA mini barcoding has recently been proposed at an international level. Starting from this evidence, we herein illustrate an investigation dealing with the evolution of this topic in Italy over the last decade. The molecular analysis of 71 commercial fish samples based on mini-COI sequencing with two different primer sets reached an amplification success rate of 87.3 and 97.2%. The investigation revealed four major frauds (5.8%) and four minor ones (5.8%). Results highlighted a decrease in incorrect labeling in Italy from 32% to 11.6% over the last decade, although a recurrent involvement of “endangered” species sensu IUCN was still observed.

Efficacy of using stable isotopes coupled with chemometrics to differentiate the production method and geographical origin of farmed salmonids

The δ²H and δ¹⁸O of 105 salmonids cultured in freshwater and seawater and from different regions were combined with linear discriminant analysis (LDA), k-nearest neighbor (KNN), and random forest (RF) to create discrimination models. To assess the stability of the discrimination models, seasonal variation in δ²H and δ¹⁸O in salmonids cultured in different systems was studied. δ²H and δ¹⁸O were significantly different between salmonids cultured in freshwater and seawater and from different geographical origins. δ²H and δ¹⁸O of salmonids cultured in an open system were vulnerable to seasonal effects. The KNN model had 100% accuracy for identifying the production methods of salmonids and was less affected by seasonal variation. The RF model had the highest accuracy for identifying the geographical origins of salmonids with an accuracy of over 80%. Thus, δ²H and δ¹⁸O were more effective for identifying the production methods of salmonids than their geographical origins.

Fraud in highly appreciated fish detected from DNA in Europe may undermine the Development Goal of sustainable fishing in Africa

Despite high effort for food traceability to ensure safe and sustainable consumption, mislabeling persists on seafood markets. Determining what drives deliberate fraud is necessary to improve food authenticity and sustainability. In this study, the relationship between consumer's appreciation and fraudulent mislabeling was assessed through a combination of a survey on consumer's preferences (N = 1608) and molecular tools applied to fish samples commercialized by European companies. We analyzed 401 samples of fish highly consumed in Europe and worldwide (i.e. tuna, hake, anchovy, and blue whiting) through PCR-amplification and sequencing of a suite of DNA markers. Results revealed low mislabeling rate (1.9%), with a higher mislabeling risk in non-recognizable products and significant mediation of fish price between consumer´s appreciation and mislabeling risk of a species. Furthermore, the use of endangered species (e.g. Thunnus thynnus), tuna juveniles for anchovy, and still not regulated Merluccius polli hake as substitutes, points towards illegal, unreported and/or unregulated fishing from African waters. These findings reveal a worrying intentional fraud that hampers the goal of sustainable seafood production and consumption, and suggest to prioritize control efforts on highly appreciated species.

DNA barcoding reveals fraud in commercial common snook (Centropomus undecimalis) products in Santa Marta, Colombia

The common snook Centropomus undecimalis is one of the main commercial fish species in the Caribbean region, including Colombia, where its populations have drastically decreased due to overfishing and environmental degradation. Thus, there is a market imbalance between the availability of snook products and their demand by consumers, which creates an opening for fraudulent actions such as species substitutions. Legislation in Colombia (and most Caribbean countries) lacks effective tools for the easy and rapid detection of frauds. Furthermore, there are very few studies published in scientific journals addressing this issue, of which none include C. undecimalis as the target species. Therefore, in order to investigate the existence of mislabeling in common snook products in Santa Marta, the present study analysed 44 frozen snook fillets from the five commercial brands available in the city. Moreover, 15 fresh snook fillets from six of the main fish markets were also analysed. To discover the frequency of possible frauds in labeling, samplings were carried out in July, September and November of 2019. Sample analyses involved the identification of each fillet at species level through molecular barcodes (16S-rRNA and COI), whose sequences were verified using BLAST and BOLD, and corroborated by a phylogenetic analysis. As a result, an astonishing 98% of the supermarkets fillets were found to be fraudulent, contrasting with a single case registered in the fish shop samples. The species used to substitute snook include the Pacific bearded brotula Brotula clarkae (38 samples), the Nile perch Lates niloticus (4 samples) and the acoupa weakfish Cynoscion acoupa (1 sample). Based on these results, there is a high rate of fraudulent labeling in the marketing of common snook in the city of Santa Marta, which calls for urgent actions to be taken by the corresponding authorities.

