PCR-RFLP of the mitochondrial cytochrome oxidase gene: a simple method for discrimination between Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss)

A DNA-based method (PCR-RFLP) has been developed for discrimination between Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss). The polymerase chain reaction (PCR) was used for amplification of a 464 bp fragment of the mitochondrial cytochrome oxidase subunit II (COII) gene. Digestion of the products with endonucleases Nci I and Sau 3AI, followed by agarose gel electrophoresis of the digested products, yielded specific restriction profiles that enabled direct visual identification of the species analysed. This PCR-RFLP methodology allowed clear discrimination of Atlantic salmon and rainbow trout samples both in raw and smoked products. © 1999 Society of Chemical Industry     

Authentication of swordfish (<Emphasis Type="Italic">Xiphias gladius</Emphasis>) by RT–PCR and FINS methodologies

In the present study, two methods for the authentication of swordfish (Xiphias gladius) were developed. The first one is based on a TaqMan probe real-time PCR technology using the cytochrome oxidase subunit I (COI), while the second one is based on the phylogenetic analysis of DNA sequences (forensically informative nucleotide sequencing, FINS) using the cytochrome b (cyt b) gene fragment. Both techniques can be applied depending on the laboratory equipment and allow the detection of fraudulent or unintentional mislabelling of this species. The developed methodologies were validated and subsequently were applied to 30 commercial samples labelled as swordfish or X. gladius in order to determinate whether the species used for their manufacturing corresponded to this species. These tools are useful to clarify questions related to the correct labelling of commercial products and to verify the correct traceability in commercial trade and for fisheries control.     

Molecular approaches for the detection of truffle species in processed food products

Molecular identification techniques were applied in order to analyse food products containing fragments of some Tuber species. Samples of fungal DNA were processed by analyses of the internal transcribed spacer (ITS) region. The polymerase chain reaction (PCR) using truffle species‐specific primers, multiplex PCR, restriction fragment length polymorphism (RFLP) analysis, sequencing of the ITS region and specific oligonucleotide probe hybridisation were used. The results obtained demonstrate the applicability of these molecular strategies to the identification of truffles, even when their morphological characteristics are difficult to interpret owing to the drastic treatments utilised in food preparation or the use of unripe fruit bodies (lacking spores). Furthermore, testing was also possible starting from very small amounts of sample and degraded DNA. The methods described have important applications in both the production and sale of such food products, in order to avoid fraud and reveal the possible presence of other fungal species. © 2002 Society of Chemical Industry     

PCR-RFLP analysis of the rpoB gene to distinguish the five species of Cronobacter

Members of the genus Cronobacter are opportunistic pathogens associated with life-threatening infections in immuno-compromised individuals. Polyphasic analysis has facilitated the classification of the novel genus Cronobacter containing five species. However, since this recent reclassification there are not many identification methods optimised for differentiation between the five Cronobacter species. This differentiation between the species is of importance as there are indications that the species may be diverse regarding their virulence. The aim of this study was to develop a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) protocol to differentiate between the five Cronobacter species. The rpoB gene of 49 Enterobacteriaceae strains, including 33 Cronobacter strains was amplified using conventional PCR, followed by digestion of these PCR products with restriction endonucleases MboI, HinP1I and Csp6I. The PCR-RFLP analysis with single digestions of each of the restriction endonucleases did not distinguish between all five Cronobacter species. This study describes the successful differentiation of the five Cronobacter species based on the amplification of the rpoB gene followed by the combined digestion with restriction endonucleases Csp6I and HinP1I. This PCR-RFLP assay is an accurate identification method that ensures rapid differentiation between the five species of Cronobacter.     

Analysis of raw meats and fats of pigs using polymerase chain reaction for Halal authentication

A method for species identification from pork and lard samples using polymerase chain reaction (PCR) analysis of a conserved region in the mitochondrial (mt) cytochrome b (cyt b) gene has been developed. Genomic DNA of pork and lard were extracted using Qiagen DNeasy^® Tissue Kits and subjected to PCR amplification targeting the mt cyt b gene. The genomic DNA from lard was found to be of good quality and produced clear PCR products on the amplification of the mt cyt b gene of approximately 360 base pairs. To distinguish between species, the amplified PCR products were cut with restriction enzyme BsaJI resulting in porcine-specific restriction fragment length polymorphisms (RFLP). The cyt b PCR-RFLP species identification assay yielded excellent results for identification of pig species. It is a potentially reliable technique for detection of pig meat and fat from other animals for Halal authentication.     

