Comparative study of DNA extraction methods from fresh and processed yellowfin tuna muscle tissue

Microbiome analyses of poultry feeds: Part I. Comparison of five different DNA extraction methods

Given extensive variability in feed composition, the absence of a dedicated DNA extraction kit for poultry feed underscores the need for an optimized extraction technique for reliable downstream sequencing analyses. This study investigates the impact of five DNA extraction techniques: Qiagen QIAamp DNA Stool Mini Kit (Qiagen), modified Qiagen with Lysing Matrix B (MQ), modified Qiagen with celite purification (MQC), polyethylene glycol (PEG), and 1-Day Direct. Genomic DNA amplification and Illumina MiSeq sequencing were conducted. QIIME2-2021.4 facilitated data analysis, revealing significant diversity and compositional differences influenced by extraction methods. Qiagen exhibited lower evenness and richness compared to other methods. 1-Day Direct and PEG enhanced bacterial diversities by employing bead beating and lysozyme. Despite similar taxonomic resolution, the Qiagen kit provides a rapid, consistent method for assessing poultry feed microbiomes. Modified techniques (MQ and MQC) improve DNA purification, reducing bias in commercial poultry feed samples. PEG and 1-Day Direct methods were effective but may require standardization. Overall, this study underscores the importance of optimized extraction techniques in poultry feed analysis, with potential implications for future standardization of effective methods.

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.

Genetic Identification and Traceability of Insect Meals

Insects have been proposed as a rich alternative source of protein for the partial or total replacement of fishmeal in aquaculture. For maximum safety and effectiveness of insect meals, control of the quality composition of these products is considered mandatory. The aim of this study was the genetic analysis of the composition of commercially available insect meals at the species level. Commercially available Hermetia illucens, Tenebrio molitor and Musca domestica individuals, as well as nine insect meals produced from these species, were analyzed. The genetic identification of insects at the species level was based on a COI fragment, and analysis of the insect meals' composition was performed with the processes of cloning and colony PCR. Genetic analysis indicated that the commercially available larvae morphologically identified as Musca domestica belonged to the species Muscina stabulans. In the commercially available insect meals, no other animal species was identified beyond the expected one. However, in the insect meal produced for research purposes, fungal growth was detected. The used methodology, herein, allows for the qualitative genetic identification of insect meals and could be included in the methods of traceability of products containing insects and other animal species.

Identification of the hazelnut cultivar in raw kernels and in semi-processed and processed products

The request for an efficient traceability system able to identify hazelnut cultivars along the entire processing chain is becoming a critical point for avoiding fraudulent practices and safeguarding the interests of growers, food processors and consumers. In this study, DNA was extracted from different hazelnut matrices, including plant material (leaf, kernel and kernel episperm), and processed foods (paste, grain, flour and different types of snacks containing hazelnuts). The efficiency of Simple Sequence Repeat (SSR) markers was tested to identify the hazelnut cultivar ‘Tonda Gentile’ in all the supply chain. The analysis at 10 SSR loci was able to verify the presence/absence of the alleles of a declared cultivar contained in these matrices. The SSR analysis of DNA from raw episperm offers the possibility of identifying the mother cultivar and is suggested as an effective way to discover frauds since DNA analysis can be performed on individual kernels. For food matrices containing hazelnuts, the presence of the mother cultivar’s DNA can be assessed based on the identification of its alleles in the sample, although the presence of multiple alleles from the pollenizers makes the interpretation of results more difficult.

Multiplex PCR assay for species identification of meat and dairy products from buffalo (Bubalus bubalis), cattle (Bos indicus and Bos taurus), goat (Capra hircus), and sheep (Ovis aries)

Cases of fraudulent meat and dairy products have increased worldwide, especially in developing countries. To determine the misrepresented animal species, appropriate tools in routine monitoring should be available for food inspections. In the present work, a multiplex polymerase chain reaction assay for species identification of products from ruminants including buffalo, cattle, goat, and sheep was developed. The primer set KUMUT_cFarmSp1 was composed of five species-specific primers and a pair of positive-control primers. The primer set amplified 106-, 163-, 232-, and 308-bp specific fragments from the cytochrome b (cyt b) gene of buffalo, cattle, goat, and sheep, respectively, and 370-bp positive-control fragment from 16S ribosomal RNA (16S rRNA). The detection limit of this PCR assay is 0.1 ng of DNA template. The developed primer set exhibited strong specificity, sensitivity, robustness, and simplicity for food verification, thus indicating its usefulness for species verification in food quality control and law enforcement.

