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1. 5 Scénarios pour la pisciculture française en 2021

Author

Barnaud, Antoine, Bonnemaire, Joseph, Clément, Olivier, Forraz, Marie, Fostier, Alexis, Gérard, Andre, Girard, Sophie, Jouan, Yannick, Lazard, Jérôme, Le Bail, Pierre-Yves, Levadoux, Marine, Médale, Françoise, Tocqueville, Aurélien, UMR INRA / IFREMER / Univ. Bordeaux 1 : Nutrition, Aquaculture et Génomique, ., Le Gouessant, ., Ecole Nationale d'Enseignement Supérieur Agronomique de Dijon, ., Viviers de France, ., Institut Français de Recherche pour l'Exploitation de la Mer, ., Filière Lorraine d'Aquaculture Continentale, ., Centre de Coopération Internationale en Recherche Agronomique pour le Développement, ., Comité interprofessionnel des produits de l'aquaculture, ., Institut Technique de l'Aviculture et des Elevages de Petits Animaux, ., ProdInra, Migration, Coopérative Le Gouessant [Lamballe], Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD), Nutrition, Aquaculture et Génomique (NUAGE), Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Viviers de France SA, Partenaires INRAE, Station commune de Recherches en Ichtyophysiologie, Biodiversité et Environnement (SCRIBE), Institut National de la Recherche Agronomique (INRA), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Filière Lorraine d'Aquaculture Continentale, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Comité Interprofessionnel des Produits de l'Aquaculture (CIPA), and ITAVI

Subjects
[SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], [INFO]Computer Science [cs], [INFO] Computer Science [cs], ETUDE PROSPECTIVE
Abstract

L’Inra a souhaité engager une réflexion prospective sur l’évolution de différentes filières animales sur le territoire national afin de mieux programmer les recherches. La prospective sur la pisciculture a été initiée au sein de la commission Inra filière Poissons avec la volonté d'associer différents acteurs de la filière. Chercheurs de l’Inra et des autres instituts de recherche dans le domaine piscicole se sont joints à des partenaires professionnels et institutionnels pour élaborer une vision partagée des futurs possibles de la pisciculture en France en 2021. L’objectif est de disposer d’images cohérentes et contrastées de l’avenir afin d’identifier les défis à relever et d’intégrer les enjeux locaux et nationaux dans le contexte international pour choisir les orientations de recherche et hiérarchiser les priorités.

Published
2007

2. Suplementing aquafeeds with new alternative ingredients: a promising solution to improve plant-based diet efficiency in rainbow trout

Author

Skiba-Cassy, Sandrine, BUREL, Christine, Kerneis, Thierry, Labbé, Laurent, Terrier, Frédéric, Corraze, Geneviève, Richard, Nadège, Marchand, Y., Dupont-Nivet, Mathilde, Nutrition, Métabolisme, Aquaculture (NuMéA), Institut National de la Recherche Agronomique (INRA)-Université de Pau et des Pays de l'Adour (UPPA), Pisciculture Expérimentale INRA des Monts d'Arrée (PEIMA), Institut National de la Recherche Agronomique (INRA), Phileo Lesaffre Animal Care, Coopérative Le Gouessant [Lamballe], Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, We thank FUI (Fonds Unique Interministériel) 2014 for financial support of the NINAqua project, European Aquaculture Society (EAS). BEL., and Le Gouessant

Subjects
oncorhynchus mykiss, alimentation végétale, alimentation animale, animal nutrition, growth, [SDV.BA]Life Sciences [q-bio]/Animal biology, animal feeding, nutrition animale, supplémentation alimentaire, rainbow trout, croissance, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition
Abstract

Session Nutrition: Additives and Ingredients; Suplementing aquafeeds with new alternative ingredients: a promising solution to improve plant-based diet efficiency in rainbow trout. Aquaculture Europe 2019

Published
2019

3. Nouveaux ingrédients et amélioration génétique : des solutions prometteuses pour améliorer les performances de croissance de la truite arc-en-ciel sur aliment végétal

Author

Skiba-Cassy, Sandrine, BUREL, Christine, Kerneis, Thierry, Labbé, Laurent, Terrier, Frédéric, Corraze, Geneviève, Richard, Nadège, Guimas, Laurence, Marchand, Y., Dupont-Nivet, Mathilde, Nutrition, Métabolisme, Aquaculture (NuMéA), Institut National de la Recherche Agronomique (INRA)-Université de Pau et des Pays de l'Adour (UPPA), Pisciculture Expérimentale INRA des Monts d'Arrée (PEIMA), Institut National de la Recherche Agronomique (INRA), Phileo Lesaffre Animal Care, Copalis Industrie, Coopérative Le Gouessant [Lamballe], Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Institut Technique de l'Aviculture et des Elevages de Petits Animaux (ITAVI). FRA., and Le Gouessant

