Next Generation Sequencing-based DNA metabarcoding for animal species profiling in fish feed

The expansion of worldwide aquaculture has been accompanied by extensive growth in the fish feed industry. However, improper labelling of many commercially available fish feeds has raised security and safety concerns over the species' origin of the ingredients. The inclusion of ruminants-derived ingredients in fish feed is prohibited according to EU legislation while porcine inclusion in fish feed has been a great concern among Muslim farmers. In contrast to the limited species that could be simultaneously determined using multiplex PCR, this study utilised Next Generation Sequencing-based DNA metabarcoding assay to determine the compositional profiles of animal species in fish feed samples in a more holistic manner. In relation to the religious issue associated with porcine-derived ingredients in fish feed, this study firstly aimed to determine the sensitivity of the methods in profiling fish feed adulterated with porcine blood and muscle tissues. Next, 10 commercially available fish feed samples were analysed. As a result, a detection limit of as low as 3% (w/w) porcine muscle and blood in the laboratory-prepared fish feed was obtained. The analysis of 10 commercial fish feeds shows surprising findings: 50% of the feeds contain Sus scrofa and 80% contain Bos taurus, a ruminant. Only one commercial fish feed was found to be solely composed of marine species. This study shows that commercial fish feeds sold in Malaysia contain undesirable animal species, and emphasises the need for accurate and legally enforced labelling of mammalian species in fish feed products.

A vertebrate-specific qPCR assay as an endogenous internal control for robust species identification

The identification of vertebrate species is important in numerous fields including archaeology, ecology, as well as food and forensic sciences. Real-time quantitative PCR (qPCR) assays specific for one vertebrate species are promising approaches for species identification, although there are several drawbacks such as difficulty determining whether the detected DNA is authentic or a contaminant. Here, we describe a qPCR assay specific for vertebrate mitochondrial DNA (mtDNA) which can overcome these drawbacks. Since we found that mitochondrial 16S rRNA contains regions that are perfectly (not highly) conserved across virtually all vertebrates, but are variable in invertebrates, we were able to design a vertebrate-specific qPCR assay by placing primers/probe within these regions. The specificity and accuracy of this assay were validated with representative vertebrate and invertebrate samples. This assay detected DNA from all vertebrate samples, but not from any invertebrate samples. In addition, this assay was able to quantify vertebrate mtDNAs as accurately as previously reported species-specific qPCR assays. The results demonstrated it is feasible to quantify vertebrate mtDNA specifically and accurately in a sample. This means that it is possible to determine the ratio of specific vertebrate species mtDNA to total vertebrate mtDNA in a sample. In conjunction with this assay as an endogenous internal control, species-specific qPCR assays will allow for the robust identification of vertebrate species.

Mitochondrial Markers for the Detection of Duck Breeds Using Polymerase Chain Reaction

Species identification of the components of various duck breeds has revealed that the lowest identifiable number of components depends on the breed. The results (shown on the agarose gel) of a species-specific PCR reaction for Rouen ducks were less intense than the results for the same amount of components from other popular duck breeds, suggesting differences in the Rouen duck genome. Therefore, the present study aimed to identify part of the Rouen duck’s gene sequences and to develop two new primer pairs. The first pair enables breed-independent identification of duck DNA, and the second distinguishes Rouen ducks from Chinese and Indian Runner ducks. The sequencing reaction yielded sequences of 1386 bp in length, and the identified sequence differs by around 7% from the sequences of Chinese duck species. The detected sequence contributes to improving species identification methods for duck DNA. On its basis, two primers for the identification of duck DNA were designed. The first allows for DNA amplification with the same sensitivity regardless of duck breed. The second primer’s pair is breed specific, and it distinguishes Rouen ducks from Chinese and Indian Runner ducks. Both methods are very sensitive (0.05%).

Improved triplex real-time PCR with endogenous control for synchronous identification of DNA from chicken, duck, and goose meat

The authentication and labeling of meat products, concerning origins and species, are key to fair trade and to protect consumer interests in the market. We developed an improved triplex real-time PCR approach to simultaneously identify chicken, duck, and goose DNA in meat, including an endogenous control to avoid false negatives. Our method specifically detected DNA from chicken, duck, and goose, and showed no cross-reaction with DNA extracted from other meat types. The detection limits of chicken, duck, and goose DNA were 0.001-0.00025 ng, 0.0025-0.0001 ng, and 0.001-0.00001 ng, respectively, and we were able to simultaneously identify DNA from two distinct origins using as little as 0.1% of total meat weight. Our newly generated triplex real-time PCR method with endogenous control exhibited high specificity, sensitivity, and efficiency for simultaneous identification of DNA from chicken, duck, and goose in meat.

