A SYBR Green real-time PCR assay to detect and quantify pork meat in processed poultry meat products

Enhancing the authenticity of animal by-products: harmonization of DNA extraction methods from novel ingredients

Introduction: The increasing global pressure to explore alternative protein sources derived from animal by-products has opened-up opportunities, but it has also created the need to assess their compliance with labelling statements, to ensure consumer's trust in the composition of both feed and food products. Assessing the authenticity of highly processed animal by-products, particularly within the rapidly expanding Halal food market, presents a significant challenge due to the lack of robust and standardized methodologies. However, the success of DNA based authenticity system is highly dependent on the extracted DNA quantity, quality, and purity ratios from heterogeneous matrices. Material and methods: In this work, nine DNA extraction methods were tested on selected processed animal by-products with high-value and interest for the feed industry: meals from poultry meat, blood and feather, and hydrolysates from swine meat and bone, fish, and black soldier fly. The proposed DNA extraction methods are developed to specifically target swine-specific mitochondrial region, as a case study. Results and discussion: Both the conventional CTAB method and the commercial kits, specifically Invisorb® Spin Tissue Mini and NucleoSpin™ Food, demonstrated superior extraction efficiency and quality ratios. Nevertheless, commercial kits enabled faster detection in comparison to the conventional methods. The absence of swine DNA was successfully validated and confirmed in all animal meals and hydrolysates that did not contain swine in their composition beforehand, demonstrating their compliance with the Halal market requirements.

Development and intralaboratory validation of three Arcidae species using a multiplex polymerase chain reaction assay combined with capillary electrophoresis

Recently, various commercial ark shell products were being sold, and in the case of processed foods, the loss of morphological traits makes species identification visually challenging, which can lead to seafood fraud. Therefore, a multiplex polymerase chain reaction (PCR) assay was developed to simultaneously identify three ark shells. The specific PCR amplicon sizes of the generated species-specific primer pairs were observed to be 99 bp for Anadara kagoshimensis, 148 bp for Anadara broughtonii, and 207 bp for Tegillarca granosa. Specificity was confirmed for 17 fish and shellfish, and only the target was amplified without cross-reactivity. The detection limit for the multiplex PCR assay was 1 pg. Furthermore, 31 commercial products were evaluated to assess the developed assay's applicability. Therefore, the analytical approach used in this study can rapidly and accurately identify ark shells in commercial food, and may be used as an authentication tool in the seafood industry.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-023-01269-2.

Towards DNA-Based Methods Analysis for Honey: An Update

Honey is a natural product widely consumed all over the world due to its relationship with healthy benefits. Additionally, environmental and ethical issues have a higher weight in the consumer's choice to buy honey as a natural product. Following the high demand of this product, several approaches have been suggested and developed aiming at the assessment of honey's quality and authenticity. Target approaches, such as pollen analysis, phenolic compounds, sugars, volatile compounds, organic acids, proteins, amino acids, minerals, and trace elements, showed an efficacy, particularly concerning the honey origin. However, a special highlight is given to DNA markers, due to their useful applicability in environmental and biodiversity studies, besides the geographical, botanical, and entomological origins. Different DNA target genes were already explored for addressing diverse sources of honey DNA, with DNA metabarcoding attaining a relevant importance. This review aims to describe the latest advances on DNA-based methods applied in honey related studies, identifying the research needs for the development of new and additional required methodologies, and to select the most adequate tools for future research projects.

Rapid On-Site Identification for Three Arcidae Species (Anadara kagoshimensis, Tegillarca granosa, and Anadara broughtonii) Using Ultrafast PCR Combined with Direct DNA Extraction