Subjects
fish, salmonidae, amélioration génétique, trout, oncorhynchus mykiss, alimentation animale, [SDV.BA]Life Sciences [q-bio]/Animal biology, performance de croissance, rainbow trout, poisson, aquaculture, rainbow, animal nutrition, salmonids, novelty foods, animal feeding, nutrition animale, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, truite arc en ciel, aliment nouveau
Abstract

Session : Génétique et Sélection; Nouveaux ingrédients et amélioration génétique : des solutions prometteuses pour améliorer les performances de croissance de la truite arc-en-ciel sur aliment végétal. 6. Journées de la Recherche Filière Piscicole

Published
2019

4. Critical assessment of metabolism and related growth and quality traits in trout fed spirulina-supplemented plant-based diets

Author

Simon Roques, Catherine Deborde, Sandrine Skiba, Olivier Cala, Yann Marchand, Annick Moing, Benoit Fauconneau, Nutrition, Métabolisme, Aquaculture (NuMéA), Université de Pau et des Pays de l'Adour (UPPA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Phileo Lesaffre Animal Care, Biologie du fruit et pathologie (BFP), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Plateforme Bordeaux Metabolome, Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-MetaboHUB-Bordeaux, MetaboHUB-MetaboHUB, Centre de RMN à très hauts champs de Lyon (CRMN), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Coopérative Le Gouessant [Lamballe], This work was supported by FUI 2014 NINAqua [grant number 15008485-056 Nouvelle-Aquitaine Regional Council] and MetaboHUB [grant number ANR-11-INBS-0010]. Simon Roques was funded by 'Phileo by Lesaffre' and the French ANRT (Association Nationale Recherche Technologie). Financial support from the IR-RMN-THC Fr3050 CNRS for conducting the research is gratefully acknowledged., and ANR-11-INBS-0010,METABOHUB,Développement d'une infrastructure française distribuée pour la métabolomique dédiée à l'innovation(2011)

Subjects
[SDV]Life Sciences [q-bio], [SDV.BA]Life Sciences [q-bio]/Animal biology, Single-cell ingredient, Proton NMR, Metabolomics, spirulina, Fish nutrition, Aquatic Science, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, ComputingMilieux_MISCELLANEOUS, Plant-based diet
Abstract

International audience

Published
2022
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5. Sustainable plant-based diets promote rainbow trout gut microbiota richness and do not alter resistance to bacterial infection

Author

Pérez-Pascual, David, Pérez-Cobas, Ana Elena, Rigaudeau, Dimitri, Rochat, Tatiana, Bernardet, Jean-François, Skiba-Cassy, Sandrine, Marchand, Yann, Duchaud, Eric, Ghigo, Jean-Marc, Génétique des Biofilms - Genetics of Biofilms, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Biologie des Bactéries intracellulaires - Biology of Intracellular Bacteria, Plateforme d'Infectiologie Expérimentale des Rongeurs et Poissons (IERP (UE 0907)), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Virologie et Immunologie Moléculaires (VIM (UR 0892)), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Nutrition, Métabolisme, Aquaculture (NuMéA), Université de Pau et des Pays de l'Adour (UPPA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Coopérative Le Gouessant [Lamballe], This research was funded by an FUI AAP n°20 NINAQUA grant, by the French government’s Investissement d’Avenir Program, Laboratoire d’Excellence 'Integrative Biology of Emerging Infectious Diseases' (grant n°ANR-10-LABX-62-IBEID) and the Fondation pour la Recherche Médicale (grant no. DEQ20180339185). D.P-P was supported by an Institut Carnot MS Postdoctoral fellowship. The Institut Pasteur C2RT is supported by a France Génomique grant (ANR-10-INBS-09-09)., We thank Frédéric Terrier and his team from the INRAE experimental fish farm at Donzacq, France, for his help in feed preparation, and Cédric Fund from the Biomics Platform from the C2RT at Institut Pasteur, Paris, France, for 16S rRNA library construction and sequencing., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Rainbow trout, Veterinary medicine, [SDV]Life Sciences [q-bio], SF600-1100, Flavobacterium psychrophilum, Gut microbiota, Microbiology, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, QR1-502, Sustainable aquaculture diet, Research Article
Abstract

