Puffer fish-based commercial fraud identification in a segment of cytochrome b region by PCR–RFLP analysis

Advances in the authentication of collagen products based on DNA technology

Collagenous products are making their way into consumer markets such as foods, nutraceuticals, cosmetics and pharmaceuticals increasingly. Collagen in a large family of proteins is ubiquitous in metazoan. The most effective way to identify biological samples including collagen is DNA technology indisputably. However, the DNA content of collagen mostly derived from connective tissue is relatively less, and commercial collagen products are usually subjected to some harsh treatments in the production process, which makes DNA damage more serious, thus tracing their origin becomes a huge challenge. At present, DNA enrichment mainly relies on silica based centrifugal columns after extraction by classical phenol chloroform method. For improving the amplification of DNA fragments, small amplicons are designed based on more stable mitochondrial genes, such as cytochrome b gene (cytb). In addition to conventional PCR for DNA amplification, some new PCR techniques have also been developed, such as DNA barcoding techniques, PCR-Southern hybridization and fluorescent PCR. These PCR techniques have their pros and cons, and are mainly used in the identification of gelatin at present. The development of a complete set of DNA authentication is of great significance for the control of collagen products quality and will contribute to sustainable development of collagen industry.

Near Infrared Reflectance Spectroscopy Coupled to Chemometrics as a Cost-Effective, Rapid, and Non-Destructive Tool for Fish Fraud Control: Monitoring Source, Condition, and Nutritional Value of Five Common Whitefish Species

Fish fraud is a problematic issue for the industry. For it to be properly addressed will require the use of accurate, rapid, and cost-effective tools. In this work, near infrared reflectance spectroscopy (NIRS) was used to predict nutritional values (protein, lipids, and moisture) as well as to discriminate between sources (farmed vs. wild fish) and conditions (fresh or defrosted fish). Samples of five whitefish species-Alaskan pollock (Gadus chalcogrammu), Atlantic cod (G. morhua), European plaice (Pleuronectes platessa), common sole (Solea solea), and turbot (Psetta maxima)-including farmed, wild, fresh, and frozen ones, were scanned by a low-cost handheld near infrared reflectance spectrometer with a spectral range between 900 and 1700 nm. Several machine learning algorithms were explored for both regression and classification tasks, achieving precisions and coefficients of determination higher than 88% and 0.78, respectively. Principal component analysis (PCA) was used to cluster samples according to classes where good linear discriminations were denoted. Loadings from PCA revealed bands at 1150, 1200, and 1400 nm as the most discriminative spectral regions regarding classification of both source and condition, suggesting the absorbance of OH, CH, CH2, and CH3 groups as the most important ones. This study shows the use of NIRS and both linear and non-linear learners as a suitable strategy to address fish fraud and fish QC.

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.

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.

Development of Species-Specific PCR Primers for the Rapid and Simultaneous Identification of the Six Species of Genus Takifugu

Pufferfish (Takifugu spp.) are economically important edible marine fish. Mistakes in pufferfish classification can lead to poisoning; therefore, accurate species identification is critical. In this study, we used the mtDNA cytochrome c oxidase subunit I gene (COI) to design specific primers for six Takifugu species among the 21 domestic or imported pufferfish species legally sold for consumption in Korea. We rapidly and simultaneously identified these pufferfish species using a highly efficient, multiplex polymerase chain reaction (PCR) system with the six species-specific primers. The results showed that species-specific multiplex PCR (multiplex species-specific polymerase chain reaction; MSS-PCR) either specifically amplified PCR products of a unique size or failed. MSS-PCR yielded amplification fragment lengths of 897 bp for Takifugu pardalis, 822 bp for T. porphyreus, 667 bp for T. niphobles, 454 bp for T. poecilonotus, 366 bp for T. rubripes, and 230 bp for T. xanthpterus using the species-specific primers and a control primer (ca. 1,200 bp). We visualized the results using agarose gel electrophoresis to obtain accurate contrasts of the six Takifugu species. MSS-PCR analysis is easily performed and provides identification results within 6 h. This technique is a powerful tool for the discrimination of Takifugu species and will help prevent falsified labeling, protect consumer rights, and reduce the risk of pufferfish poisoning..

From Fish Eggs to Fish Name: Caviar Species Discrimination by COIBar-RFLP, an Efficient Molecular Approach to Detect Fraud in the Caviar Trade

The demand for caviar is growing as is its price on the market. Due to the decline of true caviar production from sturgeons, eggs from other fish species and other animals have been used as substitutes for caviar. The labels on these products should indicate the species from which the eggs were derived, but the label can be misleading in some cases. In this context, species identification using DNA analysis is crucial for traceability and authentication of caviar products. In this work, we applied the COIBar-RFLP procedure to obtain species-specific endonuclease restriction patterns useful to discriminate “caviar” species. The tested caviar products were identified as originating from eight species: Acipenser transmontanus, A. gueldenstaedtii, A. stellatus, A. baerii, Mallotus villosus, Huso huso, Cyclopterus lumpus and Eumicrotremus orbis. The results demonstrated that 14% of the caviar products examined have a label that does not indicate the species from which the eggs were originated. The MboI restriction enzyme produced specific profiles discriminating the eight species, confirming that the COIBar-RFLP is a useful approach for routine screening of seafood products due to its ease and rapid execution, as the results of screening can be obtained within 7 h, by-passing the need for sequencing.