Granular ark (Tegillarca granosa), broughton's ribbed ark (Anadara broughtonii), and half-crenate ark (Anadara kagoshimensis) are important fishery resources throughout Asia; granular ark exhibiting a higher economic value due to its rarity. However, due to the similar morphological characteristics of the three species, the less valuable species could be exploited for food fraud. In this study, we developed a rapid on-site identification method based on a microfluidic chip for the detection of the three ark shell species. We designed new species-specific primers, targeting the genes encoding mitochondrial cytochrome b or cytochrome c oxidase I, for the identification of the three ark shells and estimated their specificity against 17 species, which amplified only the target species. The sensitivity of each primer was 0.001 ng. In addition, this method was further improved to develop a direct ultrafast polymerase chain reaction (PCR) for on-site food monitoring, which would allow for completing the entire procedure (from sampling to obtaining the results) within 25 min without DNA extraction. Our direct, ultrafast PCR was successfully applied to differentiate the three species from 29 commercial products. Therefore, this assay could be used as a rapid and cost-effective approach for the on-site identification of ark shells in commercial food products.

Identification of meat species in processed meat products by using protein based laser induced breakdown spectroscopy assay

The detection of meat fraud and mislabeling in processed meat products is a raising concern for consumers. The aim of this study was to develop and demonstrate the potential of protein-based laser induced breakdown spectroscopy (LIBS) method to be used for the identification of beef, chicken, and pork in fermented sausage and salami products. In this respect, bulk protein and protein fractions rich in sarcoplasmic and myofibrillar protein of sausage and salami products were obtained and subjected to LIBS analysis. LIBS spectrum was evaluated with chemometric methods to classify meat species and determine adulteration ratio by using principal component analysis and partial least square analysis, respectively. Limit of detection values for chicken and pork adulteration in beef sausage were found as 3.68 and 3.83% for myofibrillar fraction, while those values in beef salami were found as 3.80 and 3.47% for sarcoplasmic fraction, respectively.

Multiplex PCR Assay for Simultaneous Identification of Five Types of Tuna (Katsuwonus pelamis, Thunnus alalonga, T. albacares, T. obesus and T. thynnus)

There is a need to identify the species of similar types of fish, especially those that are commercially sold. Particularly, the price of tuna varies depending on its type, which is difficult to determine as they are sold in cut or processed forms. This study developed a multiplex polymerase chain reaction (PCR) assay to identify the five most common tuna species: bigeye, skipjack, Atlantic bluefin, albacore, and yellowfin tunas. Newly designed species-specific primer sets for these five tuna species were created. Subsequently, the amplicon sizes obtained were 270, 238, 200, 178, and 127 base pairs for bigeye, skipjack, Atlantic bluefin, albacore, and yellowfin tunas, respectively. Each primer’s specificity was further tested using 15 other fish species, and no cross-reactivity was observed. To identify multiple targets in a single reaction, multiplex PCR was optimized to increase its resolution and accuracy. The detection levels of the multiplex PCR assay were confirmed to be 1 pg for all the five tunas. Additionally, it was successfully applied to 32 types of commercial tuna products. Therefore, this multiplex PCR assay could be an efficient identification method for various tuna species.

Evaluation of High Resolution Melting (HRM) Analysis for Meat Species Identification of Raw and Cooked Meat

The current study aimed to examine a real-time PCR assay with high-resolution melting (HRM) analysis for the species identification of minced meat samples. Meat samples from several animal species were purchased and minced separately or as a mixture of two species. DNA was extracted from all meat samples and subjected to real-time PCR assay by amplifying species-specific mitochondrial cytochrome b regions. Regarding the meat mixtures, two separate melting curves with specific melt peak temperatures (Tm) were detected. Additionally, DNA from each species was quantified, based on the calibration curves. The results showed that a real-time PCR assay with HRM analysis is suitable for the species identification of meat products, and could be used for the detection of meat frauds.

Immunochromatographic Detection of Myoglobin as a Specific Biomarker of Porcine Muscle Tissues in Meat Products

An immunochromatographic detection of myoglobin (MG) as a specific marker of porcine muscle tissue has been developed. The method is based on the sandwich lateral flow immunoassay (LFIA) with gold nanoparticles (AuNPs) as a label. The developed test system determines MG with a detection limit of 5 ng mL−1 within 15 min. A specific determination of porcine MG and no cross-reactivity with MG from other tested mammals and bird species was demonstrated. The test system is able to detect pork additives, as low as 0.01% (w/w), in minced beef. A technique of MG extraction from muscle tissue has been proposed which allows for rapid and efficient MG extraction from meat samples (within 20 min). The developed test system can serve as an effective means of controlling the authenticity and quality of meat products.

