DNA Analysis Research Articles

Investigating the effectiveness of forensic genetics and population genetic diversity using a multi-InDel system in Chinese Hezhou and Southern Shaanxi Han populations.

Multiple insertion-deletion (multi-InDel) has greater potential in forensic genetics than InDel, and its efficacy in kinship testing, individual identification, DNA mixture detection and ancestry inference remains to be explored. Consequently, we designed an efficient and robust system consisting of 41 multi-InDels to evaluate its efficacy in forensic applications in Chinese Hezhou Han (HZH) and Southern Shaanxi Han (SNH) populations and explore the genetic relationships between the SNH, HZH, and 26 reference populations. The obtained results showed that 38 out of the 41 multi-InDels had fairly high genetic variations. The the cumulative probability of discrimination and exclusion values of the multi-InDels (except MI38) in HZH and SNH populations both exceeded 1-e-25 and 1-e-6, correspondingly. The genetic compositions of HZH and SNH individuals were similar to that of East Asians and the Naive Bayes model could well distinguish East Asians, Africans and Americans. These results indicated that the multi-InDel systerm can serve as an effective tool to provide important evidence for the development of multi-InDels in forensic practice and better analyse the genetic background of the Han Chinese populations.

Transmission of Genetic Material and Malignant Cells of Cutaneous Origin via Surgical Sutures.

Seeding of skin cancer cells following diagnostic or therapeutic surgical procedures can occur and might cause local recurrences. As current preferred therapy for skin malignancy is surgical excision, seeding of tumour cells by manipulating malignant tissue or suturing can be another factor leading to recurrences. To evaluate whether genetic material and malignant cells adhere to standard suture materials. This prospective study included patients who underwent excision of skin lesions. Monofilament and braided sutures were examined. Sutures were passed through the observed tumour or healthy skin margins and were examined for DNA material and cells by cytological analysis, cell culture and characterization, and DNA analysis. Twenty-two patients and 148 sutures were included. DNA quantification showed DNA material on all sutures, with no significant difference between braided and monofilament sutures. Cytological analysis showed that all slides prepared from cell blocks contained normal squamous and atypical cells. Cell culture and characterization showed viable cells adhering to the sutures under direct light microscopy. Cell cultures showed rapid proliferation of epithelial cells from squamous cell carcinoma specimens. Suture materials carry DNA material and cells, including malignant cells of cutaneous origin and may seed them at distant sites.

Epistasis facilitates functional evolution in an ancient transcription factor.

A protein's genetic architecture - the set of causal rules by which its sequence produces its functions - also determines its possible evolutionary trajectories. Prior research has proposed that the genetic architecture of proteins is very complex, with pervasive epistatic interactions that constrain evolution and make function difficult to predict from sequence. Most of this work has analyzed only the direct paths between two proteins of interest - excluding the vast majority of possible genotypes and evolutionary trajectories - and has considered only a single protein function, leaving unaddressed the genetic architecture of functional specificity and its impact on the evolution of new functions. Here, we develop a new method based on ordinal logistic regression to directly characterize the global genetic determinants of multiple protein functions from 20-state combinatorial deep mutational scanning (DMS) experiments. We use it to dissect the genetic architecture and evolution of a transcription factor's specificity for DNA, using data from a combinatorial DMS of an ancient steroid hormone receptor's capacity to activate transcription from two biologically relevant DNA elements. We show that the genetic architecture of DNA recognition consists of a dense set of main and pairwise effects that involve virtually every possible amino acid state in the protein-DNA interface, but higher-order epistasis plays only a tiny role. Pairwise interactions enlarge the set of functional sequences and are the primary determinants of specificity for different DNA elements. They also massively expand the number of opportunities for single-residue mutations to switch specificity from one DNA target to another. By bringing variants with different functions close together in sequence space, pairwise epistasis therefore facilitates rather than constrains the evolution of new functions.

Centella asiatica (L.) Urb. and Hydrocotyle umbellata L. identification and quality assessment: A methodology comparison.

