Establishment of farmed fish welfare biomarkers; a multi-omics approach

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Effect of creatine and EDTA supplemented diets on European seabass (Dicentrarchus labrax) allergenicity, fish muscle quality and omics fingerprint

Publication . Schrama, Denise; Raposo de Magalhães, Cláudia; Cerqueira, Marco; Carrilho, Raquel; Farinha, Ana Paula; Costa, Ana Rosa da; Gonçalves, Amparo; Kuehn, Annette; Revets, Dominique; Planchon, Sébastien; Engrola, Sofia; Rodrigues, Pedro

The relatively easy access to fish worldwide, alongside the increase of aquaculture production contributes to increased fish consumption which result in higher prevalence of respective allergies. Allergies to fish constitute a significant concern worldwide. beta-parvalbumin is the main elicitor for IgE-mediated reactions. Creatine, involved in the muscle energy metabolism, and ethylenediamine tetraacetic acid (EDTA), a calcium chelator, are potential molecules to modulate parvalbumin. The purpose of this study was to test creatine (2, 5 and 8%) and EDTA (1.5, 3 and 4.5%) supplementation in fish diets to modulate beta-parvalbumin expression and structure and its allergenicity in farmed European seabass (Dicentrarchus labrax) while assessing its effects on the end-product quality. Fish welfare and muscle quality parameters were evaluated by plasma metabolites, rigor mortis, muscle pH and sensory and texture analysis. Proteomics was used to assess alterations in muscle proteome profile and metabolic fingerprinting by Fourier transform infrared spectroscopy was used to assess the liver metabolic profile. In addition, IgE-reactivity to parvalbumin was analysed using fish allergic patient sera. Metabolic fingerprinting of liver tissue revealed no major alterations in infrared spectra with creatine supplementation, while with EDTA, only absorption bands characteristic of lipids were altered. Comparative proteomics showed up regulation of (tropo) myosin and phosphoglycerate mutase 2 with Creatine supplementation. In the case of EDTA proteomics showed up regulation of proteins involved in cellular and ion homeostasis. Allergenicity seems not to be modulated with creatine or EDTA supplementation as no decreased expression levels were found and IgE-binding reactivity showed no quantitative differences.

2022Journal article

Restricted access

Transcriptomic changes behind Sparus aurata hepatic response to different aquaculture challenges: An RNA-seq study and multiomics integration

Publication . Raposo de Magalhães, Cláudia; Sandoval, Kenneth; Kagan, Ferenc; McCormack, Grace; Schrama, Denise; Carrilho, Raquel; Farinha, Ana Paula; Cerqueira, Marco; Rodrigues, Pedro

Gilthead seabream (Sparus aurata) is an important species in Mediterranean aquaculture. Rapid intensification of its production and sub-optimal husbandry practices can cause stress, impairing overall fish performance and raising issues related to sustainability, animal welfare, and food safety. The advent of next-generation sequencing technologies has greatly revolutionized the study of fish stress biology, allowing a deeper understanding of the molecular stress responses. Here, we characterized for the first time, using RNA-seq, the different hepatic transcriptome responses of gilthead seabream to common aquaculture challenges, namely overcrowding, net handling, and hypoxia, further integrating them with the liver proteome and metabolome responses. After reference-guided transcriptome assembly, annotation, and differential gene expression analysis, 7, 343, and 654 genes were differentially expressed (adjusted p-value < 0.01, log2|fold-change| >1) in the fish from the overcrowding, net handling, and hypoxia challenged groups, respectively. Gene set enrichment analysis (FDR < 0.05) suggested a scenario of challenge-specific responses, that is, net handling induced ribosomal assembly stress, whereas hypoxia induced DNA replication stress in gilthead seabream hepatocytes, consistent with proteomics and metabolomics' results. However, both responses converged upon the downregulation of insulin growth factor signalling and induction of endoplasmic reticulum stress. These results demonstrate the high phenotypic plasticity of this species and its differential responses to distinct challenging environments at the transcriptomic level. Furthermore, it provides significant resources for characterizing and identifying potentially novel genes that are important for gilthead seabream resilience and aquaculture production efficiency with regard to fish welfare.

2024-03Journal article

Open access

Fish allergenicity modulation using tailored enriched diets—Where are we?

Publication . Schrama, Denise; Czolk, Rebecca; Raposo de Magalhães, Cláudia; Kuehn, Annette; Rodrigues, Pedro

Food allergy is an abnormal immune response to specific proteins in a certain food. The chronicity, prevalence, and the potential fatality of food allergy, make it a serious socio-economic problem. Fish is considered the third most allergenic food in the world, affecting part of the world population with a higher incidence in children and adolescents. The main allergen in fish, responsible for the large majority of fish-allergic reactions in sensitized patients, is a small and stable calcium-binding muscle protein named beta-parvalbumin. Targeting the expression or/and the 3D conformation of this protein by adding specific molecules to fish diets has been the innovative strategy of some researchers in the fields of fish allergies and nutrition. This has shown promising results, namely when the apo-form of beta-parvalbumin is induced, leading in the case of gilthead seabream to a 50% reduction of IgE-reactivity in fish allergic patients.

2022Journal article

Open access

Establishment of farmed fish welfare biomarkers; A multiomics approach

Publication . Magalhães, Cláudia Sofia Ferreira Raposo de; Rodrigues, Pedro Miguel

The sustainability of the aquaculture industry hinges on its ability to operate in harmony with the environment. To achieve this, it is essential to prioritize the welfare of farmed fish minimizing the stress levels associated with aquaculture practices. In this context, it is imperative to conduct a comprehensive study of fish physiological stress. The stress response in fish is initiated by an elaborate endocrine machinery that culminates in an overall metabolic reprogramming induced by the action of glucocorticoids. It can either increase fitness or induce further changes at the whole animal level and impair welfare. This process is orchestrated through a multilayered cellular program, and thus a multiomics approach can provide a holistic overview of the molecular stress response. Knowledge of the key regulators behind the adaptation mechanisms could provide valuable markers of stress to complement the existing measures. Sparus aurata, one of the most important species in Mediterranean aquaculture, was used in this study. Adult fish were subjected to three challenges: overcrowding, net handling, and hypoxia. The plasma proteome was assessed to verify the effect of the different challenges on the fish immune system and to measure the levels of typical stress indicators, i.e., cortisol, glucose, and lactate. A multiomics approach was employed to characterize the hepatic stress response, as the liver is the central organ in mounting the stress response. Lastly, skin mucus was used to identify stress biomarkers as it is easily collectable, and a mucosal tissue known to respond to stress. This work demonstrated that Sparus aurata can adapt better to high stocking densities than to net handling or hypoxia. The latter two challenges induced stress in hepatocytes and promoted several prosurvival pathways, e.g., autophagy, unfolded protein response, and DNA replication stress. Furthermore, a set of 28 candidate biomarkers was identified in the skin mucus, which could be further validated as labbased welfare indicators. This research provides scientific knowledge that can be used to develop species-specific welfare assessment protocols, promote farmed fish safety, and enhance positive societal outcomes while promoting aquaculture sustainability.

2023-09-29Doctoral thesis

Open access