Simultaneous and accurate visual identification of chicken, duck and pork components with the molecular amplification integrated lateral flow strip

We propose a visual strategy for simultaneous detection of multiple adulterated components in beef by integration of multiple polymerase chain reaction (mPCR) with the lateral flow strip (LFS). The primer sets for adulterated components are uniquely designed with different nucleic acid tags (NAT), enabling the amplicons with specific wobbled sequences at two opposite ends. The wobbled sequences will precisely hybridize with the pre-immobilized capture probes on T lines (T1, T2 and T3) and C line, contributing to the coloration of LFS. Taking advantages of extraordinary amplification efficiency of PCR and simplicity of LFS, common adulterated components including chicken, duck and pork can be easily detected with LOD as low as 0.01% (wt%), which is comparable to that of quantitative real-time polymerase chain reaction (qPCR) but with more simplified operations and reduced costs. The method can be extended to identification of other components by replacing the functional primer set. This method can be a useful candidate for meat quality control at the resource-limited setups.

Safety, Quality and Analytical Authentication of ḥalāl Meat Products, with Particular Emphasis on Salami: A Review

Only some animal species could be transformed into ḥalāl salami and the raw meat must be obtained from ritually slaughtered animals. Several scientific studies have been conducted on ritual slaughtering practices and manufacturing of meat products for Jewish and Muslim religious communities; furthermore, many projects have been funded by the European Community on this topic. The authenticity and traceability of meat is one of the priorities of ḥalāl food certification systems. The pig matrix (meat and/or lard) may be fraudulently present in ḥalāl processed meat, as well as salami, for both economic and technological purposes; in fact, the use of these raw materials reflects the easier availability and their lower cost; furthermore, it allows manufacturers to obtain final products with better quality (sensory properties) and stability (especially with respect to oxidative reactions). The aim of this review is to discuss the qualitative and technological aspects of ḥalāl raw meat for dry fermented sausages (salami); moreover, this study focuses on the most recent studies carried out on the certification system and on the analytical methods performed in order to solve problems such as fraud and adulteration of ḥalāl salami and other halal meat foods.

Comparison of Real-Time PCR Quantification Methods in the Identification of Poultry Species in Meat Products

Poultry meat is consumed worldwide and is prone to food fraud because of large price differences among meat from different poultry species. Precise and sensitive analytical methods are necessary to control poultry meat products. We chose species-specific sequences of the cytochrome b gene to develop two multiplex real-time polymerase chain reaction (real-time PCR) systems: one for chicken (Gallus gallus), guinea fowl (Numida meleagris), and pheasant (Phasianus colchicus), and one for quail (Coturnix japonica) and turkey (Meleagris gallopavo). For each species, added meat could be detected down to 0.5 % w/w. No cross reactions were seen. For these two real-time PCR systems, we applied three different quantification methods: (A) with relative standard curves, (B) with matrix-specific multiplication factors, and (C) with an internal DNA reference sequence to normalize and to control inhibition. All three quantification methods had reasonable recovery rates from 43% to 173%. Method B had more accepted recovery rates, i.e., in the range 70-130%, namely 83% compared to 75% for method A or C.

Immunotoxicity of petroleum hydrocarbons and microplastics alone or in combination to a bivalve species: Synergic impacts and potential toxication mechanisms

Both the frequent occurrence of accidental petroleum spills and the ubiquitous presence of microplastics (MPs) in the sea may pose severe threats to marine species. However, the immunotoxic impacts of these two types of pollutants and the underlying toxication mechanisms still remain largely unknown in sessile filter-feeding bivalve mollusks. Therefore, the impacts of exposure to petroleum hydrocarbons and MPs alone or in combination on the total count, cell type composition, and phagocytic activity of hemocytes were investigated in the blood clam, Tegillarca granosa. In addition, the intracellular ROS content, cell viability, degree of DNA damage, and expression levels of genes from immune-, apoptosis-, and immunotoxicity-related pathways were analyzed to reveal the potential toxication mechanisms. The results demonstrated that exposure to petroleum hydrocarbons and MPs alone or in combination at environmentally realistic concentrations could exert significant immunotoxic impacts on the blood clam, which may be caused by alterations in a series of physiological and molecular processes. In addition, the immunotoxicity of petroleum hydrocarbons could be significantly aggravated by the copresence of MPs, which suggests that coexposure to these two pollutants deserves closer attention.