Centella is an important genus in the Apiaceae family. It includes Centella asiatica, which has significant edible and medicinal values. However, this species is easily confused due to its similar morphological traits to Hydrocotyle umbellata, hindering its utilization in the consumer and pharmacological industries. The study aims to differentiate these two closely related plant species using reliable methods of confirming the authenticity of natural herbal medicines. Our work mainly focuses on the basic morphological characteristics, chemical markers, genetic fingerprints, and their biological responses. The plants can be clearly differentiated using their leaf shapes, stipules, petioles, inflorescences, and fruit structures. Although the phytochemical compositions of the C. asiatica extract were similar to that of H. umbellata which included flavonoids, tannins, and saponins important to the plant's ability to reduce inflammation and promote healing of wounds, the H. umbellata extract showed significantly higher toxicity than that of C. asiatica. High-performance liquid chromatography analysis was used to identify chemical fingerprints. The result revealed that C. asiatica had major triterpene glycoside constituents including asiaticoside, asiatic acid, madecassoside, and madecassic acid, which have a wide range of medicinal values. In contrast, triterpenoid saponins were not identified in H. umbellata. Furthermore, using SCoT1-6 primers was possible to effectively and sufficiently created a dendrogram which successfully identified the closeness of the plants and confirmed the differences between the two plant species. Therefore, differentiation can be achieved through the combination of morphometrics, molecular bioactivity, and chemical analysis.

Safe and genotyped. A non-invasive method for extraction of amphibian DNA from water baths and its application on Northern spectacled salamanders, Salamandrina perspicillata (Savi 1821)

AbstractThe global decline of amphibian populations, with 40.7% of species classified as threatened, calls for innovative and ethical approaches in conservation genetics. Molecular biology advancements have introduced environmental DNA (eDNA) analysis, primarily focusing on aquatic environments. However, the present study explores a novel non-invasive protocol using water samples to extract DNA from terrestrial and semi-terrestrial amphibians, specifically the endangered Italian endemic salamander, Salamandrina perspicillata (Savi, 1821). Unlike traditional invasive methods involving tissue sampling, this protocol immerses animals briefly, eliminating the need for digit or tail amputations or manipulation for buccal swabs. The study validated the protocol through DNA extraction, amplification, and sequencing, yielding results comparable to traditional methods. The non-invasive nature of the protocol aligns with the 3Rs principles (Replace, Reduce, Refine) and offers a streamlined, stress-minimizing alternative for studying protected and endangered species. Future experiments should also explore further refinements, including reduced soaking times and additional applications, such as skin microbiota analysis. This protocol represents a significant step towards ethical and effective research practices in amphibian conservation genetics, encouraging a paradigm shift in wildlife research ethics. Continued innovation in non-invasive methodologies is essential for comprehensive understanding and robust conservation strategies amid the ongoing biodiversity crisis.

HiChIP-based Epigenomic Footprinting Identifies a Promoter Variant of UXS1 that Confers Genetic Susceptibility to Gastroesophageal Cancer.

Genome-wide association studies (GWAS) have identified more than a hundred single nucleotide variants (SNVs) associated with the risk of gastroesophageal cancer (GEC). The majority of the identified SNVs map to noncoding regions of the genome. Uncovering the causal SNVs and the genes they modulate could help improve GEC prevention and treatment. Here, we used HiChIP against histone 3 lysine 27 acetylation (H3K27ac) to simultaneously annotate active promoters and enhancers, identify the interactions between them, and detect nucleosome free regions (NFRs) harboring potential causal SNVs in a single assay. Application of H3K27Ac HiChIP in GEC relevant models identified 61 potential functional SNVs that reside in NFRs and interact with 49 genes at 17 loci. The approach led to a 67% reduction in the number of SNVs in linkage disequilibrium at these 17 loci, and at seven loci a single putative causal SNV was identified. One SNV, rs147518036, located within the promoter of the UDP-glucuronate decarboxylase 1 (UXS1) gene appeared to underlie the GEC risk association captured by the rs75460256 index SNV. The rs147518036 SNV creates a GABPA DNA recognition motif, resulting in increased promoter activity, and CRISPR-mediated inhibition of the UXS1 promoter reduced viability of GEC cells. These findings provide a framework that simplifies the identification of potentially functional regulatory SNVs and target genes underlying risk-associated loci. In addition, the study implicates increased expression of the enzyme UXS1 and activation of its metabolic pathway as a predisposition to gastric cancer, which highlights potential therapeutic avenues to treat this disease.