Development of a method for genetic identification of four species of anchovies: E. encrasicolus, E. anchoita, E. ringens and E. japonicus

Cytochrome b has been successfully employed for genetic identification of four species of anchovies (Engraulis spp) using two methodologies: PCR–RFLP and FINS. The first method allowed the identification of Engraulis anchoita, Engraulis ringens and Engraulis japonicus–Engraulis encrasicolus. In some cases, with a determined restriction profile, this technique was able to differentiate E. japonicus from E. encrasicolus. The second method allowed the identification of those four species and demonstrates that FINS is a suitable technique for the identification of all species studied in this work. Phylogenetic trees show that sequences of E. encrasicolus are grouped into two different clusters. These results are consistent with the previously published data which suggest that some species of genus Engraulis could be cryptic species, being one specie or population distributed in the oceanic habitat and the other one around the coast.     

Comparison and evaluation of molecular methods used for identification and discrimination of lactic acid bacteria

BACKGROUND: Lactobacillus and Bifidobacterium strains are present in a great variety of habitats, including fermented products, probiotic concoctions and the human colon. Some species are so closely related that it is difficult to distinguish them by microbiological techniques. Nevertheless, discrimination of isolates is an important issue in respect of application, and molecular methods such as restriction fragment length polymorphism (RFLP), random amplification of polymorphic DNA (RAPD) or species‐specific polymerase chain reaction (PCR) might help in resolving this problem. In this study, PCR, RFLP and sequencing were applied to identify lactobacilli and bifidobacteria originating from various sources and the DSMZ strain collection. RESULTS: The microbiological composition of foods was analysed by molecular methods. Using species‐specific PCR primers, three restriction enzymes (AluI, HhaI and RsaI) and sequencing, three Bifidobacterium and six Lactobacillus reference strains could be distinguished and four additional lactobacilli of food origin were identified. CONCLUSION: A combination of three molecular methods resulted in successful discrimination of nine reference strains and four isolates of food origin. Since these methods are not always accurate owing to their high genetic homogeneity, it is advisable to use more than one method for the identification of L. casei and closely related species. Copyright © 2012 Society of Chemical Industry     

Molecular identification of five commercial flatfish species by PCR–RFLP analysis of a 12S rRNA gene fragment

Refrigerated or frozen fillets of commercial flatfish species are sometimes mislabelled, and identification of those products is needed to avoid fraudulent substitution. Molecular identification of five commercial flatfish species (order Pleuronectiformes), ie Lepidorhombus whiffiagonis (megrim), Platichthys flesus (flounder), Reinhardtius hippoglossoides (Greenland halibut), Scophthalmus maximus (turbot) and Solea vulgaris (= S solea) (sole), has been carried out on the basis of the amplification of an approximately 433 bp segment from the mitochondrial 12S rRNA gene using the polymerase chain reaction (PCR) and universal primers. Direct DNA sequencing from two PCR products for each flatfish species was carried out, and sequences were used to select six restriction enzymes. PCR products of 15 individuals of each species were cut with each enzyme, resulting in species‐specific restriction fragment length polymorphism (RFLP). The five flatfish species could be identified by application of the restriction enzyme AluI as well as by using different combinations of a pair of enzymes, ie DdeI and either AciI or MwoI. No intraspecific genetic polymorphism was found for any of the six enzymes. Results confirmed the usefulness of this technique to distinguish and genetically characterise refrigerated or frozen pieces of these five flatfish species. Copyright © 2003 Society of Chemical Industry     

Detection of pig derivatives in food products for halal authentication by polymerase chain reaction –restriction fragment length polymorphism

A method for detection of the presence of pig derivatives in three types of food products—sausages and casings, bread and biscuits—using polymerase chain reaction–restriction fragment length polymorphism (PCR‐RFLP) analysis of a conserved region in the mitochondrial (mt) cytochrome b (cyt b) gene was developed. Genomic DNA of sausages and casings, bread and biscuits were extracted. The genomic DNA from the food products were found to be of good quality for the sausages and produced clear PCR products on the amplification of the mt cyt b gene of approximately 360 base pairs (bp). However, no genomic DNA was detected from the casing samples and poor quality of genomic DNA was extracted from bread and biscuits. No amplification of mt cyt b gene was produced from bread and biscuit samples. To differentiate between samples, the amplified PCR products were digested with restriction enzyme (RE) BsaJI, resulting in species‐specific RFLP. The cyt b PCR‐RFLP species identification assay gave excellent results for detection of pork adulteration in food products and is a potentially reliable technique to avoid species adulteration or fraudulent species substitution for halal authentication. Copyright © 2006 Society of Chemical Industry     

