DNA barcoding reveals mislabeling of game meat species on the U.S. commercial market

Development of ion torrent-based targeted next-generation sequencing panel for identification of animal species in pet foods

Manufacturers may intentionally or unintentionally incorporate ingredients not specified on the label of canned pet foods. Including any unacknowledged ingredients in a food product is considered food fraud or misbranding. Contamination of pet foods may occur in the processing of the foods, including potential cross-contamination in packaging facilities. Of the methods available to identify meat species in food products, Sanger sequencing and several next-generation sequencing methods are available, but there are limitations including the number of targets analyzed at a time and the method specificity. In this study, we developed a targeted next-generation sequencing panel to detect meat species in canned pet foods using Ion Torrent technology. The panel contains multiple primers targeting mitochondrial genes from as many as 27 animal species, of which 7 major animal species were validated. The meat species targets could be identified from samples spiked with as low as 0.01% w/w of the contaminating meat species in a vegetarian food matrix material. Targeted NGS in the current study enriches species-specific multiple target areas in the mitochondrial genome of the target material, which gives high accuracy in the sequencing results.

DNA barcoding for the identification and authentication of medicinal deer (Cervus sp.) products in China

Deer products from sika deer (Cervus nippon) and red deer (C. elaphus) are considered genuine and used for Traditional Chinese Medicine (TCM) materials in China. Deer has a very high economic and ornamental value, resulting in the formation of a characteristic deer industry in the prescription preparation of traditional Chinese medicine, health food, cosmetics, and other areas of development and utilization. Due to the high demand for deer products, the products are expensive and have limited production, but the legal use of deer is limited to only two species of sika deer and red deer; other wild deer are prohibited from hunting, so there are numerous cases of mixing and adulteration of counterfeit products and so on. There have been many reports that other animal (pig, cow, sheep, etc.) tissues or organs are often used for adulteration and confusion, resulting in poor efficacy of deer traditional medicine and trade fraud in deer products. To authenticate the deer products in a rapid and effective manner, the analysis used 22 deer products (antler, meat, bone, fetus, penis, tail, skin, and wool) that were in the form of blind samples. Total DNA extraction using a modified protocol successfully yielded DNA from the blind samples that was useful for PCR. Three candidate DNA barcoding loci, cox1, Cyt b, and rrn12, were evaluated for their discrimination strength through BLAST and phylogenetic clustering analyses. For the BLAST analysis, the 22 blind samples obtained 100% match identity across the three gene loci tested. It was revealed that 12 blind samples were correctly labeled for their species of origin, while three blind samples that were thought to originate from red deer were identified as C. nippon, and seven blind samples that were thought to originate from sika deer were identified as C. elaphus, Dama dama, and Rangifer tarandus. DNA barcoding analysis showed that all three gene loci were able to distinguish the two Cervus species and to identify the presence of adulterant species. The DNA barcoding technique was able to provide a useful and sensitive approach in identifying the species of origin in deer products.

Development and Application of a Visual Duck Meat Detection Strategy for Molecular Diagnosis of Duck-Derived Components

To make meat adulteration detection systems faster, simpler and more efficient, we established a duck-derived meat rapid detection Recombinase Polymerase Amplification (dRPA) method by using interleukin 2 (IL-2) from nuclear genomic DNA as the target gene to design specific primers. We tested the dRPA detection system by comparing its sensitivity and specificity using real-time fluorescent PCR technology. By adjusting the ratio of reagents, this method shortens the time of DNA extraction and visualizes results in combination with colloidal gold immunoassay strips. Our results demonstrate that this dRPA method could specifically detect duck-derived components with a sensitivity of up to 23 copies/μL and the accuracy of the results is consistent with real-time fluorescent PCR. Additionally, dRPA can detect at least 1% of the duck meat content by mixing beef and mutton with duck meat in different proportions, which was verified by spot-check market samples. These results can be visualized with colloidal gold immunoassay strips with the same accuracy as real-time fluorescent RPA. dRPA can complete detection within 30 min, which shortens existing detection time and quickly visualizes the detection results on-site. This lays the groundwork for future large-scale standardized duck origin detection.