Structure and genome editing of type I-B CRISPR-Cas

Type I CRISPR-Cas systems employ multi-subunit effector Cascade and helicase-nuclease Cas3 to target and degrade foreign nucleic acids, representing the most abundant RNA-guided adaptive immune systems in prokaryotes. Their ability to cause long fragment deletions have led to increasing interests in eukaryotic genome editing. While the Cascade structures of all other six type I systems have been determined, the structure of the most evolutionarily conserved type I-B Cascade is still missing. Here, we present two cryo-EM structures of the Synechocystis sp. PCC 6714 (Syn) type I-B Cascade, revealing the molecular mechanisms that underlie RNA-directed Cascade assembly, target DNA recognition, and local conformational changes of the effector complex upon R-loop formation. Remarkably, a loop of Cas5 directly intercalated into the major groove of the PAM and facilitated PAM recognition. We further characterized the genome editing profiles of this I-B Cascade-Cas3 in human CD3+ T cells using mRNA-mediated delivery, which led to unidirectional 4.5 kb deletion in TRAC locus and achieved an editing efficiency up to 41.2%. Our study provides the structural basis for understanding target DNA recognition by type I-B Cascade and lays foundation for harnessing this system for long range genome editing in human T cells.

DORA: an interactive map for the visualization and analysis of ancient human DNA and associated data.

The ability to sequence ancient genomes has revolutionized the way we study evolutionary history by providing access to the most important aspect of evolution-time. Until recently, studying human demography, ecology, biology, and history using population genomic inference relied on contemporary genomic datasets. Over the past decade, the availability of human ancient DNA (aDNA) has increased rapidly, almost doubling every year, opening the way for spatiotemporal studies of ancient human populations. However, the multidimensionality of aDNA, with genotypes having temporal, spatial and genomic coordinates, and integrating multiple sources of data, poses a challenge for developing meta-analyses pipelines. To address this challenge, we developed a publicly-available interactive tool, DORA, which integrates multiple data types, genomic and non-genomic, in a unified interface. This web-based tool enables browsing sample metadata alongside additional layers of information, such as population structure, climatic data, and unpublished samples. Users can perform analyses on genotypes of these samples, or export sample subsets for external analyses. DORA integrates analyses and visualizations in a single intuitive interface, resolving the technical issues of combining datasets from different sources and formats, and allowing researchers to focus on the scientific questions that can be addressed through analysis of aDNA datasets.

Comparative Study of Sex Estimation by Mesiodistal width of Mandibular Canine and Mesiodistal width of Maxillary Canine in North Indian Population

Abbreviations: MD: Mesiodistal, SD: Standard deviation, mm: millimetres. Introduction: Various methods of identification such as anthropometry, stature estimation, dactylography, sex estimation, age estimation, DNA analysis, differentiation by blood groups and odontology are used in forensic medicine to create biological profile of an unknown individual. Estimation of sex is the first step towards identification of person. Determination of sex from skeletal remains is an essential task in medicolegal examination.Teeth are highly indestructible and reveal minimal turnover of natural substance hence teeth can be used for sex estimation. Mesiodistal parameter of mandibular and maxillary canine gave evidence of sex estimation due to sexual dimorphism. Aim: The aim of our study was to evaluate the sex estimation by mesiodistal width of mandibular canine and mesiodistal width of maxillary canine in north Indian population. Materials and Methods: The sample comprised of dental impression from 120 individuals (60 males and 60 females), all young adults between 20 and 35 years of age. Impressions of the teeth were made using irreversible hydrocolloid (alginate) material and casts poured in dental stone. Mesiodistal (MD) dimensions of mandibular and maxillary canine of both right and left side is measure by caliper. Results: Mean mandibular canine width of both right and left sidewere higher in male than female and were statistically significant whereas, mean maxillary canine width of both right and left side were slightly higher in male than female but were not statistically significant in young north Indian population. Left mandibular canine width (6%) was more sexually dimorphic than right mandibular canine width (5.1%). Whereas negligible sexual dimorphism shown by maxillary canine. Conclusion: The study confirmed that among maxillary and mandibular canine, mandibular canine can be used for sex estimation and shows significant sexual dimorphism.

Top predator status and trends: ecological implications, monitoring and mitigation strategies to promote ecosystem-based management