Development of novel species‐specific primers for species identification of the Lactobacillus casei group based on RAPD fingerprints

BACKGROUND: It is difficult to clearly distinguish and identify specific species of the Lactobacillus casei group using phenotypic and genotypic (16S ribosomal DNA sequence analysis) techniques alone. Some species of this group are probiotic and are widely used in the food and feed industries. The objective of this study was to develop species‐specific primers based on randomly amplified polymorphic DNA (RAPD) fingerprinting for species identification within the closely related L. casei group of bacteria. RESULTS: Three random primers termed OPT‐14, OPA‐11 and OPT‐16 were developed for analysis. The primer pairs each produced a species‐specific band found only in the tested Lactobacillus rhamnosus, Lactobacillus paracasei subsp. tolerans and Lactobacillus zeae isolates respectively. These specific fragments were then sequenced for further analysis. The species‐specific primers were designed according to cloned sequencing, which was employed for polymerase chain reaction (PCR) with the template DNA of Lactobacillus strains. Single 102, 179 and 451 bp species‐specific bands were found only in L. rhamnosus, L. paracasei subsp. tolerans and L. zeae respectively. CONCLUSION: Using PCR, the novel species‐specific primers have been shown to rapidly, accurately and effectively identify species of L. rhamnosus, L. paracasei subsp. tolerans and L. zeae from within the L. casei group of probiotic bacteria. Copyright © 2009 Society of Chemical Industry     

Detection of Panax quinquefolius in Panax ginseng using 'subtracted diversity array'

BACKGROUND: Food adulteration remains a major global concern. DNA fingerprinting has several advantages over chemical and morphological identification techniques. DNA microarray‐based fingerprinting techniques have not been used previously to detect adulteration involving dried commercial samples of closely related species. Here we report amplification of low‐level DNA obtained from dried commercial ginseng samples using the Qiagen^? REPLI‐g^® Kit. Further, we used a subtracted diversity array (SDA) to fingerprint the two ginseng species, Panax ginseng and Panax quinquefolius, that are frequently mixed for adulteration. RESULTS: The two ginseng species were successfully discriminated using SDA. Further, SDA was sensitive enough to detect a deliberate adulteration of 10% P. quinquefolius in P. ginseng. Thirty‐nine species‐specific features including 30 P. ginseng‐specific and nine P. quinquefolius‐specific were obtained. This resulted in a feature polymorphism rate of 10.5% from the 376 features used for fingerprinting the two ginseng species. The functional characterization of 14 Panax species‐specific features by sequencing revealed one putative ATP synthase, six putative uncharacterized proteins, and two retroelements to be different in these two species. CONCLUSION: SDA can be employed to detect adulterations in a broad range of plant samples. Copyright © 2011 Society of Chemical Industry     

Molecular identification of dried squid products sold in China using DNA barcoding and SYBR green real time PCR

ABSTRACT

Dried squid products are popular in China as a snack food, side dishes, or refreshments, and the market appeal can be reflected by the high price that occasionally reaches 497 RMB per kg. However, the absence of harmonisation around the definition of squid, as well as the problems with visual inspection for processed seafood products, make alternative species substitution for dried squid products a frequent occurrence. The aim of the present study was to apply a DNA barcoding approach for species identification of 48 dried squid products collected from the largest online shopping platform in China. Moreover, we also developed a novel SYBR green real-time PCR assay (simplex and duplex followed by a melting curve analysis) specific for Illex argentinus and Todarodes pacificus based on cytochrome C oxidase subunit I (COI) gene.

Results highlighted the successful DNA extraction and PCR amplification of a 655 bp COI gene fragment from all products. A maximum similarity value in the range of 98-100% was obtained for all readable sequences using the BOLD and BLAST public databases and four species (Dosidicus gigas, Uroteuthis edulis, I. argentinus, and T. pacificus) were identified. The specificity of the designed primer sets was confirmed against 23 non-target species, and the newly developed methods were successfully applied to screen I. argentinus and T. pacificus in dried squid products.

Overall, DNA barcoding is a robust tool for seafood species identification and the novel method is effective in screening I. argentinus and T. pacificus in food products.     