Background Farmed fish food with reduced fish-derived products are gaining growing interest due to the ecological impact of fish-derived protein utilization and the necessity to increase aquaculture sustainability. Although different terrestrial plant proteins could replace fishmeal proteins, their use is associated with adverse effects. Here, we investigated how diets composed of terrestrial vegetal sources supplemented with proteins originating from insect, yeast or terrestrial animal by-products affect rainbow trout (Onchorynchus mykiss) gut microbiota composition, growth performance and resistance to bacterial infection by the fish pathogen Flavobacterium psychrophilum responsible for frequent outbreaks in aquaculture settings. Results We showed that the tested regimes significantly increased gut bacterial richness compared to full vegetal or commercial-like diets, and that vegetal diet supplemented with insect and yeast proteins improves growth performance compared to full vegetal diet without altering rainbow trout susceptibility to F. psychrophilum infection. Conclusion Our results demonstrate that the use of insect and yeast protein complements to vegetal fish feeds maintain microbiota functions, growth performance and fish health, therefore identifying promising alternative diets to improve aquaculture’s sustainability. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-021-00107-2.

Published
2021
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6. Growth Performance and Adaptability of European Sea Bass (Dicentrarchus labrax) Gut Microbiota to Alternative Diets Free of Fish Products

Author

Gilbert Dutto, Charles Rodde, Jean-Marc Ghigo, David Pérez-Pascual, Jordi Estellé, Jean-François Bernardet, Cyrille Przybyla, Yann Marchand, Eric Duchaud, Génétique des Biofilms - Genetics of Biofilms, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Station IFREMER de Palavas-les-Flots, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Virologie et Immunologie Moléculaires (VIM (UR 0892)), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Coopérative Le Gouessant [Lamballe], FUI AAP n°20 NINAQUA/Fonds Unique Interministériel, DEQ20180339185/Fondation pour la Recherche Médicale NA/Institut Carnot Pasteur MS, ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay-AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD)

Subjects
0301 basic medicine, Microbiology (medical), Firmicutes, Fish farming, Gut flora, Microbiology, Feed conversion ratio, Commercial fish feed, 03 medical and health sciences, fish gut microbiota, Virology, 14. Life underwater, Food science, Sea bass, European sea bass, bacteria, lcsh:QH301-705.5, 2. Zero hunger, biology, 04 agricultural and veterinary sciences, biology.organism_classification, Fish products, 030104 developmental biology, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, lcsh:Biology (General), [SDV.SA.SPA]Life Sciences [q-bio]/Agricultural sciences/Animal production studies, 040102 fisheries, 0401 agriculture, forestry, and fisheries, Dicentrarchus, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition
Abstract

Innovative fish diets made of terrestrial plants supplemented with sustainable protein sources free of fish-derived proteins could contribute to reducing the environmental impact of the farmed fish industry. However, such alternative diets may influence fish gut microbial community, health, and, ultimately, growth performance. Here, we developed five fish feed formulas composed of terrestrial plant-based nutrients, in which fish-derived proteins were substituted with sustainable protein sources, including insect larvae, cyanobacteria, yeast, or recycled processed poultry protein. We then analyzed the growth performance of European sea bass (Dicentrarchus labrax L.) and the evolution of gut microbiota of fish fed the five formulations. We showed that replacement of 15% protein of a vegetal formulation by insect or yeast proteins led to a significantly higher fish growth performance and feed intake when compared with the full vegetal formulation, with feed conversion ratio similar to a commercial diet. 16S rRNA gene sequencing monitoring of the sea bass gut microbial community showed a predominance of Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes phyla. The partial replacement of protein source in fish diets was not associated with significant differences on gut microbial richness. Overall, our study highlights the adaptability of European sea bass gut microbiota composition to changes in fish diet and identifies promising alternative protein sources for sustainable aquafeeds with terrestrial vegetal complements.

Published
2020
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7. Integrative Metabolomics for Assessing the Effect of Insect (Hermetia illucens) Protein Extract on Rainbow Trout Metabolism

Author

Annick Moing, Yann Marchand, Nadège Richard, Laurence Guimas, Benoit Fauconneau, Simon Roques, Daniel J. Jacob, Sandrine Skiba-Cassy, Catherine Deborde, Nutrition, Métabolisme, Aquaculture (NuMéA), Université de Pau et des Pays de l'Adour (UPPA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Phileo Lesaffre Animal Care, Plateforme Metabolome Bordeaux, INRAE, 2018, MetaboHUB, Centre INRAE Nouvelle Aquitaine Bordeaux, doi: 10.15454/1.5572412770331912E12 (PMB), Institut National de la Recherche Agronomique (INRA), Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Copalis Industrie, Coopérative Le Gouessant [Lamballe], Biologie du fruit et pathologie (BFP), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Moing, Annick