The conservation and management of marine ecosystems hinge on a comprehensive understanding of the status and trends of top predators. This review delves into the ecological significance of marine top predators, examining their roles in maintaining ecosystem stability and functioning through an integrated analysis of current scientific literature. We first assess the efficacy of various monitoring methods, ranging from traditional field observations to cutting-edge technologies like satellite tracking and environmental DNA (eDNA) analysis and evaluating their strengths and limitations in terms of accuracy, spatial coverage, and cost-effectiveness, providing resource managers with essential insights for informed decision-making. Then, by synthesizing data from diverse marine ecosystems, this study offers a comprehensive overview of the trends affecting top predator populations worldwide. We explore the multifaceted impacts of human activities, climate change, and habitat degradation on the abundance and distribution of these key species. In doing so, we shed light on the broader implications of declining top predator populations, such as trophic cascades and altered community structures. Following a thorough assessment of successful strategies for reversing the decline of top predators, a compilation of recommendations is presented, encompassing effective governance interventions. A crucial aspect of effective ecosystem-based management is the implementation of robust monitoring strategies. Mitigation measures are imperative to reverse the adverse impacts on marine top predators. We present a comprehensive array of mitigation options based on successful case studies. These include the establishment of marine protected areas, the enforcement of fisheries regulations, and the promotion of sustainable fishing practices. We deepen the synergies between these strategies and their potential to mitigate human-induced stressors on top predator populations to safeguard their pivotal role in maintaining marine ecosystem structure and function. By examining marine top predators’ ecological significance, analyzing population trends, discussing monitoring techniques, and outlining effective mitigation strategies, we provide a comprehensive resource for researchers, policymakers, and stakeholders engaged in fostering ecosystem-based management approaches. We conclude that integrating these insights into current management frameworks will be essential to safeguard both top predators and the broader marine environment for future generations.

Plasmid targeting and destruction by the DdmDE bacterial defence system.

While eukaryotic Argonautes play a pivotal role in post-transcriptional gene regulation through nucleic acid cleavage, some short prokaryotic Argonaute variants (pAgos) rely on auxiliary nuclease factors for efficient foreign DNA degradation (1). Here, we elucidate the activation pathway of the DNA Defense Module DdmDE system, which rapidly eliminates small, multicopy plasmids from Vibrio cholerae Seventh Pandemic Strain (7PET) (2). Through a combination of cryo-EM, biochemistry and in vivo plasmid clearance assays, we demonstrate DdmE is a catalytically inactive, DNA-guided, DNA-targeting pAgo with a distinctive insertion domain. We observe that DdmD transitions from an autoinhibited, dimeric protein to monomers upon loading of single-stranded DNA targets. Furthermore, the complete structure of the DdmDE-guide-target handover complex provides a comprehensive view into how DNA recognition triggers processive plasmid destruction. Our work establishes a mechanistic foundation for how pAgo utilize ancillary factors to achieve plasmid clearance, and provides insights into anti-plasmid immunity in bacteria.

The tombs of wind (Những ngôi mộ giό)

This article details the remarkable involvement of the Vietnamese population in finding and naming half a million Vietnamese missing-in-action (MIAs). The secrecy that characterised Vietnam’s military operations during wartime, and the overlapping claims and therefore control of the MIAs by the army and civil administrations in the aftermath of the wars, are the reasons behind unsolvable quagmires in Vietnam’s current war-accounting effort. The myriad of state actors involved who often work at cross purposes raises the public’s awareness of the incompetence of the state and calls for the participation of non-state actors. The latest potential avenue to solve the MIA problem, DNA forensics, is facing all kinds of challenges, such as the quality of the bone samples and the scale of the effort. War accounting has therefore become an open arena of public engagement and popular dissent, while significantly transforming the cult of the dead in Vietnam.

Predictive genome-wide association and economic analyses of pooled DNA in a commercial feedlot setting

Understanding the genetic profile of cattle allows producers to make predictions of performance and disease. However, it is often fiscally and logistically unfeasible for commercial cattle producers to individually genotype animals. As such, our objec­tive was to utilize prospectively-pooled DNA from commercial feedlot cattle for a genome-wide association study (GWAS) of ec­onomically-important carcass traits and measure the economic efficiency of this technique.

Bioaerosol Sampling Devices and Pretreatment for Bacterial Characterization: Theoretical Differences and a Field Experience in a Wastewater Treatment Plant

Studies on bioaerosol bacterial biodiversity have relevance in both ecological and health contexts, and molecular methods, such as 16S rRNA gene-based barcoded sequencing, provide efficient tools for the analysis of airborne bacterial communities. Standardized methods for sampling and analysis of bioaerosol DNA are lacking, thus hampering the comparison of results from studies implementing different devices and procedures. Three samplers that use gelatin filtration, swirling aerosol collection, and condensation growth tubes for collecting bioaerosol at an aeration tank of a wastewater treatment plant in Trieste (Italy) were used to determine the bacterial biodiversity. Wastewater samples were collected directly from the untreated sewage to obtain a true representation of the microbiological community present in the plant. Different samplers and collection media provide an indication of the different grades of biodiversity, with condensation growth tubes and DNA/RNA shieldTM capturing the richer bacterial genera. Overall, in terms of relative abundance, the air samples have a lower number of bacterial genera (64 OTUs) than the wastewater ones (75 OTUs). Using the metabarcoding approach to aerosol samples, we provide the first preliminary step toward the understanding of a significant diversity between different air sampling systems, enabling the scientific community to orient research towards the most informative sampling strategy.

