Towards improved traceability in the seafood industry

Demand for seafood products is increasing worldwide, contributing to ever more complex supply chains and hampering traceability efforts. Despite marked improvements in seafood traceability and transparency, the fisheries industry is still victim to fraudulent behaviours and malpractice. This thesis examines some of the societal factors that may affect seafood traceability and explores DNA-based methods that have the potential to greatly improve the continuous and regular monitoring of transparency and traceability along the supply chain. Each chapter is dedicated to a given driver which might allow mislabelling to persevere (i.e. lack of consumer knowledge, shortcomings of species identification methods, absence of a framework for the use of point-of-origin detection tools) and explores some of the associated solutions that could help strengthen the monitoring of seafood products, verify compliance, and tackle fraud in the seafood industry. Educational tools and DNA-based methods can empower both consumers and enforcement officers respectively in the quest to combat fraudulent practices in the seafood industry; yet most enforcement bodies still struggle to identify which tools to work with. This highlights a potential mismatch between what the scientific community proposes and what the users really need. This thesis attempts to bridge the increasing demand for simple traceability and transparency tools with some of the existing technologies and proposes frameworks and strategies for their adoptions in practical contexts. It emphasises that if interested parties invest in coordinated efforts to develop robust and comprehensive authentication methods for an increasing number of commercial species, the benefits would largely outweigh the costs. Marine resources are under tremendous pressure and the need for good stewardship is now critical. Effective tools do exist, and it is crucial to demonstrate their practical application and expose the reach they may have within the fisheries and seafood industry

A future for seafood point-of-origin testing using DNA and stable isotope signatures

Demand for seafood products is increasing worldwide, contributing to ever more complex supply chains and posing challenges to trace their origin and guarantee legal, well-managed, sustainable sources from confirmed locations. While DNA-based methods have proven to be reliable in verifying seafood authenticity at the species level, the verification of geographic origin remains inherently more complex. Both genetic and stable isotope analyses have been employed for determining point-of-origin with varying degrees of success, highlighting that their application can be effective when the right tool is selected for a given application. Developing an a priori prediction of their discrimination power for different applications can help avoid the financial cost of developing inappropriate reference datasets. Here, we reviewed the application of both techniques to seafood point-of-origin for 63 commercial finfish species certified by the Marine Stewardship Council, and showed that, even for those species where baseline data exist, real applications are scarce. To fill these gaps, we synthesised current knowledge on biological and biogeochemical mechanisms that underpin spatial variations in genetic and isotopic signatures. We describe which species’ biological and distribution traits are most helpful in predicting effectiveness of each tool. Building on this, we applied a mechanistic approach to predicting the potential for successful validation of origin to three case study fisheries, using combined genetic and isotopic methodologies to distinguish individuals from certified versus non-certified regions. Beyond ecolabelling applications, the framework we describe could be reproduced by governments and industries to select the most cost-effective techniques

A future for seafood point-of-origin testing using DNA and stable isotope signatures

Demand for seafood products is increasing worldwide, contributing to ever more complex supply chains and posing challenges to trace their origin and guarantee legal, well-managed, sustainable sources from confirmed locations. While DNA-based methods have proven to be reliable in verifying seafood authenticity at the species level, the verification of geographic origin remains inherently more complex. Both genetic and stable isotope analyses have been employed for determining point-of-origin with varying degrees of success, highlighting that their application can be effective when the right tool is selected for a given application. Developing an a priori prediction of their discrimination power for different applications can help avoid the financial cost of developing inappropriate reference datasets. Here, we reviewed the application of both techniques to seafood point-of-origin for 63 commercial finfish species certified by the Marine Stewardship Council, and showed that, even for those species where baseline data exist, real applications are scarce. To fill these gaps, we synthesised current knowledge on biological and biogeochemical mechanisms that underpin spatial variations in genetic and isotopic signatures. We describe which species’ biological and distribution traits are most helpful in predicting effectiveness of each tool. Building on this, we applied a mechanistic approach to predicting the potential for successful validation of origin to three case study fisheries, using combined genetic and isotopic methodologies to distinguish individuals from certified versus non-certified regions. Beyond ecolabelling applications, the framework we describe could be reproduced by governments and industries to select the most cost-effective techniques. Graphic abstract: [Figure not available: see fulltext.

Validation of FASTFISH-ID: A new commercial platform for rapid fish species authentication via universal closed-tube barcoding

Seafood represents up to 20% of animal protein consumption in global food consumption and is a critical dietary and income resource for the world's population. Currently, over 30% of marine fish stocks are harvested at unsustainable levels, and the industry faces challenges related to Illegal, Unregulated and Unreported (IUU) fishing. Accurate species identification is one critical component of successful stock management and helps combat fraud. Existing DNA-based technologies permit identification of seafood even when morphological features are removed, but are either too time-consuming, too expensive, or too specific for widespread use throughout the seafood supply chain. FASTFISH-ID is an innovative commercial platform for fish species authentication, employing closed-tube barcoding in a portable device. This method begins with asymmetric PCR amplification of the full length DNA barcode sequence and subsequently interrogates the resulting single-stranded DNA with a universal set of Positive/Negative probes labeled in two fluorescent colors. Each closed-tube reaction generates two species-specific fluorescent signatures that are then compared to a cloud-based library of previously validated fluorescent signatures. This novel approach results in rapid, automated species authentication without the need for complex, time consuming, identification by DNA sequencing, or repeated analysis with a panel of species-specific tests. Performance of the FASTFISH-ID platform was assessed in a blinded study carried out in three laboratories located in the UK and North America. The method exhibited a 98% success rate among the participating laboratories when compared to species identification via conventional DNA barcoding by sequencing. Thus, FASTFISH-ID is a promising new platform for combating seafood fraud across the global seafood supply chain. © 2021 The Author

