Aquaculture is facing a strategic challenge to improve feed suitability and support the global increase in fish production. Improvements in diet formulation for sustainable nutritional strategies have focused to date on the partial substitution of marine resources by plant resources but will now include other alternative feedstuffs. Growth trials and body composition data provide valuable indicators of fish nutritional status, while omics technologies may contribute to a better understanding of fish nutrition and help to demonstrate how feed and nutrients act in fish metabolism. Metabolomic approaches give an insight into fish metabolism through a non‐targeted analysis of metabolites in tissues or biofluids that involve multiple factors affecting fish, such as nutrition. In this review, we highlight the outcomes of publications in metabolomics applied to fish nutrition. We explain the concept of metabolomics and discuss specific technical considerations related to sample type, sampling and sample preparation. We show how metabolomic studies help to elucidate the impact of nutrition on fish fillet composition and fish metabolism. Finally, we describe the potential applications of metabolomic approaches for the non‐invasive monitoring of fish nutritional status.

Mitigation of methane emission, a potent greenhouse gas, is a worldwide priority to limit global warming. A substantial part of anthropogenic methane is emitted by the livestock sector, as methane is a normal product of ruminant digestion. We present the latest developments and challenges ahead of the main efficient mitigation strategies of enteric methane production in ruminants. Numerous mitigation strategies have been developed in the last decades, from dietary manipulation and breeding to targeting of methanogens, the microbes that produce methane. The most recent advances focus on specific inhibition of key enzymes involved in methanogenesis. But these inhibitors, although efficient, are not affordable and not adapted to the extensive farming systems prevalent in low- and middle-income countries. Effective global mitigation of methane emissions from livestock should be based not only on scientific progress but also on the feasibility and accessibility of mitigation strategies.

Nutrition of high trophic species in aquaculture is faced with the development of sustainable plant-based diets. Insects seem particularly promising for supplementing plant-based diets. However, the complex effect of whole insect meal on fish metabolism is not well understood, and even less is known about insect meal extracts. The purpose of this work was to decipher the metabolic utilization of a plant-based diet supplemented with the gradual addition of an insect protein extract (insect hydrolysate at 0%, 5%, 10% and 15%). ¹H-NMR profiling was used to assess metabolites in experimental diets and in fish plasma, liver and muscle. A significant dose-dependent increase in growth and feed efficiency with increasing insect extract amounts was observed. The incremental incorporation of the insect extract in diet had a significant and progressive impact on the profile of dietary soluble compounds and trout metabolome. The metabolites modulated by dietary insect extracts in plasma and tissues were involved in protein and energy metabolism. This was associated with the efficient metabolic use of dietary free amino acids toward protein synthesis through the concomitant supply of balanced free amino acids and energy substrates in muscle. The findings provide new insights into how the dietary food metabolome affects fish metabolism.

An experiment was performed to study the effects of a low inclusion level of Chlorella vulgaris (CV) biomass in broiler diets on performance, immune response related to inflammatory status, and the intestinal histomorphology. The study was performed with 120 Ross 308 male broiler chickens from 0–35 days of age. The broilers were housed in 12 floor pens (1.5 m²) bedded with wood shavings. The broilers received a three phase diet program, either with 0.8% CV biomass (CV) or without CV (CON). Each diet program was replicated in six pens. The final body weight increased (p = 0.053), and the feed conversion ratio (FCR), corrected for body weight, was reduced (p = 0.02) in birds fed CV compared to birds fed CON. In addition, decreased haptoglobins (p = 0.02) and interleukin-13 (p < 0.01) responses were observed during the grower phase of birds fed CV compared to the birds fed CON. A strong correlation (r = 0.82, p < 0.01) was observed between haptoglobin response and FCR. Histomorphology parameters of the jejunum were not different between the groups. It was concluded that the inclusion of 0.8% CV biomass in broiler diets is effective in influencing immune responses related to inflammatory status and promoting broiler growth.