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

HIGHLIGHTS

75.5% of products were identified as species outside the expected family. Six products were identified as containing multiple species from distinct families. Species from distinct families were verified in products of same brand for six groups. Identification of potentially toxic pufferfish species highlighted health concerns.

Tracing individuals and populations of the tambaqui, Colossoma macropomum (Cuvier, 1818), from Brazilian hatcheries using microsatellite markers

BACKGROUND

In recent years, tracing of alimentary produce of animal origin has become increasingly important, for economic, food safety and ecological reasons. The tambaqui, Colossoma macropomum, is the native fish most farmed in Brazil. The reliable identification of the origin of tambaquis (wild or farmed) offered for sale to the general public has become necessary to satisfy regulatory norms and uphold consumer confidence. Molecular methods based on the analysis of DNA sequences have often been used to evaluate the potential for tracing farmed fish, given their reliability and precision.

RESULTS

Full likelihood and Bayesian approaches proved to be the most efficient for the identification, respectively, of individuals and populations for most of the fish sampled from seven hatcheries and one wild stock. The exclusion method and genetic distances were the least effective approaches for the identification of individuals and populations. The Bayesian method identified correctly more than 99% of the fry from most stocks, except those of the Santarém hatchery and River Amazon wild stock, which presented the best results for individual identification.

CONCLUSIONS

The identification of populations was effective for most hatcheries, although the identification of individuals from most stocks was hampered by the reduced genetic variability. © 2018 Society of Chemical Industry.

Development of standardized methodology for identifying toxins in clinical samples and fish species associated with tetrodotoxin-borne poisoning incidents

Tetrodotoxin (TTX) is a naturally occurring toxin in food, especially in puffer fish. TTX poisoning is observed frequently in South East Asian regions. In TTX-derived food poisoning outbreaks, the amount of TTX recovered from suspicious fish samples or leftovers, and residual levels from biological fluids of victims are typically trace. However, liquid chromatography–mass spectrometry and liquid chromatography–tandem mass spectrometry methods have been demonstrated to qualitatively and quantitatively determine TTX in clinical samples from victims. Identification and validation of the TTX-originating seafood species responsible for a food poisoning incident is needed. A polymerase chain reaction-based method on mitochondrial DNA analysis is useful for identification of fish species. This review aims to collect pertinent information available on TTX-borne food poisoning incidents with a special emphasis on the analytical methods employed for TTX detection in clinical laboratories as well as for the identification of TTX-bearing species.

Genotyping of Toxic Pufferfish Based on Specific PCR-RFLP Products As Determined by Liquid Chromatography/Quadrupole-Orbitrap Hybrid Mass Spectrometry

A method based on liquid chromatography-electrospray mass spectrometric analysis of the enzymatically digested amplicons derived from the mitochondrial 16S rRNA gene was established for the discrimination of toxic pufferfish. A MonoBis C18 narrow-bore silica monolith column (Kyoto Monotech) and a Q Exactive mass spectrometer (Thermo Fisher) were employed for separation and detection, respectively. Monoisotopic masses of the oligonucleotides were calculated using Protein Deconvolution 3.0 software (Thermo Fisher). Although a lock mass standard was not used, excellent accuracy (mass error, 0.83 ppm on average) and precision (relative standard deviation, 0.49 ppm on average) were achieved, and a mass accuracy of <2.8 ppm was maintained for at least 180 h without additional calibration. The present method was applied to 29 pufferfish samples, and results were consistent with Sanger sequencing.

Lactic acid bacterial population dynamics during fermentation and storage of Thai fermented sausage according to restriction fragment length polymorphism analysis

This study applied restriction fragment length polymorphism (RFLP) analysis to identify the lactic acid bacteria (LAB) isolated from "mum" Thai fermented sausages during fermentation and storage. A total of 630 lactic acid bacteria were isolated from the sausages prepared using 2 methods. In Method 1, after stuffing, the sausages were stored at 30 °C for 14 days. In Method 2, after stuffing and storage at 30 °C for 3 days, the sausages were vacuum-packed and stored at 4 °C until Day 28. The sausages were sampled on Days 0, 3, 14, and 28 for analyses. The 16S rDNA was amplified and digested using restriction enzymes. Of the restriction enzymes evaluated, Dde I displayed the highest discrimination capacity. The LAB were classified and 7 species were identified For Methods 1 and 2, during fermentation, the Lactobacillus sakei and Lactobacillus plantarum species were dominant. For Method 2, the proportion of Leuconostoc mesenteroides markedly increased during storage, until L. sakei and Ln. mesenteroides represented the dominant species. The identification of LAB in the sausage samples could facilitate the selection of appropriate microorganisms for candidate starter cultures for future controlled mum production.

