DNA Barcoding Revealed Mislabeling and Potential Health Concerns with Roasted Fish Products Sold across China

DNA mini-barcoding reveals the mislabeling rate of canned cat food in Taiwan

Background

Domestic cats are important companion animals in modern society that live closely with their owners. Mislabeling of pet food can not only harm pets but also cause issues in areas such as religious beliefs and natural resource management. Currently, the cat food market is booming. However, despite the risk that mislabeling poses to cats and humans, few studies have focused on species misrepresentation in cat food products.

Methods

To address this issue, we used DNA barcoding, a highly effective identification methodology that can be applied to even highly processed products. We targeted a short segment (~85 basepairs) of the mitochondrial 16S rRNA (16S) gene as a barcode and employed Sanger or next generation sequencing (NGS) to inspect 138 canned cat food products in the Taiwanese market.

Results

We discovered that the majority of mislabeling incidents were related to replacement of tuna with other species. Moreover, our metabarcoding revealed that numerous undeclared ingredients were present in all examined canned products. One product contained CITES Appendix II-listed shortfin mako shark (Isurus oxyrinchus). Overall, we uncovered a mislabeling rate of at least 28.99%. To verify cases of mislabeling, an official standardized list of vernacular names, along with the corresponding scientific species names, as well as a dependable barcoding reference sequence database are necessary.

DNA Barcodes Using a Dual Nanopore Device

We report a novel method based on the current blockade (CB) characteristics obtained from a dual nanopore device that can determine DNA barcodes with near-perfect accuracy using a Brownian dynamics simulation strategy. The method supersedes our previously reported velocity correction algorithm (S. Seth and A. Bhattacharya, RSC Advances, 11:20781-20787, 2021), taking advantage of the better measurement of the time-of-flight (TOF) protocol offered by the dual nanopore setup. We demonstrate the efficacy of the method by comparing our simulation data from a coarse-grained model of a polymer chain consisting of 2048 excluded volume beads of diameter 𝜎 = 24 bp using with those obtained from experimental CB data from a 48,500 bp λ-phage DNA, providing a 48500 2400 ≅ 24 base pair resolution in simulation. The simulation time scale is compared to the experimental time scale by matching the simulated time-of-flight (TOF) velocity distributions with those obtained experimentally (Rand et al., ACS Nano, 16:5258-5273, 2022). We then use the evolving coordinates of the dsDNA and the molecular features to reconstruct the current blockade characteristics on the fly using a volumetric model based on the effective van der Waal radii of the species inside and in the immediate vicinity of the pore. Our BD simulation mimics the control-zoom-in-logic to understand the origin of the TOF distributions due to the relaxation of the out-of-equilibrium conformations followed by a reversal of the electric fields. The simulation algorithm is quite general and can be applied to differentiate DNA barcodes from different 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.

Integration of Innovative Technologies in the Agri-Food Sector: The Fundamentals and Practical Case of DNA-Based Traceability of Olives from Fruit to Oil

Several socio-economic problems have been hidden by the COVID-19 pandemic crisis. Particularly, the agricultural and food industrial sectors have been harshly affected by this devastating disease. Moreover, with the worldwide population increase and the agricultural production technologies being inefficient or obsolete, there is a great need to find new and successful ways to fulfill the increasing food demand. A new era of agriculture and food industry is forthcoming, with revolutionary concepts, processes and technologies, referred to as Agri-food 4.0, which enables the next level of agri-food production and trade. In addition, consumers are becoming more and more aware about the origin, traceability, healthy and high-quality of agri-food products. The integration of new process of production and data management is a mandatory step to meet consumer and market requirements. DNA traceability may provide strong approach to certify and authenticate healthy food products, particularly for olive oil. With this approach, the origin and authenticity of products are confirmed by the means of unique nucleic acid sequences. Selected tools, methods and technologies involved in and contributing to the advance of the agri-food sector are presented and discussed in this paper. Moreover, the application of DNA traceability as an innovative approach to authenticate olive products is reported in this paper as an application and promising case of smart agriculture.

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.