Identification of Selected Tuna Species in Commercial Products

This study was conducted to develop systems for the identification of four tuna species (skipjack tuna Katsuwonus pelamis, yellowfin tuna Thunnus albacares, bullet tuna Auxis sp. and Atlantic bonito Sarda sp). At first, raw samples of these species and a mix intended as internal control were prepared for the authentication of fish muscle tissue of the genus Thunnus sp., Auxis sp. and Sarda sp. DNA from raw muscle tissue, the mix and samples was extracted with the DNeasy mericon Food Kit (Qiagen GmbH, Hilden, Germany). The concentration and purity of DNA in raw samples were evaluated using a spectrophotometer. Primers and probe sequences were specifically designed to identify the selected species. In addition, primers and a probe for the endogenous 12S rRNA gene were designed to determine the presence of amplifiable fish (especially tuna) DNA in samples. Furthermore, the species specificity of the designed primers and probes was verified in DNA samples of various tuna and bonito species. Limit of detection for the selected species was calculated as well as the coefficient of determination R² and efficiency of real-time PCR testing was determined. To evaluate the developed real-time PCR methods, 70 commercial tuna products were analysed. The results show that mislabelling of fish products can still be encountered and, moreover, the presence of an additional species can be identified.

Dual-output toehold-mediated strand displacement amplification for sensitive homogeneous electrochemical detection of specie-specific DNA sequences for species identification

The determination of specie-specific DNA sequences is a key factor for identification of animal species and detection of meat adulteration. Herein, a simple homogeneous electrochemical biosensor was developed for sensitive detection of specie-specific DNA sequences from meat products based on high efficient and specific dual-output toehold-mediated strand displacement (TMSD). After incubation with target DNA, large amount of methylene blue (electrochemical signal molecule) labeled probes (MB-P) were released from preformed DNA duplex structures by the process of dual-output TMSD amplification. The free MB-P could be further digested by Exonuclease I, and the enzymatic products contain little negative charge could diffuse to the surface of indium tin oxide electrode, generating significantly electrochemical signal. As a result, the designed biosensor showed a broad dynamic range from 0.01 pM to 100 pM, with a low detection limit of 8.2 fM, and ideal selectivity and reproducibility. Meanwhile, the approach exhibited acceptable accuracy for the detection of specie-specific DNA sequences, and possessed the potential application for the identification of animal species from meat products.

A quantitative comparison of two kits for DNA extraction from canned tuna

The most common methods that can be used for species identification of tuna include methods based on detection of species-specific DNA via the polymerase chain reaction (PCR) method. The problem with DNA detection in processed products is the possibility of DNA fragmentation during the technological process. The quantity and quality of extracted DNA is a crucial step for species identification based on the DNA analysis. In this study, two DNA extraction methods (DNeasy Blood & Tissue Kit and DNeasy mericon Food Kit) for tuna DNA isolation were compared. Eight food products of canned tuna (three of them were declared as Thunnus albacares and five products were declared as Katsuwonus pelamis) with a different addition of various ingredients were tested. Furthermore, three different times of proteolysis (30 min, 60 min, overnight) for each sample and each extraction kit were evaluated. The DNA concentration was determined by a Qubit dsDNA HS Assay Kit fluorescence method and quantified using a Qubit fluorometer. The DNA purity was evaluated using the A260/A280 ratio of absorbances measured on a spectrophotometer. The main indicator of DNA quality and quantity was its amplifiability in the subsequent real-time PCR for Thunnus species, Thunnus albacares and Katsuwonus pelamis. Based on the results, both kits can be used for tuna species determination in highly heat-treated products with different composition, nevertheless, the DNeasy mericon Food Kit provided better statistical values in some parameters. The effect of different times of proteolysis was significant in most of the samples with regard to the crossing point values determined by real-time PCR.

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.