Species Identification of Red Deer (Cervus elaphus), Roe Deer (Capreolus capreolus), and Water Deer (Hydropotes inermis) Using Capillary Electrophoresis-Based Multiplex PCR

To provide consumers correct information on meat species, specific and sensitive detection methods are needed. Thus, we developed a capillary electrophoresis-based multiplex PCR assay to simultaneously detect red deer (Cervus elaphus), roe deer (Capreolus capreolus), and water deer (Hydropotes inermis). Specific primer sets for these three species were newly designed. Each primer set only amplified target species without any reactivity against non-target species. To identify multiple targets in a single reaction, multiplex PCR was optimized and combined with capillary electrophoresis to increase resolution and accuracy for the detection of multiple targets. The detection levels of this assay were 0.1 pg for red deer and roe deer and 1 pg for water deer. In addition, its applicability was demonstrated using various concentrations of meat DNA mixtures. Consequently, as low as 0.1% of the target species was detectable using the developed method. This capillary electrophoresis-based multiplex PCR assay for simultaneous detection of three types of deer meat could authenticate deer species labeled on products, thus protecting consumers from meat adulteration.

Potential authentication of various meat-based products using simple and efficient DNA extraction method

BACKGROUND

The growth of halal food consumption worldwide has resulted in an increase in the request for halal authentication. DNA-based detection using powerful real-time polymerase chain reaction (PCR) technique has been shown to be highly specific and sensitive authentication tool. The efficient DNA extraction method in terms of quality and quantity is a backbone step to obtain successful real-time PCR assays. In this study, different DNA extraction methods using three lysis buffers were evaluated and developed to recommend a much more efficient method as well as achieve a successful detection using real-time PCR.

RESULTS

The lysis buffer 2 (LB2) has been shown to be the best lysis buffer for DNA extraction from both raw and processed meat samples comparing to other lysis buffers tested. Hence, the LB2 has been found to be ideal to detect meat and porcine DNAs by real-time PCR using pairs of porcine specific primers and universal primers which amplified at 119 bp fragment and 93 bp fragment, respectively. This assay allows detection as low as 0.0001 ng of DNA. Higher efficiency and sensitivity of real-time PCR via a simplified DNA extraction method using LB2 have been observed, as well as a reproducible and high correlation coefficient (R²  = 0.9979) based on the regression analysis of the standard curve have been obtained.

CONCLUSION

This study has established a fast, simple, inexpensive and efficient DNA extraction method that is feasible for raw and processed meat products. This extraction technique allows an accurate DNA detection by real-time PCR and can also be implemented to assist the halal authentication of various meat-based products available in the market. © 2019 Society of Chemical Industry.

Development of a PCR-based lateral flow strip assay for the simple, rapid, and accurate detection of pork in meat and meat products

In recent years, adulteration of meat and meat products has become a major food safety issue. PCR and real-time PCR technologies are mainstream methods used to identify animal-derived components. However, these technologies rely highly on costly equipment and professional technicians; they are therefore difficult to use in resource-limited settings. In this study, a novel, highly sensitive molecular assay, Pig-PCR-Strip (Pig specific polymerase chain reaction-Lateral flow strip), was developed for rapid detection of pig and swine-derived components. The assay is based on PCR amplification, hybridization of the PCR product to the probe, followed by detection using a strip format. Using this format, the PCR product can be detected by the naked eye within 3 min, and provides a basis for the migration of species-specific detection to a point-of-care (POC) microfluidic format. The Pig-PCR-Strip can detect pork components at a concentration of 0.01% in adulterated meat, and the limit of detection is up to 10 fg of target DNA. The assay was specific to pork and did not cross-react with other non-target species. It also can be used for commercial samples and complex food samples. It is a promising new tool for detection of pig-derived meat and can be rapidly modified for identifying other species. It could be widely used for solving problems related to meat quality assurance, species authentication, and traceability.