Fish out of water : consumers’ unfamiliarity with the appearance of commercial fish species

Seafood labels play an increasingly key role in assisting consumers in purchasing processed and featureless fish products, and in encouraging sustainable fishing and aquaculture practices. While informed purchasing choices are typically influenced by traceability and labelling awareness, they also depend on the consumers’ ability to identify and discriminate the fish species available on the market, which to date remains notably unexplored. We asked 720 people across six European countries to identify pictures of six fish species commonly sold in Europe. We reveal that European consumers have a poor understanding of the appearance of the fish they consume (overall ∼ 30% correct identification), with British consumers performing the poorest and Spanish ones doing best. We noted cultural association with some species, whereby the most regionally consumed fish are more easily recognized. We argue that despite recent improvements in technological solutions, stakeholder dialogue, and policy implementation, seafood market transparency will remain open to malpractice until consumers restore connection with their food

Fish out of water: consumers' unfamiliarity with the appearance of commercial fish species

Seafood labels play an increasingly key role in assisting consumers in purchasing processed and featureless fish products, and in encouraging sustainable fishing and aquaculture practices. While informed purchasing choices are typically influenced by traceability and labelling awareness, they also depend on the consumers’ ability to identify and discriminate the fish species available on the market, which to date remains notably unexplored. We asked 720 people across six European countries to identify pictures of six fish species commonly sold in Europe. We reveal that European consumers have a poor understanding of the appearance of the fish they consume (overall ∼ 30% correct identification), with British consumers performing the poorest and Spanish ones doing best. We noted cultural association with some species, whereby the most regionally consumed fish are more easily recognized. We argue that despite recent improvements in technological solutions, stakeholder dialogue, and policy implementation, seafood market transparency will remain open to malpractice until consumers restore connection with their food

The CanOE Strategy: Integrating Genomic and Metabolic Contexts across Multiple Prokaryote Genomes to Find Candidate Genes for Orphan Enzymes

Of all biochemically characterized metabolic reactions formalized by the IUBMB, over one out of four have yet to be associated with a nucleic or protein sequence, i.e. are sequence-orphan enzymatic activities. Few bioinformatics annotation tools are able to propose candidate genes for such activities by exploiting context-dependent rather than sequence-dependent data, and none are readily accessible and propose result integration across multiple genomes. Here, we present CanOE (Candidate genes for Orphan Enzymes), a four-step bioinformatics strategy that proposes ranked candidate genes for sequence-orphan enzymatic activities (or orphan enzymes for short). The first step locates “genomic metabolons”, i.e. groups of co-localized genes coding proteins catalyzing reactions linked by shared metabolites, in one genome at a time. These metabolons can be particularly helpful for aiding bioanalysts to visualize relevant metabolic data. In the second step, they are used to generate candidate associations between un-annotated genes and gene-less reactions. The third step integrates these gene-reaction associations over several genomes using gene families, and summarizes the strength of family-reaction associations by several scores. In the final step, these scores are used to rank members of gene families which are proposed for metabolic reactions. These associations are of particular interest when the metabolic reaction is a sequence-orphan enzymatic activity. Our strategy found over 60,000 genomic metabolons in more than 1,000 prokaryote organisms from the MicroScope platform, generating candidate genes for many metabolic reactions, of which more than 70 distinct orphan reactions. A computational validation of the approach is discussed. Finally, we present a case study on the anaerobic allantoin degradation pathway in Escherichia coli K-12

Genome sequencing reveals diversification of virulence factor content and possible host adaptation in distinct subpopulations of Salmonella enterica

<p>Abstract</p> <p>Background</p> <p>Divergence of bacterial populations into distinct subpopulations is often the result of ecological isolation. While some studies have suggested the existence of <it>Salmonella enterica </it>subsp. <it>enterica </it>subclades, evidence for these subdivisions has been ambiguous. Here we used a comparative genomics approach to define the population structure of <it>Salmonella enterica </it>subsp. <it>enterica</it>, and identify clade-specific genes that may be the result of ecological specialization.</p> <p>Results</p> <p>Multi-locus sequence analysis (MLSA) and single nucleotide polymorphisms (SNPs) data for 16 newly sequenced and 30 publicly available genomes showed an unambiguous subdivision of <it>S. enterica </it>subsp. <it>enterica </it>into at least two subpopulations, which we refer to as clade A and clade B. Clade B strains contain several clade-specific genes or operons, including a β-glucuronidase operon, a S-fimbrial operon, and cell surface related genes, which strongly suggests niche specialization of this subpopulation. An additional set of 123 isolates was assigned to clades A and B by using qPCR assays targeting subpopulation-specific SNPs and genes of interest. Among 98 serovars examined, approximately 20% belonged to clade B. All clade B isolates contained two pathogenicity related genomic islands, SPI-18 and a cytolethal distending toxin islet; a combination of these two islands was previously thought to be exclusive to serovars Typhi and Paratyphi A. Presence of β-glucuronidase in clade B isolates specifically suggests an adaptation of this clade to the vertebrate gastrointestinal environment.</p> <p>Conclusions</p> <p><it>S. enterica </it>subsp. <it>enterica </it>consists of at least two subpopulations that differ specifically in genes involved in host and tissue tropism, utilization of host specific carbon and nitrogen sources and are therefore likely to differ in ecology and transmission characteristics.</p