Fingerprint Approaches Coupled with Chemometrics to Discriminate Geographic Origin of Imported Salmon in China's Consumer Market

Of the salmon sold in China’s consumer market, 92% was labelled as Norwegian salmon, but was in fact was mainly imported from Chile. The aim of this study was to establish an effective method for discriminating the geographic origin of imported salmon using two fingerprint approaches, Near-infrared (NIR) spectroscopy and mineral element fingerprint (MEF). In total, 80 salmon (40 from Norway and 40 from Chile) were tested, and data generated by NIR and MEF were analysed via various chemometrics. Four spectral preprocessing methods, including vector normalization (VN), Savitzky Golay (SG) smoothing, first derivative (FD) and second derivative (SD), were employed on the raw NIR data, and a partial least squares (PLS) model based on the FD + SG9 pretreatment could successfully differentiate Norwegian salmons from Chilean salmons, with a R² value of 98.5%. Analysis of variance (ANOVA) and multiple comparative analysis were employed on the contents of 16 mineral elements including Pb, Fe, Cu, Zn, Al, Sr, Ni, As, Cr, V, Se, Mn, K, Ca, Na and Mg. The results showed that Fe, Zn, Al, Ni, As, Cr, V, Se, Ca and Na could be used as characteristic elements to discriminate the geographical origin of the imported salmon, and the discrimination rate of the linear discriminant analysis (LDA) model, trained on the above 10 elements, could reach up to 98.8%. The results demonstrate that both NIR and MEF could be effective tools for the rapid discrimination of geographic origin of imported salmon in China’s consumer market.

Development and successful real-world use of a transfer DNA technique to identify species involved in shark bite incidents

Identifying the species involved in shark bite incidents is an ongoing challenge but is important to mitigate risk. We developed a sampling protocol to identify shark species from DNA transferred to inanimate objects during bite incidents. To develop and refine the technique, we swabbed shark bite impressions on surfboards and wetsuit neoprene collected under semicontrolled conditions. Methods were tested experimentally and then successfully used to identify the species involved in a real-world shark bite incident. Thirty-two of 33 bite impressions yielded sufficient DNA sequences for species identification, producing barcodes from five test species, including dusky, Galapagos, bull, tiger, and white shark. The latter three species collectively account for a majority of shark bites worldwide. Our method successfully identified the species (Galeocerdo cuvier) responsible for a fatal shark bite on December 8th, 2020 on the island of Maui, from swab samples collected from the victim's surfboard 49 h after the bite incident. Our experimental results demonstrate that shark species can be accurately identified from transfer DNA recovered from bite impressions on surfboards and wetsuit neoprene. The successful use of our method in the real-world incident shows great potential for the practicality of this tool. We recommend DNA swabbing as a routine part of the forensic analysis of shark bites to help identify the species involved in human-shark interactions.

International Wildlife Trafficking: A perspective on the challenges and potential forensic genetics solutions

International wildlife trafficking (IWT) is a thriving and pervasive illegal enterprise that adversely affects modern societies. Yet, despite being globally recognized as a threat to biodiversity, national security, economy, and biosecurity, IWT remains largely unabated and is proliferating at an alarming rate. The increase in IWT is generally attributed to a lack of prioritization to curb wildlife crime through legal and scientific infrastructure. This review: (1) lays out the damaging scope and influence of IWT; (2) discusses the potential of DNA marker systems, barcodes, and emerging molecular technologies, such as long-read portable sequencing, to facilitate rapid, in situ identification of species and individuals; and (3) encourages initiatives that promote quality and innovation. Interdisciplinary collaboration promises to be one of the most effective ways forward to surmounting the complex scientific and legal challenges posed by IWT.

Use of DNA Barcoding Combined with PCR-SFLP to Authenticate Species in Bison Meat Products

American bison (Bison bison) meat is susceptible to species mislabeling due to its high value and similar appearance to meat from domestic cattle (Bos taurus). DNA barcoding is commonly used to identify animal species. However, as a result of the historical hybridization of American bison and domestic cattle, additional genetic testing is required for species confirmation. The objective of this study was to perform a market survey of bison meat products and verify the species using DNA barcoding combined with polymerase chain reaction-satellite fragment length polymorphism (PCR-SFLP). Bison products (n = 45) were purchased from a variety of retailers. Samples that were positive for domestic cattle with DNA barcoding were further analyzed with PCR-SFLP. DNA barcoding identified bison in 41 products, red deer (Cervus elaphus) in one product, and domestic cattle in three products. PCR-SFLP confirmed the identification of domestic cattle in two samples, while the third sample was identified as bison with ancestral cattle DNA. Overall, mislabeling was detected in 3 of the 45 samples (6.7%). This study revealed that additional DNA testing of species that have undergone historical hybridization provides improved identification results compared to DNA barcoding alone.

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.