Geographic Pattern of Sushi Product Misdescription in Italy-A Crosstalk between Citizen Science and DNA Barcoding

The food safety of sushi and the health of consumers are currently of high concern for food safety agencies across the world due to the globally widespread consumption of these products. The microbiological and toxicological risks derived from the consumption of raw fish and seafood have been highlighted worldwide, while the practice of species substitution in sushi products has attracted the interest of researchers more than food safety agencies. In this study, samples of sushi were processed for species authentication using the Cytochrome Oxidase I (COI) gene as a DNA barcode. The approach of Citizen Science was used to obtain the sushi samples by involving people from eighteen different Italian cities (Northern, Central and Southern Italy). The results indicate that a considerable rate of species substitution exists with a percentage of misdescription ranging from 31.8% in Northern Italy to 40% in Central Italy. The species most affected by replacement was Thunnus thynnus followed by the flying fish roe substituted by eggs of Mallotus villosus. These results indicate that a standardization of fish market names should be realized at the international level and that the indication of the scientific names of species should be mandatory for all products of the seafood supply chain.

Dentex dentex Frauds: Establishment of a New DNA Barcoding Marker

The common dentex (Dentex dentex (Linnaeus, 1758)) is an iconic fish in the Mediterranean diet. Due to its commercial and organoleptic importance, this sparid is highly appreciated in European markets and is often subjected to species substitution frauds. Comparative mitogenomics is a suitable approach for identifying new and effective barcode markers. This study aimed to find a molecular tag useful for unequivocally discriminating the sparid species D. dentex. The comparison of the complete mitochondrial DNA (mtDNA) sequences of 16 sparid species allowed us to highlight the potential of the NAD2 gene for direct identification purposes. Common dentex-specific primers were created and successfully evaluated by end-point and real-rime PCR (Polymerase Chain Reaction) for several fish species, achieving amplification only in the D. dentex. The method proposed in this study appears fast, simple, and inexpensive and requires affordable instrumentation. This approach provides unambiguous results for the common dentex authentication without the sequencing step. The presence/absence assay for D. dentex can be executed in a few hours of lab work. Therefore, national authorities responsible for food safety and traceability could apply and make full use of DNA-testing methods for deterring operators from false seafood declarations.

Identification and Authentication of Commercial Mi-iuy Croaker (Miichthys miiuy) Products by Two PCR-Based Methods

ABSTRACT

Mi-iuy croaker (Miichthys miiuy) is one of the most important ingredients of Korean cuisine and, thus, has a high economic value. However, the similar morphological traits among croaker fish belonging to family Sciaenidae are often exploited for seafood fraud. In this study, an M. miiuy-specific primer set was designed and further improved by the development of a rapid and cost-effective duplex PCR method. The specificity of M. miiuy-specific duplex PCR was tested using 22 seafood species, and no cross-reactivity was observed. The sensitivity of the PCR assay was found to be 0.1 ng/μL. For the first time, labeling compliance of 43 commercial mi-iuy croaker products was verified using both full DNA barcoding and M. miiuy-specific duplex PCR methods. For species identification, BOLDSYSTEMS and GenBank database were screened with the consensus sequences of each PCR product as a query. This identification result was further confirmed using the M. miiuy-specific duplex PCR method. The findings of this study revealed that principal species substituted were law croaker (Pseudotolithus senegallus, n = 4), bigeye croaker (Micropogonias megalops, n = 3), whitemouth croaker (Micropogonias furnieri, n = 1), and tigertoothed croaker (Otolithes ruber, n = 1). A significant percentage (21%) of mislabeling was present in commercial mi-iuy products sold on the South Korean market.