Development of RAPD-PCR assay for identifying Holstein, Angus, and Taiwan Yellow Cattle for meat adulteration detection

Incidents of food fraud have occurred worldwide, particularly in the form of meat adulteration. In this study, molecular probes were developed using the Random amplification of polymorphic DNA (RAPD) polymerase chain reaction (PCR) technique in order to identify three beef subspecies-Holstein, Angus, and Taiwan Yellow Cattle. Four RAPD-PCR 10-nucleotide primers were chosen out of a total of 60 primers. The selection was based on the reproducibility of species-specific amplicons able to detect various origins of cattle breeds. The results demonstrated that primer OPK12 produced three unique amplicons (1100 bp, 1000 bp and 480 bp) in Holstein; primer OPK14 generated one amplicon that only appeared in Holstein and Angus (200 bp); primer OPK19 amplified two species-specific amplicons in Holstein measuring 550 bp and 650 bp, respectively. However, due to the relatively lower repeatability of RAPD-PCR, higher and more specific testing repeats were required to increase the accuracy of the conclusion.

Detection and Quantification of Milk Ingredients as Hidden Allergens in Meat Products by a Novel Specific Real-Time PCR Method

Milk ingredients are often included in a wide range of meat products, such as cooked hams and sausages, to improve technological characteristics. However, milk proteins are also important food allergens. The aim of this study was the development of a highly sensitive and specific real-time PCR system targeting the 12S rRNA gene of Bos domesticus for the detection and quantification of milk as an allergenic ingredient in processed meat products. The method was able to achieve an absolute limit of detection (LOD) of 6 fg of milk DNA. Using a normalized approach (∆Ct method) for the detection of milk protein concentrate (MPC), it was possible to obtain sensitivities down to 0.01% (w/w) of MPC in model hams (raw and cooked) and autoclaved sausages, and 0.005% in raw sausage mixtures. The developed systems generally presented acceptable PCR performance parameters, being successfully validated with blind samples, applied to commercial samples, and further compared with an immunochemical assay. Trace amounts of milk material were quantified in two out of 13 samples, but the results mostly infer the excessive practice of the precautionary labeling.

Rapid Identification of Rainbow Trout Adulteration in Atlantic Salmon by Raman Spectroscopy Combined with Machine Learning

This study intends to evaluate the utilization potential of the combined Raman spectroscopy and machine learning approach to quickly identify the rainbow trout adulteration in Atlantic salmon. The adulterated samples contained various concentrations (0-100% w/w at 10% intervals) of rainbow trout mixed into Atlantic salmon. Spectral preprocessing methods, such as first derivative, second derivative, multiple scattering correction (MSC), and standard normal variate, were employed. Unsupervised algorithms, such as recursive feature elimination, genetic algorithm (GA), and simulated annealing, and supervised K-means clustering (KM) algorithm were used for selecting important spectral bands to reduce the spectral complexity and improve the model stability. Finally, the performances of various machine learning models, including linear regression, nonlinear regression, regression tree, and rule-based models, were verified and compared. The results denoted that the developed GA-KM-Cubist machine learning model achieved satisfactory results based on MSC preprocessing. The determination coefficient (R2) and root mean square error of prediction sets (RMSEP) in the test sets were 0.87 and 10.93, respectively. These results indicate that Raman spectroscopy can be used as an effective Atlantic salmon adulteration identification method; further, the developed model can be used for quantitatively analyzing the rainbow trout adulteration in Atlantic salmon.