Subjects
0301 basic medicine, Hermetia illucens, Endocrinology, Diabetes and Metabolism, lcsh:QR1-502, profiling oncorhynchus mykiss, hermetia illucens, Biochemistry, Feed conversion ratio, lcsh:Microbiology, Hydrolysate, 03 medical and health sciences, Metabolomics, Aquaculture, integrative metabolomics, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, Biologie animale, Metabolome, fish nutrition, insect, profiling Oncorhynchus mykiss, Hermetia illucens, proton NMR, Food science, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Molecular Biology, Animal biology, 2. Zero hunger, biology, business.industry, fungi, 04 agricultural and veterinary sciences, Metabolism, biology.organism_classification, Trout, 030104 developmental biology, Oncorhynchus mykiss, [SDV.SA.SPA]Life Sciences [q-bio]/Agricultural sciences/Animal production studies, 040102 fisheries, 0401 agriculture, forestry, and fisheries, Hermetia illucens ▼ Show Figures, profiling, business, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, métabolomique
Abstract

UMR BFP - Equipe BFP; 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.

Published
2020
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8. Inclusion of a protein-rich yeast fraction in rainbow trout plant-based diet: Consequences on growth performances, flesh fatty acid profile and health-related parameters

Author

Jorge Dias, Marina Machado, Nadège Richard, Sergio Fernández-Boo, Yann Marchand, Sandrine Skiba-Cassy, Geneviève Corraze, Albert Girons, Frédéric Terrier, Benjamín Costas, Phileo Lesaffre Animal Care, Interdisciplinary Centre of Marine and Environmental Research [Matosinhos, Portugal] (CIIMAR), Universidade do Porto, Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), ICTIOVET, Sparos Lda, Nutrition, Métabolisme, Aquaculture (NuMéA), Université de Pau et des Pays de l'Adour (UPPA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Coopérative Le Gouessant [Lamballe], FUI 2014 (Grant N◦2014-NINAQUA) NINAqua project, and Portuguese national funds through FCT –Foundation for Science and Technology within the scope of UIDB/04423/2020 and UIDP/04423/2020

Subjects
Aquatic Science, Feed conversion ratio, Commercial fish feed, 03 medical and health sciences, Fish meal, Aquaculture, 14. Life underwater, Food science, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, biology, business.industry, [SDV.BA]Life Sciences [q-bio]/Animal biology, 04 agricultural and veterinary sciences, Fatty acid, Fish oil, biology.organism_classification, Yeast, Plant-based diet, Trout, Rainbow trout, 040102 fisheries, 0401 agriculture, forestry, and fisheries, Gut health, business, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition
Abstract

International audience; Fast development of the aquaculture sector in the last decades conducted to a shortage in traditional ingredients (fishmeal and fish oil) that were not anymore avaible in sufficient quantity to purvey such growing aquafeeds needs. Ingredients of plant-derived raw materials, thus started to be preferentially incorporated into aquafeed formulas, and are nowadays being routinely used in most fish feed formulas. However, the total replacement of fishmeal and fish oil has not yet been reached due to negative impacts on feed intake and feed efficiency, perturbations of metabolic and health status, impacts on flesh quality, and growth performances slowdown. Single cell protein sources such as yeast protein products could be an alternative solution to complement and mitigate detrimental effects of plant proteins. This was assessed in a 12 weeks trial in which rainbow trout (Oncorhynchus mykiss) juveniles were fed with a plant-based diet (totally devoid of fishmeal and fish oil), containing 0, 5, 10 or 15% of a protein-rich yeast fraction and microalgae as DHA source.Results indicated that a 15% protein-rich yeast fraction inclusion may upgrade growth performance of trout fed plant-based diets by improving feed conversion ratio and body nitrogen retention. Surprisingly, 5% yeast incorporation in the diet leaded to enhanced accumulation of DHA in whole body that could be linked to a higher expression of the fatty acid elongase 2. Immune status and gut health of fish were also assessed through histological analyses and transcript expression level measurements of immune-related genes in distal intestine complemented by measurement of some plasma immune-related parameters. A lower score of lymphocytes infiltrates in lamina propria of fish distal intestine was observed from 10% inclusion level of the yeast fraction and the calculated overall inflammation score was greatly reduced with 15% inclusion level. In fish fed diets containing 5% and 15% yeast fraction, a higher internal perimeter: external perimeter ratio was measured compared to fish fed the control plant-based group. Inclusion of 15% yeast fraction in the plant-based diet also lead to an increased expression of mucin 5 and claudin a compared to 5% inclusion level. A statistically negative linear correlation was revealed between plasma neutrophils proportions and dietary yeast content. Plasma lysozyme concentration was lower in trouts fed diets containing 10% and 15% yeast fraction. All together, those results revealed that inclusion of yeast in a plant-based diet enables to improve rainbow trout gut health and global immune status