HIGHLIGHTS

Multiple drivers behind mislabeling of fish from artisanal fisheries in La Paz, Mexico

Seafood mislabeling has the potential to mask changes in the supply of species due to overfishing, while also preventing consumers from making informed choices about the origin, quality and sustainability of their food. Thus, there is a need to understand mislabeling and analyze the potential causes behind it to propose solutions. We conducted a COI DNA barcoding study in La Paz, Baja California Sur, Mexico, with 74 samples from fish markets and 50 samples from restaurants. We identified 38 species sold under 19 commercial names, from which at least ∼80% came from local small-scale fisheries. Overall, 49 samples, representing 40% (95% CI [31.4-48.3]) were considered mislabeled in our samples. Based on analyses where species were assigned to three price categories, economic incentives were associated with approximately half of the mislabeling events observed, suggesting that other motivating factors might simultaneously be at play. Using a network approach to describe both mislabeling (when species are mislabeled as the focal species) and substitution (when the focal species is used as substitute for others), we calculated proxies for the net availability of each species in the market. We found that local fish landings were a significant predictor of the net availability of the 10 most important commercial species at retail, but this true availability was masked to the eyes of the final consumer by both mislabeling and substitution. We hypothesize that the level of supply of each species could help explain mislabeling and substitution rates, where species in low supply and high demand could show higher mislabeling rates and rarely be used as substitutes, while species in high supply and low demand could be used as substitutes for the preferred species. Other factors affecting mislabeling include national regulations that restrict the fishing or commercialization of certain species and local and global campaigns that discourage specific patterns of consumption. We discuss how these factors might influence mislabeling and propose some solutions related to communication and education efforts to this local and global challenge.

DNA barcoding: a modern age tool for detection of adulteration in food

Globalization of the food trade requires precise and exact information about the origin, methods of production, transformation technologies, authentication, and the traceability of foodstuffs. New challenges in food supply chains such as deliberate fraudulent substitution, tampering or mislabeling of food and its ingredients or food packaging incapacitates the market and eventually the national economy. Currently, no proper standards have been established for the authentication of most of the food materials. However, in order to control food fraud, various robust and cost-effective technologies have been employed, like a spectrophotometer, GC-MS, HPLC, and DNA barcoding. Among these techniques, DNA barcoding is a biotechnology advantage with the principle of using 400-800 bp long standardized unique DNA sequences of mitochondrial (e.g. COI) or plastidial (e.g. rbcL) of nuclear origin (e.g. ITS) to analyze and classify the food commodities. This review covers several traded food commodities like legumes, seafood, oils, herbal products, spices, fruits, cereals, meat, and their unique barcodes which are critically analyzed to detect adulteration or fraud. DNA barcoding is a global initiative and it is being accepted as a global standard/marker for species identification or authentication. The research laboratories and industries should collaborate to realize its potential in setting standards for quality assurance, quality control, and food safety for different food products.

Investigating seafood substitution problems and consequences in Taiwan using molecular barcoding and deep microbiome profiling

Seafood is commonly seen in cuisines of the Asia–Pacific regions. The rates and consequences of seafood substitution frauds in Taiwan were elusive. To address this, we conducted a consumer-centered study, collecting seafood dishes and cooking materials from restaurants and markets easily accessible to the residents in Taiwan. Seafood substitutions were evaluated using DNA barcodes in the mitochondrial MT-CO1 gene. Among the 127 samples collected, 24 samples were mislabeled (18.9%, 95% Confidence interval [CI] = [12.5–26.8%]). The mislabel rates vary in different fish and product types (snapper [84.6%, 54.6–98.1%], cod [25%, 5.5–57.2%], swordfish [16.7%, 2.1–48.4%], cobia [16.7%, 0.4–64.1%], surimi products [100.0%]). A deep microbiome profiling was performed in 8 correctly-labeled conventional sushi and 2 tilapia sashimi mislabeled as snapper, with sequencing depths greater than 100,000 reads for every sample. The relative abundance of Pseudomonas genus is significantly higher in tilapia sashimi than in conventional sushi (P = 0.044). In conclusion, the gross seafood mislabel rate in Taiwan is 18.9% (12.5–26.8%). Snapper, cod and surimi products are particularly vulnerable to fraudulent substitutions. The high abundance of Pseudomonas in tilapia sashimi mislabeled as snapper unveils a potential health issue pertaining to the consumption of raw mislabeled seafood.