PCR-RFLP Analysis of Mitochondrial DNA for Identification of Snail Meat Species

Several species of land snails, including Helix pomatia and Helix lucorum are consumed as food products. The main source of commercial competition is an imported African snail, Achatina fulica. The only way to distinguish between these species has been morphologically. We hypothesized a reliable method for identifying canned snails could be based on using PCR-RFLP analysis of mito-chondrial DNA. The molecular weights of the amplified fragments were perfectly identical, regardless of low extraction (fresh snails or cooked and canned samples). The whole amplified products (16S rRNA and 12S rRNA) made it possible to check any fraudulent label and identify the three species using four restriction enzymes (RFLP).     

Survey of authenticity of meat species in food products subjected to different technological processes,by means of PCR-RFLP analysis

Polymerase chain reaction (PCR) coupled to restriction-fragment length polymorphism analysis (RFLP) was considered for exploring the incidence of incorrect labelling in food products containing one or more meat species. Universal primers CYT b1/CYT b2, which amplify a variable region of the mitochondrial cytochrome b of vertebrates, and endonucleases PalI, MboI, HinfI and AluI were used for this purpose. Fifty food products, nine of them raw or cured and the other 41 subjected to a variety of technological processes such as pre-cooking and freezing, cooking and smoking, dehydration or sterilisation, were investigated. Twenty of the 50 products declared mixtures of meat species on their labels. Fifteen (30%) of the 50 food samples investigated displayed an incorrect qualitative labelling. While this affected only one (11.1%) of the nine raw/cured products, 14 (34.2%) of the 41 products subjected to some type of heat-processing were not correctly labelled. The undeclared presence of turkey was the most frequent concern, since it was detected in seven food products. The complete absence of a declared species of high commercial value—such as beef or roe-deer—was observed in another four cases. The PCR-RFLP method used here proved to be a rapid and easy-to-perform two-step analytical approach to achieve qualitative meat species identification in raw and cooked food products containing one or more different species.     

Species identification of ruminant milk by genotyping of the κ-casein gene

The development of molecular genetic and bioinformatic systems for identifying the species of milk and the raw material composition of dairy products is of great scientific and practical importance with the purpose of introducing developments in the system for controlling the turnover of falsified products. The aim of the research is to develop a method of PCR-RFLP analysis for species identification of milk and dairy products from agricultural ruminant animals by the κ-casein gene (CSN3) with the possibility of qualitative and relative quantitative assessment of species-specific DNA of the tested biomaterial. The objects of research were samples of raw milk and milk powder, pasteurized cream, and hard and semi-hard cheeses. The developed method of species identification of milk and dairy products includes sample preparation of the studied samples, nucleic acid extraction, combined PCR-RFLP technique, detection of obtained results by the method of horizontal electrophoresis in agarose gel and their analysis, including using the developed mathematical algorithms and software. The synergistic effect established in combined operation of 2 restriction enzymes ensured their application in a mix with increased performance in an ergonomic way in the context of DNA authentication of cow, goat, and sheep milk and dairy products based on them. The specificity and sensitivity of the proposed method is potentially suitable for implementing the development of a system to control the turnover of falsified and counterfeit goods.     

主要进出口经济鱼类及其制品分子鉴定技术的研究进展

随着我国进出口贸易的不断发展,进出口鱼类品种繁多,数量巨大。但部分国内外企业受高额利润驱使,以假充真、以劣充好事件时有发生,鱼类制品更是真伪难辨,掺假状况极其普遍。通过形态学和生物学方法已经不能满足对鱼类种属鉴定。近年来,随着分子生物技术的迅猛发展,分子检测技术在鱼类品种鉴定领域得到广泛应用。本文针对不同分子鉴定技术进行阐述,包括普通聚合酶链反应(polymerase chain reaction,PCR)技术、多重PCR技术、实时定量PCR技术、DNA条形码技术、环介导等温扩增检测技术(loop-mediated isothermal amplification,LAMP)、聚合酶链反应-限制性酶切多态性技术(polymerase chain reaction-restriction fragment length polymorphism,PCR-RFLP)以及随机扩增多态性DNA检测技术(random amplified polymorphic DNA),并根据不同检测技术的特点进行分析,为进出口鱼类鉴定提供技术支撑。     

Species identification of Wickerhamomyces anomalus and related taxa using β‐tubulin (β‐tub) DNA barcode marker

Wickerhamomyces anomalus is used in food and feed processing, although the species has been reported as an opportunistic human pathogen, predominantly in neonates. Neither phenotypic nor the most frequently applied genotypic marker (D1/D2 LSU ribosomal DNA) provide sufficient resolution for accurate identification of this yeast. In this study, the β‐tubulin gene was used for species identification by direct DNA sequencing and as marker in a species‐specific PCR assay. The results showed that all examined W. anomalus strains were clearly distinguished from the closely related species by comparative sequence analysis of the β‐tubulin gene. In addition, the species‐specific primers were also developed based on the β‐tubulin gene, which was employed for polymerase chain reaction with the template DNA of Wickerhamomyces strains. A single 218 bp species‐specific band was found only in W. anomalus. Our data indicate that the phylogenetic relationships between these strains are easily resolved by sequencing of the β‐tubulin gene and combined with species‐specific PCR assay. Copyright © 2012 John Wiley & Sons, Ltd.     