PCR-RFLP identification of four Chinese soft-shelled turtle Pelodiscus sinensis strains using mitochondrial genes

A PCR-RFLP method to confirm the identification of four Pelodiscus sinensis strains (Taihu Lake strain, Taiwan strain, Yellow River strain and Japanese strain) was developed and evaluated. In this study, we sequenced and analyzed the partial sequences of mitochondrial NADH4, COX I and NADH5-NADH6 genes of 60 individuals from the four P. sinensis strains. Bgl I, Hpa II and Cla I were selected for cutting NADH4, COX I and NADH5-NADH6 PCR products, respectively, and each strain has its unique restriction band patterns. The result showed that all the 140 samples tested can be correctly identified based on the combination of the three digested fragments pattern. This study provides an effective method to distinguish the four main strains of P. sinensis.

Identifications of captive and wild tilapia species existing in Hawaii by mitochondrial DNA control region sequence

Background

The tilapia family of the Cichlidae includes many fish species, which live in freshwater and saltwater environments. Several species, such as O. niloticus, O. aureus, and O. mossambicus, are excellent for aquaculture because these fish are easily reproduced and readily adapt to diverse environments. Historically, tilapia species, including O. mossambicus, S. melanotheron, and O. aureus, were introduced to Hawaii many decades ago, and the state of Hawaii uses the import permit policy to prevent O. niloticus from coming into the islands. However, hybrids produced from O. niloticus may already be present in the freshwater and marine environments of the islands. The purpose of this study was to identify tilapia species that exist in Hawaii using mitochondrial DNA analysis.

Methodology/Principal Findings

In this study, we analyzed 382 samples collected from 13 farm (captive) and wild tilapia populations in Oahu and the Hawaii Islands. Comparison of intraspecies variation between the mitochondrial DNA control region (mtDNA CR) and cytochrome c oxidase I (COI) gene from five populations indicated that mtDNA CR had higher nucleotide diversity than COI. A phylogenetic tree of all sampled tilapia was generated using mtDNA CR sequences. The neighbor-joining tree analysis identified seven distinctive tilapia species: O. aureus, O. mossambicus, O. niloticus, S. melanotheron, O. urolepies, T. redalli, and a hybrid of O. massambicus and O. niloticus. Of all the populations examined, 10 populations consisting of O. aureus, O. mossambicus, O. urolepis, and O. niloticus from the farmed sites were relatively pure, whereas three wild populations showed some degree of introgression and hybridization.

Conclusions/Significance

This DNA-based tilapia species identification is the first report that confirmed tilapia species identities in the wild and captive populations in Hawaii. The DNA sequence comparisons of mtDNA CR appear to be a valid method for tilapia species identification. The suspected tilapia hybrids that consist of O. niloticus are present in captive and wild populations in Hawaii.

Liquid chromatography-tandem mass spectrometry determination of the toxicity and identification of fish species in a suspected tetrodotoxin fish poisoning

Suspected tetrodotoxin (TTX) poisoning was associated with eating unknown fish in April 2009 in Taiwan. After ingestion of the fish, symptoms of the victim included perioral paresthesia, nausea, vomiting, ataxia, weakness of all limbs, respiration failure, and death within several hours. The toxicity in the remaining fish was determined, with the mice exhibiting symptoms of neurotoxin poisoning. The implicated fish and deceased victim tissues were analyzed for TTX by liquid chromatography-tandem mass spectrometry. The urine, bile, cerebrospinal fluid (spinal cord), pleural effusion, and pericardial effusion of the victim contained TTX. In addition, the partial cytochrome b gene of the implicated fish was determined by PCR. The DNA sequence in the partial 465-bp cytochrome b gene identified the implicated fish as Chelonodon patoca (puffer fish). These results indicate that people should avoid eating unknown fish species from fish markets where harvested fish may include toxic species.

Advances in DNA-based techniques for the detection of seafood species substitution on the commercial market

Increased worldwide trade and processing of seafood has increased the potential for species substitution on the commercial market. To detect and prevent species substitution, several deoxyribonucleic acid (DNA)-based methods have been developed that can be used to identify species in a variety of food types. For large-scale applications, such as regulatory screening, these methods must be rapid, cost-effective, reliable, and have high potential for automation. This review highlights recent technological advances in DNA-based identification methods, with a focus on seafood species identification in automated, high-throughput settings. Advances in DNA isolation methods include silica-based columns for use in high-throughput operations and magnetic bead particles for increased and targeted recovery of DNA. The three most widely used methods for seafood species identification (polymerase chain reaction [PCR] sequencing, PCR-restriction fragment length polymorphism, and species-specific PCR) will be discussed, with a focus on the incorporation of technologies such as rapid PCR cycling, microfluidic chips, and real-time PCR. Emerging methods, including DNA microarrays and next-generation sequencing will also be explored for their potential to identify seafood species on a large scale. Overall, many of the technological advances discussed here offer complementary properties that will enable species identification in a variety of settings and with a range of products.