Fabrication of multicolored patterns based on dye-doped cholesteric liquid crystals

We developed a type of dye-doped cholesteric liquid crystal, which were used for fluorescence enhancement and dual-mode multicolor patterns. We added dye molecules (BBOT, coumarin 6 (C6) and rhodamine B (RhB)) to liquid crystals, and cholesteric liquid crystals (CLC) exhibited selective reflection characteristics. When the reflection wavelength overlaps with the peak of the fluorescent dye, the luminescence intensity of the dye molecules could be adjusted. We used two methods to adjust the reflection wavelength of the cholesteric liquid crystals by changing the content of chiral additives and the isomerization degree of azo molecules. We used the screen printing and stencil printing methods to combine liquid crystal particles containing different fluorescent colors to prepare multicolor patterns. Moreover, the photoisomerization characteristics of the azo molecules were also used to achieve brilliant firework-like images upon exposure to ultraviolet and visible light. In addition, we also realized a face-changing stunt with facial makeup during a performance in the Sichuan Opera, a traditional Chinese folk art. We made use of the difference between reflection color and luminescence intensity upon light irradiation to present orange, green, blue and dark-blue facial effects.

Detection and quantification of salep with real time PCR utilizing the nr-ITS2 region

BACKGROUND

Salep is a highly valued food product, susceptible to adulteration with less costly additives such as starch. The aim of this study is to develop a real-time polymerase chain reaction (PCR) method for the detection and quantification of authentic salep using primers designed from the nr-ITS2 region.

RESULTS

The designed primers were shown to amplify selectively with salep DNA and cloning/sequencing of end-point PCR products obtained with authentic salep (Orchideceae) confirmed amplimers to be copies of the intended target region. Detection of salep DNA using the designed primer set was possible at levels as low as 20 pg. After initial evaluation of the real-time PCR method with binary DNA mixtures of salep and cornflour, quantification of salep was conducted in binary mixtures of potato starch (a more likely adulterant) and salep, showing that quantification within the range 25%-100% could be achieved. The real-time assay was performed using the 18S rDNA region co-amplified as an internal standard and evaluated using the ΔΔCt method. The calibration curves obtained as a result of real-time PCR runs showed linearity, with R² values above 99%.

CONCLUSION

A real-time PCR method using SybreGreen intercalating dye was established for salep detection and quantification based on the specific amplification of salep DNA. Method validation was performed utilizing blind and commercial samples. © 2018 Society of Chemical Industry.

The employment of Fourier transform infrared spectroscopy coupled with chemometrics techniques for traceability and authentication of meat and meat products

Meat-based food such as meatball and sausages are important sources of protein needed for the human body. Due to different prices, some unethical producers try to adulterate high-price meat such as beef with lower priced meat like pork and rat meat to gain economical profits, therefore, reliable and fast analytical techniques should be developed, validated, and applied for meat traceability and authenticity. Some instrumental techniques have been applied for the detection of meat adulteration, mainly relied on DNA and protein using polymerase chain reaction and chromatographic methods, respectively. But, this method is time-consuming, needs a sophisticated instrument, involves complex sample preparation which make the method is not suitable for routine analysis. As a consequence, a simpler method based on spectroscopic principles should be continuously developed. Food samples are sometimes complex which resulted in complex chemical responses. Fortunately, a statistical method called with chemometrics could solve the problems related to complex chemical data. This mini-review highlights the application of Fourier-transform infrared spectroscopy coupled with numerous chemometrics techniques for authenticity and traceability of meat and meat-based products.

Design and Validation of Short-Amplicon Length PCR Assay for the Detection of Porcine Gelatin in Commercial Candy and Marshmallow Products

Porcine gelatin has been used in many food products. To ensure the compliance of food products with halal regulations and label description, reliable analytical methods are required. In this study, Porcine-specific short amplicon-size for conventional PCR assay was developed for the detection of gelatin in commercial candy and marshmallow products. A pair of porcine-specific primers defining a 74 bp region of the mitochondrial D-loop sequence were designed. One hundred and three samples including seventy six samples from candies and twenty seven samples from marshmallow were purchased from local market in Amman, Jordan. The results revealed that seventeen samples were found to contain porcine gelatin ingredients and the rest 86 were found to be negative. Nine of the positive samples were Gelatin labeled, and eight were not identified to contain gelatin. Of these samples. Five were also labeled as Halal. So, we demonstrated that the authentication of commercial sweet ingredients using PCR assay is effective and protect consumers from being mislead due to mislabels.