Reliability of Listeria monocytogenes Identification by Specific PCR Assessed by Phenotypic and Genotypic Techniques

This study evaluates the possibility of using polymerase chain reaction (PCR) for rapid identification of food-borne Listeria monocytogenes as an alternative to API Listeria system and estimates the incidence of API Listeria misidentifications in food-borne Listeria species. A total of 198 strains, 11 L. monocytogenes, 28 other Listeria species, and 159 food isolates were phenotypically and genotypically characterized by API Listeria profiles and randomly amplified polymorphic DNA (RAPD) profiles, respectively. They were also tested for PCR amplification using genus- and species-specific primers. Clustering analysis of phenotypic and genotypic data showed discrepancies in species identification of some isolates by API Listeria profiles. Their identities were confirmed by 16S rDNA sequencing, and thus, it was revealed that 33% of Listeria innocua and 19% of Listeria welshimeri were misidentified as L. monocytogenes by API Listeria profiles. Reliable identification of L. monocytogenes was obtained by LM1–LM2 specific primers which allowed PCR amplification only in reference strains and isolates previously identified as L. monocytogenes by RAPD and 16S rDNA sequence analysis. These results corroborate the suitability of specific PCR as a rapid and accurate test for the identification of L. monocytogenes, avoiding misidentification with other Listeria species commonly found in food products.     

Nuclear DNA barcodes for cod identification in mildly-treated and processed food products

Gadoids are a group of fish with historical importance in the fishing industry. The high demand for cod is one of the reasons why cod products are often mislabelled, and numerous observations have been made on the replacement of Atlantic cod (Gadus morhua) by cheaper species or its illegal capture in contravention of fish quotas. Fish species identification is traditionally based on morphological features, but this may be difficult in case of heat-treated or processed products, or where the species look similar, as in the Gadoid group. DNA-based approaches (using either nuclear or mitochondrial DNA) are most commonly used in this case, due to their high specificity and to the high resilience of the target molecules to food processing techniques. In this article, we identified, using an automated screening approach, novel barcode regions and their associated primers in the nuclear genome, to be used for the efficient identification of Gadoids. The barcode regions were tested on official and commercial samples, raw or mildly treated products, like frozen, or salted, as well as pre-cooked complex mixtures and processed samples, using next-generation sequencing (NGS) technique. The method proposed could complement existing fish identification strategies in establishing an efficient framework to detect and prevent frauds along the food chain.     

Microbiological evaluation and molecular characterization of bifidobacteria strains in commercial fermented milks

The aim of this study was to evaluate the presence of Bifidobacterium animalis subsp. lactis in commercial dairy products using different molecular techniques. We analyzed the microbiological composition of 13 commercial fermented milks available in the Spanish market. Thirteen strains of genus Bifidobacterium were isolated from these products and were identified by genus-specific PCR, by fluorescence in situ hybridization (FISH), by multiplex PCR and amplified ribosomal DNA restriction analysis (ARDRA). The same sets of strains were typed by randomly amplified polymorphic DNA (RAPD) analysis and by amplified fragment length polymorphism technique (AFLP). All strains were identified as B. animalis subsp. lactis using ARDRA and multiplex PCR techniques. Similarity between strains was evaluated based on RAPD and AFLP profiles. The isolated strains showed similar profiles by using these techniques, revealing the reduced genetic variability existing among commercial strains, and all these profiles were reproducible in repeated analysis. ARDRA and multiplex PCR are techniques that allow differentiation of the bifidobacteria at genus and species level, but do not indicate if they are different strains, for which reason the RAPD technique is very useful. All bifidobacteria isolated from commercial fermented milks in Spain belong to the same species B. animalis subsp. lactis. Our results demonstrate the necessity to control the presence of bifidobacteria in commercial fermented milks, not only at species level but also at strain level. Multiplex PCR and RAPDs are the most suitable, rapid and precise techniques to identify all bifidobacteria contained in fermented milk products at genus-, species-, and strain levels.