Rapid point-of-care testing methods/devices for meat species identification: A review

The authentication of animal species is an important issue due to an increasing trend of adulteration and mislabeling of animal species in processed meat products. Polymerase chain reaction is the most sensitive and specific technique for nucleic acid-based animal species detection. However, it is a time-consuming technique that requires costly thermocyclers and sophisticated labs. In recent times, there is a need of on-site detection by point-of-care (POC) testing methods and devices under low-resource settings. These POC devices must be affordable, sensitive, specific, user-friendly, rapid and robust, equipment free, and delivered to the end users. POC devices should also confirm the concept of micro total analysis system. This review discusses POC testing methods and devices that have been developed for meat species identification. Recent developments in lateral flow assay-based devices for the identification of animal species in meat products are also reviewed. Advancements in increasing the efficiency of lateral flow detection are also discussed.

Multiplex PCR and 12S rRNA gene sequencing for detection of meat adulteration: A case study in the Egyptian markets

Recently, DNA-based methods have proved to be accurate, fast and sensitive for meat authentication. According to the European Union, the food safety standards require accurate and detailed composition information of the meat products. Therefore, an accurate, fast and cost-effective identification methodology is needed. In this study, multiplex PCR coupled with 12S rDNA sequencing was employed for the detection of meat adulteration in two red meat products (frozen beef liver and cold cut samples, respectively) in Egypt. Multiplex PCR allowed the identification of ruminant, poultry, pork, and donkey residuals in processed red meat products (cold cuts) in a single step PCR reaction. Preliminary uniplex PCR was performed to evaluate primers specificity using DNA extracted from the positive control samples. The primers produced specific fragments for ruminant, poultry, pork, and donkey as follows: 271, 183, 531 and 145 bp, respectively. Multiplex PCR revealed that none of the samples was contaminated by porcine or donkey residuals, but 62.5% of all tested processed beef samples contained poultry contaminants. The sensitivity of this method was 0.01 ng/μL for beef, poultry and donkey and 0.1 ng/μL for pig. Another promising finding is the identification of all frozen beef liver samples as a cattle species (Bos taurus) through PCR-sequencing of a short fragment of 12S rRNA gene. Finally, we recommend the employment of multiplex PCR and PCR-sequencing of 12S rDNA for quality control in routine analysis of processed and frozen meat products.

DNA barcoding reveals incorrect labelling of insects sold as food in the UK

Background

Insects form an established part of the diet in many parts of the world and insect food products are emerging into the European and North American marketplaces. Consumer confidence in product is key in developing this market, and accurate labelling of content identity is an important component of this. We used DNA barcoding to assess the accuracy of insect food products sold in the UK.

Methods

We purchased insects sold for human consumption from online retailers in the UK and compared the identity of the material ascertained from DNA barcoding to that stated on the product packaging. To this end, the COI sequence of mitochondrial DNA was amplified and sequenced, and compared the sequences produced to reference sequences in NCBI and the Barcode of Life Data System (BOLD).

Results

The barcode identity of all insects that were farmed was consistent with the packaging label. In contrast, disparity between barcode identity and package contents was revealed in two cases of foraged material (mopane worm and winged termites). One case of very broad family-level description was also highlighted, where material described as grasshopper was identified as Locusta migratoria from DNA barcode.

Conclusion

Overall these data indicate the need to establish tight protocols to validate product identity in this developing market. Maintaining biosafety and consumer confidence rely on accurate and consistent product labelling that provides a clear chain of information from producer to consumer.

DNA barcoding and mini-barcoding in authenticating processed animal-derived food: A case study involving the Chinese market

This study used DNA barcoding and DNA mini-barcoding to test a variety of animal-derived food products sold in the Chinese market for potential mislabeling. Samples (52) including meat, poultry, and fish purchased from retail and online sources were examined. Regions of cytochrome C oxidase I (COI) gene (~650 bp) and 16S rRNA (~220 bp) were used as full- and mini-barcode markers, respectively. Approximately 94% (49 of 52) of the samples generated barcode sequences. The failure rate for full COI full-barcodes was 44%, but we obtained the 16S rRNA mini-barcode from 87% of the COI-failed cases. Overall, the survey revealed that 23% (12 of 52) of animal-derived products were mislabeled and, in most cases, contain undeclared species. Thus, regulatory measures and continuous monitoring for mislabeling of animal-derived products should be conducted.

