Integrative "omic" approaches to improve fish nutrition and individual phenotyping

Abstract

The production of environmentally sustainable aquaculture feeds starts with the selection of high-quality raw materials that may need to be supplemented with specific nutrients (amino acids, phospholipids, vitamins and minerals). It is crucial to identify which nutrients (and in which forms) have to be added to plant-based diets to allow maximum growth in all production stages. Nevertheless, different competences for developing tools and methodologies are needed to assess and predict nutrient requirements or status of fish, going further than just identifying differences in growth parameters. The challenge is not only to screen and make the best use of a given tool, but also to integrate new knowledge arising from transcriptomics, proteomics, metabolomics and metagenomics in order to define a reliable healthy fish phenotype. Of particular value are biomarkers that precede the onset of metabolic disturbances or predict the capacity of the animal to cope dietary, environmental and age-related stresses. Currently, we are still far from establishing the normal range of variation for most valuable biomarkers through the full productive cycle, but ARRAINA, AQUAEXCEL and AQUAEXCEL2020 EU projects contributed significantly to progress in this area. Very often, the application of targeted analyses is the prevailing strategy for qualitative and quantitative detection of different biomarkers. However, this strategy restricts the possibilities to detect other unpredictable effects that could result directly or indirectly from the changes in diet composition. This limitation has encouraged the development and application of new and powerful analytical approaches to face the complexity of this problem and to improve the chance to detect unintended effects. A good example is the strategy used in gilthead sea bream to assess and prevent the drawback effects of environmental stressors and extreme diet formulations. This overview intends to present recent advances in this field showing the usefulness of targeted and nontargeted approaches for the risk assessment of food quality and safety and the proper phenotyping of fish growth performance and fish health and welfare, including prospective approaches for remote and nondisturbing fish monitoring.