The Quality of DNA Isolated from Processed Food and Feed via Different Extraction Procedures

The extraction of DNA is a critical step for species identification by PCR analysis in processed food and feed products. In this study, eight DNA extraction procedures were compared—DNeasy Blood and Tissue Kit, DNeasy mericon Food Kit, chemagic DNA Tissue 10 Kit, Food DNA Isolation Kit, UltraPrep Genomic DNA Food Mini Prep Kit, High Pure PCR Template Preparation Kit, phenol—chloroform extraction, and NucleoSpin Food—Using self-prepared samples from both raw and heat-processed and/or mechanically treated muscles and different types of meat products and pet food (pork, beef, and chicken). The yield, purity, and suitability of DNA for PCR amplification was evaluated. Additionally, comparisons between the effectiveness of various extraction methods were made with regard to price, and labor- and time-intensiveness. It was found that the DNeasy mericon Food Kit was the optimal choice for the extraction of DNA from raw muscle, heat-treated muscle, and homemade meat products from multiple and single species.

Bridging legal requirements and analytical methods: a review of monitoring opportunities of animal proteins in feed

Availability and safety of food ranks among the basic requirements for human beings. The importance of the food producing sector, inclusive of feed manufacturing, demands a high level of regulation and control. This paper will present and discuss the relationships in the triangle of legislation, the background of hazards with a biological nature, and opportunities for monitoring methods, most notable for prion-based diseases as primary issue. The European Union legislation for prevention of prion-based diseases since 2000 is presented and discussed. The definitions and circumscriptions of groups of species will be analysed in the view biological classification and evolutionary relationships. The state of the art of monitoring methods is presented and discussed. Methods based on visual markers (microscopy), DNA-based methods (PCR), protein-based methods (ELISA, mass spectroscopy, proteomics), near infrared oriented methods and combinations thereof are being evaluated. It is argued that the use in legislation of non-homogeneous groups of species in a biological sense will hamper the optimal design of monitoring methods. Proper definitions are considered to act as bridges between legal demands and suitable analytical methods for effective monitoring. Definitions including specified groups of species instead of single species are more effective for monitoring in a range of cases. Besides the desire of precise circumscription of animal groups targeted by legislation, processed products need well defined definitions as well. Most notable examples are blood versus blood products, and hydrolysis of several types of material. The WISE principle for harmonising the design of legislation and of analytical methods is discussed. This principle includes the elements Witful (reasonable legal principles), Indicative (clear limits between prohibition and authorisation), Societal demands (public health, environment, economy), and Enforceable (presence of suited monitoring methods) in order to promote a balanced effort for reaching the desired level of safety in the food production chain.

A quantitative polymerase chain reaction assay for the detection of equine (horse and donkey)-originated meat in processed bovine meat products

Meat is one of the most important basic foodstuffs in human nutrition. Nowadays, adulteration and authenticity are common problems for meat products. Identification of meat species is important in terms of consumer protection and prevention of adulteration. There are different methods to determine adulteration of meat and meat products. These methods are histological controls, serological tests, and quantitative polymerase chain reaction. In this study, species identification and quantification analysis of meat and meat products were done by using horse-, donkey-, and bovine-specific primers with quantitative polymerase chain reaction method. Triple meat mixtures containing horse and donkey meat ranging from 0.1 to 50% levels were prepared within a bovine mixture for using species identification and quantification analysis. The method specificity was confirmed by melting curve analysis. In conclusion, quantitative polymerase chain reaction is an easy, rapid, and reliable method for meat species identification, and with this study an applicable method was developed for the detection and quantification of equine-originated meat in bovine meat products.

Rapid bovine and caprine species identification in ruminant feeds by duplex real-time PCR melting curve analysis using EvaGreen fluorescence dye

A duplex real-time PCR assay with melting curve analysis, using the EvaGreen fluorescence dye, was developed for rapid and reliable identification of bovine and caprine in ruminant feeds. The method merges the use of bovine (Bos taurus) and caprine (Capra hircus) specific primers that amplify small fragments (bovine 96 bp and caprine 142 bp) of the mitochondrial 16S rRNA and 12S rRNA genes, respectively. DNA was isolated from heat-treated meats (133 °C/3 bar for 20 min) mixtures of bovine and caprine and was used to optimize the assay. Gene products of caprine and bovine produced two distinct melting peaks simultaneously at 82 and 86.8 °C, respectively. Duplex analysis of the reference samples showed that the detection limit of the assay was 0.003 % for bovine and 0.005 % for caprine species. The aim of this study was to develop a duplex real-time PCR assay followed by a melt curve step for sensitive, rapid, specific, and cost-effective detection of bovine and caprine species based on the amplicon melting peak in ruminant feeds to prevent Transmissible Spongiform Encephalopathies.