Identification of the original species of cubilose based on DNA barcode

Cubilose, a valuable traditional Chinese medicine, is mainly composed of the saliva by several species of Aerodramus or Collocalia in the Apodidae. Due to rarity, high economic value and huge market demand, its fake or adulteration is frequently found in the market. Therefore, it is urgent to establish a simple and accurate method for authenticating cubilose. DNA barcoding, which is an easy, quick and reliable method, is widely used to trace the origin of traditional Chinese medicine. For identifying the original species of cubilose, cytb gene of 18 cubilose samples including 15 officer cubilose and 3 feather cubilose were amplified and entered into the GenBank database using the BLAST search tool. The genetic distances among 18 cubilose samples were calculated based on the Kimura two parameter (K2P) model. To construct the reference database, 18 cytb sequences of Aerodramus or Collocalia were downloaded from GenBank. The neighbor-joining (NJ) and unweighted pair group method with arithmetic average (UPGMA) trees were constructed based on sequences from GenBank and our dataset. Blast analysis showed that all cubilose samples had the highest similarity with A. fuciphagus, and the sequence similarity reached over 99%. Genetic distance of 18 cubilose samples ranged from 0.000-0.010. Trees constructed by NJ and UPGMA gave similar topology: all cubilose samples clustered together with A. fuciphagus. These result demonstrated that the original species of all 18 cubilose samples were A. fuciphagus, and cytb gene is a good candidate for identifying cubilose.

Re-visiting the occurrence of undeclared species in sausage products sold in Canada

Meat and poultry are major protein sources for humans worldwide. Undeclared ingredients in processed meat products, like sausage, continue to be identified in retail products all over the world. In collaboration with the Canadian Food Inspection Agency, a previous study of products purchased in Canada showed 20% mislabelling rate in sausage meats when tested for beef, pork, chicken, turkey and horse using DNA barcoding and digital PCR. In a follow-up to this study, an additional 100 "single species" sausage products were collected from Canadian retail markets, one year after our earlier study, to determine the prevalence of undeclared meat species in sausage. A new hierarchy of complementary molecular methods was applied in this study, including the testing of new target species (sheep and goat), in addition to beef, pork, chicken, turkey and horse. First, all samples were tested using DNA barcoding using universal primers, which revealed that 97% of the samples contained the declared species, presumably as the predominant species. Second, all samples were tested using ddPCR assays specifically targeting beef, pork, chicken, and turkey, which revealed that five beef samples, three chicken samples and two turkey samples contained undeclared species. Additionally, ddPCR revealed the presence of undeclared sheep in five samples. Overall, using complementary molecular methods, 14% of the samples contained additional undeclared species. It was encouraging to find a reduced rate of mislabelling compared to the previous study, though it remains clear that meat mislabelling is still an issue affecting Canadian consumers. The results from this study can be used to support decision-making processes for future inspection and monitoring activities in order to control species substitution or adulteration to protect consumers.

DNA Barcodes for Forensically Important Fly Species in Brazil

Here, we analyze 248 DNA barcode sequences of 35 fly species of forensic importance in Brazil. DNA barcoding can be effectively used for specimen identification of these species, allowing the unambiguous identification of 31 species, an overall success rate of 88%. Our results show a high rate of success for molecular identification using DNA barcoding sequences and open new perspectives for immature species identification, a subject on which limited forensic investigations exist in Tropical regions. We also address the implications of building a robust forensic DNA barcode database. A geographic bias is recognized for the COI dataset available for forensically important fly species in Brazil, with concentration of sequences from specimens collected mainly in sites located in the Cerrado, Mata Atlântica, and Pampa biomes.

Game meat authentication through rare earth elements fingerprinting

Accurate labelling of meat (e.g. wild versus farmed, geographical and genetic origin, organic versus conventional, processing treatment) is important to inform the consumers about the products they buy. Meat and meat products declared as game have higher commercial value making them target to fraudulent labelling practices and replacement with non-game meat. We have developed and validated a new method for authentication of wild rabbit meat using elemental metabolomics approach. Elemental analysis was performed using rapid ultra-trace multi-element measurement by inductively coupled plasma mass spectrometry (ICP-MS). Elemental signatures showed excellent ability to discriminate the wild rabbit from non-wild rabbit meat. Our results demonstrate the usefulness of metabolic markers -rare earth signatures, as well as other trace element signatures for game meat authentication.

Towards a Universal Approach Based on Omics Technologies for the Quality Control of Food

In the last decades, food science has greatly developed, turning from the consideration of food as mere source of energy to a growing awareness on its importance for health and particularly in reducing the risk of diseases. Such vision led to an increasing attention towards the origin and quality of raw materials as well as their derived food products. The continuous advance in molecular biology allowed setting up efficient and universal omics tools to unequivocally identify the origin of food items and their traceability. In this review, we considered the application of a genomics approach known as DNA barcoding in characterizing the composition of foodstuffs and its traceability along the food supply chain. Moreover, metabolomics analytical strategies based on Nuclear Magnetic Resonance (NMR) and Mass Spectroscopy (MS) were discussed as they also work well in evaluating food quality. The combination of both approaches allows us to define a sort of molecular labelling of food that is easily understandable by the operators involved in the food sector: producers, distributors, and consumers. Current technologies based on digital information systems such as web platforms and smartphone apps can facilitate the adoption of such molecular labelling.