The ITS region provides a reliable DNA barcode for identifying reishi/lingzhi (Ganoderma) from herbal supplements

The dietary supplement industry is rapidly growing yet, a recent study revealed that up to 60% of supplements may have substituted ingredients, some of which can be harmful contaminants or additives. When ingredients cannot be verified morphologically or biochemically, DNA barcoding complemented with a molecular phylogenetic analysis can be a powerful method for species authentication. We employed a molecular phylogenetic analysis for species authentication of the commonly used fungal supplement, reishi (Ganoderma lingzhi), by amplifying and sequencing the nuclear ribosomal internal transcribed spacer regions (ITS) with genus-specific primers. PCR of six powdered samples and one dried sample all sold as G. lucidum representing independent suppliers produced single, strong amplification products in the expected size-range for Ganoderma. Both best-hit BLAST and molecular phylogenetic analyses clearly identified the presence of G. lingzhi DNA in all seven herbal supplements. We detected variation in the ITS sequences among our samples, but all herbal supplement samples fall within a large clade of G. lingzhi ITS sequences. ITS-based phylogenetic analysis is a successful and cost-effective method for DNA-based species authentication that could be used in the herbal supplement industry for this and other fungal and plant species that are otherwise difficult to identify.

DNA-based techniques for seafood species authentication

Global trade of seafood has increased in the last decade, leading to significant concerns associated with seafood fraud. Seafood fraud involves the intentional misrepresentation of fish or shellfish for the purpose of economic gain and includes acts such as species substitution, illegal transshipment, overtreatment/short weighting, and mislabeling country of origin or production method. These fraudulent acts have had economic, environmental, and public health consequences on a global level. DNA-based techniques for seafood authentication are utilized by regulatory agencies and can be employed as part of a food fraud risk mitigation plan. This chapter will focus specifically on the use of DNA-based methods for the detection of seafood species substitution. Various methods have been developed for DNA-based species identification of seafood, including polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), species-specific PCR, real-time PCR, Sanger sequencing, microarrays, and high-resolution melting (HRM). Emerging techniques for seafood authentication include droplet digital PCR, isothermal amplification, PCR-enzyme-linked immunosorbent assay (ELISA), and high-throughput or next-generation sequencing. Some of these DNA-based methods target specific species, such as real-time PCR and droplet digital PCR, while other methods allow for simultaneous differentiation of a wide range of fish species, including Sanger sequencing and high-throughput sequencing. This chapter will begin with an introduction on seafood fraud and species substitution, followed by an analysis of the main DNA-based authentication methods and emerging techniques for species identification.

Fish-Based Baby Food Concern-From Species Authentication to Exposure Risk Assessment

In this work, two different but complementary approaches were used to evaluate the reliability of fish-based baby foods as a source of safe nourishment for babies. More specifically, barcoding analysis based on the Cytochrome Oxidase I sequences was used for fish species authentication and an analysis of metal/metalloid levels was performed to estimate the exposure risk assessment derived from consumption of selected fish-based baby food in infants and toddlers. COI DNA barcoding revealed that in three samples the species detected did not match the common name of the species shown on the label. In particular, G. chalcogrammus and M. australis were found in place of M. merluccius and O. mykiss was found in place of S. salar. The analysis of exposure risk assessment indicated a low risk for developing chronic systemic and carcinogenic effects in infants and toddler, under an exposure scenario based on daily consumption of a single box of fish-based baby food. However, it is important to highlight that in order to provide a comprehensive risk assessment it would be important to supplement the levels of exposure resulting from the total diet. Overall, our results suggest that more attention should be paid by authorities to ensure the safety of food for infants and toddlers.