Product Authentication Using Two Mitochondrial Markers Reveals Inconsistent Labeling and Substitution of Canned Tuna Products in the Taiwanese Market

Fish of the tribe Thunnini represent a significant proportion of the stock caught by the fishing industry, with many of these fishes being collectively called tuna. However, only certain species can be used legally as an ingredient in canned tuna products, depending on regional food regulations. In Taiwan, only Thunnus species or Katsuwonus pelamis can be used as canned tuna. Here, we authenticated 90 canned tuna products, including 25 cat food samples, by sequencing two mitochondrial regions, 16S rRNA (16S) and the control region (CR). BLAST analysis revealed that Sarda orientalis, Euthynnus affinis, Auxis rochei, and Auxis thazard are all used as substitutes for legitimate tuna products. We found that 63.33% of investigated samples are true canned tuna, i.e., contain Thunnus species or skipjack tuna. We advocate that the Taiwanese government publishes an official standardized list of fishes, especially so that scientific, Chinese and vernacular names can be assigned unambiguously based on a “one species-one name policy”, thereby clarifying which species can be used in seafood products such as tuna. Furthermore, we feel that the large-scale and long-term monitoring of canned tuna products is warranted to fully assess the extent of tuna product adulteration in Taiwan.

DNA barcode by flossing through a cylindrical nanopore

We report an accurate method to determine DNA barcodes from the dwell time measurement of protein tags (barcodes) along the DNA backbone using Brownian dynamics simulation of a model DNA and use a recursive theoretical scheme which improves the measurements to almost 100% accuracy. The heavier protein tags along the DNA backbone introduce a large speed variation in the chain that can be understood using the idea of non-equilibrium tension propagation theory. However, from an initial rough characterization of velocities into “fast” (nucleotides) and “slow” (protein tags) domains, we introduce a physically motivated interpolation scheme that enables us to determine the barcode velocities rather accurately. Our theoretical analysis of the motion of the DNA through a cylindrical nanopore opens up the possibility of its experimental realization and carries over to multi-nanopore devices used for barcoding.

We report a method for DNA barcoding from the dwell time measurement of protein tags (barcodes) along the DNA backbone using Brownian dynamics simulation of a model DNA and use a recursive scheme to improve the measurements to almost 100% accuracy.

Rapid identification of pufferfish in roast fish fillet by real-time PCR

The purpose of this study was to develop a rapid method based on a real-time PCR assay designed to identify the presence of pufferfish in roasted fish fillet. Specific primers and probes were designed targeting Takifugu spp. and Lagocephalus spp., the most common genera in China. Specificity and sensitivity of this assay design were tested by using artificially spikes of pufferfish mixed in with other fish, such as Gadus and Thamnaconus septentrionalis,among others. Fifteen samples of retail roasted fish fillet and six samples from a 1999 poisoning event that occurred in Fujian province China were analysed for pufferfish. When the assay design was validated, no cross-reaction was observed between pufferfish and other species of fish. The limit of detection (LOD) was determined to be 0.001 ng pufferfish template, and the sensitivity of the method was 1%. Lagocephalus lunari was detected in six samples assayed from 1999 and no pufferfish was detected in the 15 retail roasted fish fillet samples tested. These results showed that the method was efficient for screening for pufferfish contamination in the roasted fish fillet and it could benefit public health protection by reducing the risk of tetrodotoxin poisoning.

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.

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.

Exploring the possible reasons for fish fraud in China based on results from monitoring sardine products sold on Chinese markets using DNA barcoding and real time PCR

Sardine is the common name for several small-sized pelagic species from Clupeiformes, representing a resource of great importance in the global fishery. Great efforts have been made to utilise these species as dried, smoked, and restructured fish products. However, in most of these products, it is quite challenging to identify the individual species as the external features are lost during processing, paving the way for species mislabelling. In this study, DNA barcoding (max, using about 650 bp, described as FDB; mini, of about 192 bp, described as MDB) was used for species identification of 139 specimens taken from 48 sardine products (canned and dried seasoning) randomly collected from local markets in Nanjing, China. Moreover, species specific primers were designed for Sardina pilchardus, with the aim to screen the species of S. pilchardus in mixed products. Results highlighted a success rate of amplification from 38.1% for FDB to 97.9% for MDB. Only one sample failed the Sanger-sequencing, and species-specific real time PCR confirmed the existence of S. pilchardus in the product. A maximum species identity in the range of 98-100% was obtained for all readable sequences and 11 species/genera were identified, belonging to 5 orders (Scorpaeniformes, Perciformes, Clupeiformes, Aulopiformes, Scombriformes). Significant legislative and managerial shortcomings and incentives to facilitate the market access of certain species, together with public indifference, represent the main reasons for fish fraud in China.