A Proteomics and other Omics approach in the context of farmed fish welfare and biomarker discovery

Abstract

The rapid and intensive growth of aquaculture over the last decade, poses a tremendous challenge to this industry in order to comply with the latest guidelines, established to minimise its negative effects on the environment, animal welfare and public health. Farmed fish welfare has become one of the main priorities towards sustainable aquaculture production with several initiatives launched by the European Union within the framework of the 2030 agenda. It is clear that an unbiased and reliable way to access farmed fish welfare needs to be implemented due to the lack of reliable indicators and standardised methods that are used at present. In this review, we start by addressing the status quo of animal and fish welfare definition in particular, describing the methods and assays currently used to measure it. We then explain why we believe these methods are unreliable and why there is a need to establish new ones that will promote productivity and consumer's acceptance of farmed fish. The establishment of a new type of welfare biomarkers using cutting‐edge technologies like proteomics and other omics technologies is proposed as a solution to this issue. Therefore, we provide a brief description of these new methodologies, describing for each one how they can improve our scientific knowledge and the role they can play in farmed fish welfare biomarker discovery.

Data_Sheet_2.pdf

“…Furthermore, the different magnitude of regulatory changes observed among trials suggests a specific response influenced by its severity. This scenario is in agreement with a previous Fourier-transformed infrared spectroscopy (FTIR) exploratory analysis performed on the liver of these fish, where a metabolic reprogramming was proposed to meet the energy demands required during the physiological stress response (Raposo de Magalhães et al, 2020).…”

“…In this sense, we exposed gilthead seabream (Sparus aurata) adults to different suboptimal rearing conditions and physical challenges, specifically high rearing densities, net handling and hypoxia. A previous metabolic fingerprinting of these same fish's liver samples demonstrated alterations in the hepatic infrared spectra of the challenged fish, compared with undisturbed fish, suggesting a challenge-specific metabolic reprogramming (Raposo de Magalhães et al, 2020). Here, a 2D-DIGE gel-based proteomics analysis was employed to disclose the set of liver proteins involved in the gilthead seabream adaptive response to these challenges.…”

“…As these changes occur over a slower timescale, comparing with endocrine responses, proteomics can thus be a promising alternative to find indicators of an adaptive long-term stress response instead of an early response (e.g., hormones), as that used in acute stress assessment (Cowan and Vera, 2008;Marco-Ramell et al, 2016). The number of studies employing a proteome-wide characterization to unveil the molecular adaptations behind the physiological response to stress in fish has been considerably increasing (Raposo de Magalhães et al, 2020a). However, the effects on metabolism and hepatic proteome have been studied mainly as a response to environmental stimuli, xenobiotics, diseases and acute stressors (Wiseman et al, 2007;Ibarz et al, 2010;Malécot et al, 2011;Mahanty et al, 2016;Gandar et al, 2017;Pédron et al, 2017;Zhang et al, 2017;Causey et al, 2018;Naderi et al, 2018;Ghisaura et al, 2019).…”

Physiology: An Important Tool to Assess the Welfare of Aquatic Animals

“…However, external factors such as the unavoidable noise of visitors can increase cortisol levels, as has been described for the lined seahorse (Hippocampus erectus) [131]. It is noteworthy that apart from the study of classical biomarkers [61,132], recent reviews addressed new approaches using transcriptomics, proteomics, and metabolomics to assess long-term welfare of teleosts [133,134].…”

Domestic animal proteomics in the 21st century: A global retrospective and viewpoint analysis

“…This type of collaboration is extremely important, and Eurastip provided a structured basis within the aquaculture community for the joint Portugal and Thailand effort. Judging by the number of students visiting our laboratories as well as the three publications in peer-review journals resulting from this research on Nile tilapia nutrition and health [88][89][90], the collaboration was certainly a successful and prosperous one. However, like other bilateral initiatives such as one described between Portugal and Argentina [33], it was very dependent on the establishment of informal but solid research relations between scientists.…”