Feeding fiction: Fraud vulnerability in the food service industry

This study examines fraud vulnerability in the food service industry; identifies underlying fraud vulnerability factors; and studies the differences in fraud vulnerability between casual dining restaurants, fine dining restaurants and mass caterers for four product groups. Vulnerability was assessed by an adapted SSAFE food fraud vulnerability assessment, tailored to the food service sector situation. The 15 food service operators rated high vulnerability for 40% of the fraud indicators. This is considerably more than food manufacturers, wholesalers and retailers did previously. In particular, more opportunities and fewer controls were noted. Overall fraud vulnerability was more determined by the type of food service operator than by the type of food product. Casual dining restaurants appeared most vulnerable, followed by fine dining restaurants. Mass caterers seemed the least vulnerable operators, because they had more adequate food fraud controls in place. Considering its high vulnerability, reinforcement of mitigation measures in the food service industry is urgently recommended.

MinION-Based DNA Barcoding of Preserved and Non-Invasively Collected Wildlife Samples

The ability to sequence a variety of wildlife samples with portable, field-friendly equipment will have significant impacts on wildlife conservation and health applications. However, the only currently available field-friendly DNA sequencer, the MinION by Oxford Nanopore Technologies, has a high error rate compared to standard laboratory-based sequencing platforms and has not been systematically validated for DNA barcoding accuracy for preserved and non-invasively collected tissue samples. We tested whether various wildlife sample types, field-friendly methods, and our clustering-based bioinformatics pipeline, SAIGA, can be used to generate consistent and accurate consensus sequences for species identification. Here, we systematically evaluate variation in cytochrome b sequences amplified from scat, hair, feather, fresh frozen liver, and formalin-fixed paraffin-embedded (FFPE) liver. Each sample was processed by three DNA extraction protocols. For all sample types tested, the MinION consensus sequences matched the Sanger references with 99.29%-100% sequence similarity, even for samples that were difficult to amplify, such as scat and FFPE tissue extracted with Chelex resin. Sequencing errors occurred primarily in homopolymer regions, as identified in previous MinION studies. We demonstrate that it is possible to generate accurate DNA barcode sequences from preserved and non-invasively collected wildlife samples using portable MinION sequencing, creating more opportunities to apply portable sequencing technology for species identification.

Assessing species diversity of Coral Triangle artisanal fisheries: A DNA barcode reference library for the shore fishes retailed at Ambon harbor (Indonesia)

The Coral Triangle (CT), a region spanning across Indonesia and Philippines, is home to about 4,350 marine fish species and is among the world's most emblematic regions in terms of conservation. Threatened by overfishing and oceans warming, the CT fisheries have faced drastic declines over the last decades. Usually monitored through a biomass-based approach, fisheries trends have rarely been characterized at the species level due to the high number of taxa involved and the difficulty to accurately and routinely identify individuals to the species level. Biomass, however, is a poor proxy of species richness, and automated methods of species identification are required to move beyond biomass-based approaches. Recent meta-analyses have demonstrated that species richness peaks at intermediary levels of biomass. Consequently, preserving biomass is not equal to preserving biodiversity. We present the results of a survey to estimate the shore fish diversity retailed at the harbor of Ambon Island, an island located at the center of the CT that display exceptionally high biomass despite high levels of threat, while building a DNA barcode reference library of CT shore fishes targeted by artisanal fisheries. We sampled 1,187 specimens and successfully barcoded 696 of the 760 selected specimens that represent 202 species. Our results show that DNA barcodes were effective in capturing species boundaries for 96% of the species examined, which opens new perspectives for the routine monitoring of the CT fisheries.