A Review on Bridging Molecular Biology and Ecological Dynamics through Integrative Approaches in Zoology

The integration of molecular biology with ecological dynamics has emerged as a transformative approach in zoology, enhancing our understanding of biodiversity, ecosystem health, and the adaptive responses of species to environmental changes. This review synthesizes key developments and methodological innovations at the intersection of molecular biology and ecological dynamics, highlighting the application of DNA barcoding, environmental DNA (eDNA) analyses, molecular phylogenetics, and advanced computational models in elucidating complex biological interactions and evolutionary patterns. Significant advancements include the use of high-throughput sequencing technologies and CRISPR-Cas systems that have expanded our ability to explore genetic diversity and manipulate genetic material for conservation purposes. The review discusses the predictive capabilities of integrative models that combine genetic with ecological data, offering insights into species resilience and ecosystem stability under varying environmental scenarios. Challenges in data integration, such as issues of scale, complexity, and the necessity for interdisciplinary cooperation, are critically examined. Technical limitations related to data management and ethical considerations in the use of genetic information are also explored. Looking forward, the review identifies emerging technologies and their potential impacts on ecological and conservation biology, emphasizing the need for policies that support sustainable management and conservation strategies. This review underscores the profound impact of integrating molecular biology with ecological dynamics, which not only enhances our scientific understanding but also provides practical frameworks for addressing global environmental challenges.

Comprehensive molecular profiling identifies actionable biomarkers for patients from Thailand and the United Arab Emirates with advanced malignancies

BackgroundComprehensive molecular profiling of tissue samples that can help guide therapy management is not widely available across the globe.MethodsComprehensive molecular profiling through Caris Molecular Intelligence involves the analysis of DNA through next-generation sequencing, chromogenic or fluorescent in situ hybridization, pyrosequencing, and copy number alterations; RNA through whole-transcriptome sequencing and multiplex PCR of RNA; and protein through immunohistochemistry.ResultsHere we describe the experience of molecular profiling of tumor tissue samples from patients diagnosed with advanced solid tumors and treated in two countries, the United Arab Emirates and Thailand. Tumor cancer cases submitted to Caris Life Sciences (Phoenix, Arizona, USA) for molecular profiling from the UAE and Thailand were retrospectively analyzed (data accessed between 2019 and 2020) for their molecular alterations and clinical biomarkers, without regard to ethnicity. A total of 451 samples from 35 distinct types of advanced cancers were examined for mutations, amplifications, overexpression, exon copy number alterations, microsatellite instability, deficient mismatch repair, tumor mutational burden, and fusions. Interrogating each step of the biological pathway, from DNA to RNA to distinct protein, identified an alteration with an associated therapy for 75% of these tumor samples. The most common alterations identified included elevated PDL-1 that can be targeted with an immune checkpoint inhibitors and amplification of HER2 for which a variety of anti HER2 therapies are available.ConclusionComprehensive molecular profiling in patients with advanced malignancies can help optimize therapeutic management allowing for improved prognostic outcome.

Individual identification method using samples associated with doping tests: A comparison of mitochondrial and nuclear genetic data.

Doping offenses involve the use or attempted use of any prohibited method or substance as well as substituting samples. Consequently, it has been recommended that short tandem repeat (STR) analysis be used to determine if the doping control samples are from the same athlete. However, it has been recognized that it may be difficult to obtain full STR analysis using negligible amounts of DNA samples. Mitochondrial DNA (mtDNA) is characterized by its stability and high cellular copy number. Therefore, mtDNA testing in urine is expected to be used to analyze samples that cannot be analyzed using STR analysis. The objective of this study was to compare mtDNA testing with STR analysis by conducting sensitivity, concordance (whole blood, dried blood spot, and urine), and case-type studies. In sensitivity studies, mtDNA testing exhibited greater sensitivity compared with STR analysis. Concordance studies indicated that all samples were consistent with the mtDNA sequences and STR profiles. Allelic dropout occurred in some urine samples that were examined for STR analysis. Case-type sample studies demonstrated that mtDNA testing could be used to obtain DNA profiles of all the samples tested, including blood, dried blood spots, urine, blood residues on needles, and blood stains. In conclusion, mtDNA testing is valuable for analyzing highly degraded DNA samples, such as urine samples, compared with STR analysis. Urine testing should be performed for the initial testing procedure, because mtDNA is inherited maternally. In situations where the DNA match is detrimental to the athlete, additional blood STR analysis may be required.