A new specific reference gene based on growth hormone gene (GH1) used for detection and relative quantification of Aquadvantage® GM salmon (Salmo salar L.) in food products

Genetic transformation of fish is mainly oriented towards the improvement of growth for the benefit of the aquaculture. Actually, Atlantic salmon (Salmo salar) is the species most transformed to achieve growth rates quite large compared to the wild. To anticipate the presence of contaminations with GM salmon in fish markets and the lack of labeling regulations with a mandatory threshold, the proper methods are needed to test the authenticity of the ingredients. A quantitative real-time polymerase chain reaction (QRT-PCR) method was used in this study. Ct values were obtained and validated using 15 processed food containing salmon. The relative and absolute limits of detection were 0.01% and 0.01 ng/μl of genomic DNA, respectively. Results demonstrate that the developed QRT-PCR method is suitable specifically for identification of S. salar in food ingredients based on the salmon growth hormone gene 1 (GH1). The processes used to develop the specific salmon reference gene case study are intended to serve as a model for performing quantification of Aquadvantage® GM salmon on future genetically modified (GM) fish to be commercialized.

Development of a sensitive and specific multiplex PCR method for the simultaneous detection of chicken, duck and goose DNA in meat products

Identifying the origin of animal species in manufactured meat products is of considerable economic, religious and sanitary importance. In this study, we developed a multiplex PCR method to simultaneously detect chicken, duck and goose DNA in meat products derived from beef, pork, mutton or quail. The PCR primers were designed based on the sequence of mitochondrial genes of each avian species, and the amplicon sizes were 131, 283 and 387bp for chicken, duck and goose, respectively. The method had no cross-reaction with DNA isolated from beef, mutton, pork or quail, and generated products at a target DNA content as low as 0.05ng, or a target meat content of 1% of total meat weight. Moreover, screening of 24 commercial meat samples using this method indicated that six, two and one samples were contaminated with chicken, duck, or both, respectively, suggesting its usefulness for the simultaneous identification of chicken, duck and goose DNA in commercial meat products.

Detection of rabbit and hare processed material in compound feeds by TaqMan real-time PCR

Food and feed traceability has become a priority for governments due to consumer demand for comprehensive and integrated safety policies. In the present work, a TaqMan real-time PCR assay targeting the mitochondrial 12S rRNA gene was developed for specific detection of rabbit and hare material in animal feeds and pet foods. The technique is based on the use of three species-specific primer/probe detection systems targeting three 12S rRNA gene fragments: one from rabbit species, another one from hare species and a third fragment common to rabbit and hare (62, 102 and 75 bp length, respectively). A nuclear 18S rRNA PCR system, detecting a 77-bp amplicon, was used as positive amplification control. Assay performance and sensitivity were assessed through the analysis of a batch of laboratory-scale feeds treated at 133°C at 3 bar for 20 min to reproduce feed processing conditions dictated by European regulations. Successful detection of highly degraded rabbit and hare material was achieved at the lowest target concentration assayed (0.1%). Furthermore, the method was applied to 96 processed commercial pet food products to determine whether correct labelling had been used at the market level. The reported real-time PCR technique detected the presence of rabbit tissues in 80 of the 96 samples analysed (83.3%), indicating a possible labelling fraud in some pet foods. The real-time PCR method reported may be a useful tool for traceability purposes within the framework of feed control.

Novel real-time PCR method based on growth hormone gene for identification of Salmonidae ingredient in food

To avoid fraudulent substitutions in fish markets, the proper methods are needed to test the authenticity of the ingredients. As a preferable methodology, a quantitative real-time polymerase chain reaction (qPCR) method was used in this study to identify species from the Salmonidae family based on the salmon growth hormone gene. Fish samples of six genera from the Salmonidae family were tested to identify the specificity, sensitivity, and applicability of the established method. Results showed that the method was highly specific for salmonid detection. Ct values were obtained only from 31 Salmonidae fish species samples. The relative and absolute limits of detection were 0.01% and 25 pg of genomic DNA, respectively, which could meet with the requirements of routine detections. To test the applicability of the method, the content of salmonid ingredients in 16 commercial food products was quantified from standard curves constructed from DNA of two Salmonidae species. The results revealed that the salmonid ingredient was detected in 12 samples, indicating that 25% of the labels are inauthentic. These results demonstrate that the developed qPCR method is suitable for identification of Salmonidae ingredients.