Introduction Fish feed formulations are constantly evolving to improve the quality of diets for farmed fish and to ensure the sustainability of the aquaculture sector. Nowadays, insect, microalgae and yeast are feedstuff candidates for new feeds. However, the characterization of aquafeed is still based on proximate and targeted analyses which may not be sufficient to assess feed quality. Objectives Our aim was to highlight the soluble compounds that specifically differ between selected plant-based feeds complemented with alternative feedstuffs and discuss their origin and potential for fish nutrition. Methods A growth trial was carried out to evaluate growth performances and feed conversion ratios of fish fed plant-based, commercial, insect, spirulina and yeast feeds. ¹H NMR metabolomics profiling of each feed was performed using a CPMG sequence on polar extracts. Spectra were processed, and data were analyzed using multivariate and univariate analyses to compare alternative feeds to a plant-based feed. Results Fish fed insect or yeast feed showed the best growth performances associated with the lowest feed conversion ratios compared to plant-based feed. Soluble compound ¹H NMR profiles of insect and spirulina alternative feeds differed significantly from the plant-based one that clustered with yeast feed. In insect and spirulina feeds, specific differences compared to plant-based feed concerned glycerol and 3-hydroxybutyrate, respectively. Conclusion This strategy based on compositional differences between plant-based and alternative feeds can be useful for detecting compounds unsuspected until now that could impact fish metabolism.

Cette thèse s’inscrit dans le contexte du développement d’une alimentation durable en aquaculture. Les aliments aquacoles, historiquement à base de ressources marines, sont aujourd’hui principalement à base de ressources végétales. Cependant, l’utilisation d’aliments exclusivement végétaux chez les espèces carnivores est limitée par les faibles performances de croissance résultant notamment d’effets négatifs sur la digestion et le métabolisme. De nouveaux aliments à base de matières premières végétales complétés par des ingrédients alternatifs, extraits protéiques de levures (Saccharomyces cerevisiae), insectes (Hermetia illucens) et microalgues (Spirulina platensis), ont été formulés pour proposer des aliments performants sans ressources marines. L’objectif de cette thèse est de caractériser les composés solubles de ces aliments alternatifs testés pour les performances de croissance de la truite en pisciculture expérimentale, et d’évaluer les effets engendrés sur le métabolisme par une approche métabolomique basée sur la RMN du proton. Ce type d’approche intégrée combinant les métabolomes de l’aliment et de l’animal est original chez les poissons. La caractérisation des composés solubles des aliments alternatifs a permis de mettre en évidence des marqueurs des matières premières alternatives et des composés jusque-là non identifiés par les techniques d’analyses ciblées utilisées en routine pour la caractérisation des aliments : par exemple marqueur de type quinone pour les microalgues, et composé glycérol pour les insectes. Certains de ces composés sont également actifs sur le métabolisme de la truite. Les effets métaboliques ont été étudiés spécifiquement pour les aliments comprenant des taux d’incorporation croissants d’ingrédient levure et insecte ayant des effets significatifs sur la croissance. Les effets métaboliques observés au niveau du métabolome plasmatique, hépatique et musculaire des truites nourries avec ces aliments alternatifs suggèrent que l’amélioration de la croissance résulte de la réduction des matières premières végétales des aliments, et d’effets spécifiques des matières premières alternatives. La réduction de la teneur en farines végétales affecte le métabolisme musculaire notamment par des modifications des teneurs en histidine et taurine. Ces métabolites attestent de la restauration de fonctions importantes dans le muscle : la régulation du pouvoir tampon et de l’osmolarité. Les aliments contenant l’ingrédient levure induisent un effet spécifique sur le métabolisme énergétique et sur le statut de la bétaïne hépatique. Les aliments contenant l’ingrédient insecte induisent un effet sur le métabolisme protéique musculaire grâce à l’apport d’acides aminés libres utilisés pour la protéosynthèse et la fourniture d’énergie. L’intégration des données métabolomiques et zootechniques montre l’histidine comme un marqueur original de la croissance. Afin de proposer une méthode d’analyse non-invasive du métabolome hépatique et musculaire, nous avons testé la prédiction de la variation des métabolites tissulaires à partir du métabolome plasmatique. Cette thèse ouvre de nouvelles perspectives pour améliorer l’évaluation (i) de la qualité des aliments aquacoles, et (ii) des effets nutritionnels de nouveaux aliments par l’identification de voies métaboliques et de fonctions utiles en relation avec la croissance chez la truite.