Machine learning based DNA melt curve profiling enables automated novel genotype detection

Surveillance for genetic variation of microbial pathogens, both within and among species, plays an important role in informing research, diagnostic, prevention, and treatment activities for disease control. However, large-scale systematic screening for novel genotypes remains challenging in part due to technological limitations. Towards addressing this challenge, we present an advancement in universal microbial high resolution melting (HRM) analysis that is capable of accomplishing both known genotype identification and novel genotype detection. Specifically, this novel surveillance functionality is achieved through time-series modeling of sequence-defined HRM curves, which is uniquely enabled by the large-scale melt curve datasets generated using our high-throughput digital HRM platform. Taking the detection of bacterial genotypes as a model application, we demonstrate that our algorithms accomplish an overall classification accuracy over 99.7% and perform novelty detection with a sensitivity of 0.96, specificity of 0.96 and Youden index of 0.92. Since HRM-based DNA profiling is an inexpensive and rapid technique, our results add support for the feasibility of its use in surveillance applications.

Circulating tumour DNA analysis and new uses of anti-EGFR monoclonal antibodies in patients with metastatic colorectal cancer

Currently, tumour tissue biopsy to determine RAS/BRAF gene alterations, assess microsatellite instability status, and determine HER‑2/neu gene amplification/hyperexpression is the gold standard of diagnosis and allows the selection of optimal molecularly targeted therapy when considering treatment strategies for patients with metastatic colorectal cancer. However, biopsy does not fully reflect the existing intratumoural heterogeneity and clonal evolution of tumour cells, which can often be the cause of therapeutic failures. In recent years, liquid biopsy has attracted increasing attention as an additional and potentially alternative non-invasive tool for molecular tumour profiling. Assessment of circulating tumour DNA allows changes in the genetic status of the tumour to be monitored and the «burden» of disease to be measured dynamically in real time. Advances in liquid biopsy technology have led to promising new strategies for the management of patients with metastatic colorectal cancer in late-line therapy. The standard drug arsenal in this group of patients is limited to either repeat administration of previously effective therapy or regorafenib and the combination of trifluridine/tipiracil with bevacizumab, which are characterized by limited clinical activity. However, thanks to the discovery of the NeoRAS wild-type phenomenon and the rechallenge strategy of anti-EGFR monoclonal antibodies based on the study of clonal selection and evolution of tumour cells, the administration of epidermal growth factor inhibitors in a molecularly selected by liquid biopsy population is accompanied by good tolerability and efficacy. Numerous clinical studies are ongoing to further understand the mechanisms of tumour resistance and to develop new evidence-based treatment approaches in order to realise the concept of personalised medicine.

Increasing marine trophic web knowledge through DNA analyses of fish stomach content: a step towards an ecosystem-based approach to fisheries research.

Multispecies and ecosystem models, which are key for the implementation of ecosystem-based approaches to fisheries management, require extensive data on the trophic interactions between marine organisms, including changes over time. DNA metabarcoding, by allowing the simultaneous taxonomic identification of the community present in hundreds of samples, could be used for speeding up large-scale stomach content data collection. Yet, for DNA metabarcoding to be routinely implemented, technical challenges should be addressed, such as the potentially complicated sampling logistics, the detection of a high proportion of predator DNA, and the inability to provide reliable abundance estimations. Here, we present a DNA metabarcoding assay developed to examine the diet of five commercially important fish, which can be feasibly incorporated into routinary samplings. The method is devised to speed up the analysis process by avoiding the stomach dissection and content extraction steps, while preventing the amplification of predator DNA by using blocking primers. Tested in mock samples and in real stomach samples, the method has proven effective and shows great effectiveness discerning diet variations due to predator ecology or prey availability. Additionally, by applying our protocol to mackerel stomachs previously analyzed by visual inspection, we showcase how DNA metabarcoding could complement visually based data by detecting overlooked prey by the visual approach. We finally discuss how DNA metabarcoding-based data can contribute to trophic data collection. Our work reinforces the potential of DNA metabarcoding for the study and monitoring of fish trophic interactions and provides a basis for its incorporation into routine monitoring programs, which will be critical for the implementation of ecosystem-based approaches to fisheries management.