Published
2021
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9. Proton-NMR Metabolomics of Rainbow Trout Fed a Plant-Based Diet Supplemented with Graded Levels of a Protein-Rich Yeast Fraction Reveal Several Metabolic Processes Involved in Growth

Author

Benoit Fauconneau, Nadège Richard, Yann Marchand, Annick Moing, Sandrine Skiba-Cassy, Catherine Deborde, Sylvain Prigent, Simon Roques, Laurence Larroquet, Biologie du fruit et pathologie (BFP), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Bordeaux (UB), Nutrition, Métabolisme, Aquaculture (NuMéA), Université de Pau et des Pays de l'Adour (UPPA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Phileo Lesaffre Animal Care, Plateforme Metabolome Bordeaux, Institut National de la Recherche Agronomique (INRA), Coopérative Le Gouessant [Lamballe], Phileo by Lesaffre, Association Nationale de la Recherche et de la Technologie, Grant No. CIFRE 2016/0775, FUI 2014 NINAqua (Nouvelle-Aquitaine Regional Council funding 15008485-056), and ANR-11-INBS-0010,METABOHUB,Développement d'une infrastructure française distribuée pour la métabolomique dédiée à l'innovation(2011)

Subjects
Magnetic Resonance Spectroscopy, [SDV]Life Sciences [q-bio], Metabolite, Medicine (miscellaneous), Saccharomyces cerevisiae, yeast, Feed conversion ratio, Fungal Proteins, 03 medical and health sciences, chemistry.chemical_compound, Betaine, Metabolomics, Animals, 14. Life underwater, Food science, Muscle, Skeletal, 030304 developmental biology, 0303 health sciences, metabolic process, Nutrition and Dietetics, Dose-Response Relationship, Drug, biology, fish nutrition, [SDV.BA]Life Sciences [q-bio]/Animal biology, Body Weight, 04 agricultural and veterinary sciences, Metabolism, Plants, biology.organism_classification, Animal Feed, metabolomics, rainbow trout, NMR, Yeast, Diet, Trout, Liver, chemistry, Oncorhynchus mykiss, Dietary Supplements, 040102 fisheries, 0401 agriculture, forestry, and fisheries, Female, Rainbow trout, Dietary Proteins, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition
Abstract

Background Plant raw materials are commonly used in aquafeeds, as marine resources are unsustainable. However, full plant-based diets lead to poorer fish growth performance. Objective We aimed to understand the metabolic effects of a yeast fraction as a protein supplement in a plant-based diet and to integrate such effects with phenotypic traits as a new approach to assess the interest of this raw material. Methods Juvenile (49 g) rainbow trout (Oncorhynchus mykiss) were fed graded levels of a yeast protein-rich fraction (5% YST05, 10% YST10, 15% YST15) in a plant-based diet (PB) for 84 d. Final body weight, feed conversion ratio, and hepatosomatic and viscerosomatic indexes were measured. Plasma, liver, and muscle 1H-NMR fingerprints were analyzed with principal component analyses, and their metabolite patterns were clustered according to the yeast level to identify concomitant metabolic effects. A regression modeling approach was used to predict tissue metabolite changes from plasma fingerprints. Results In tissues, the patterns of metabolite changes followed either linear trends with the gradual inclusion of a yeast fraction (2 patterns out of 6 in muscle, 1 in liver) or quadratic trends (4 patterns in muscle, 5 in liver). Muscle aspartate and glucose (395 and 138% maximum increase in relative content compared with PB, respectively) revealing modification in energy metabolism, as well as modification of liver betaine (163% maximum increase) and muscle histidine (57% maximum decrease) related functions, indicates that the yeast fraction could improve growth in several ways. The highest correlation between measured and predicted metabolite intensities in a tissue based on plasma fingerprints was observed for betaine in liver (r = 0.80). Conclusions These findings herald a new approach to assess the plurality of metabolic effects induced by diets and establish the optimal level of raw materials. They open the way for using plasma as a noninvasive matrix in trout nutrition studies.

Published
2020
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10. NINAQUA : nouveaux ingrédients pour de nouveaux aliments aquacoles – effets sur la qualité des truitesau stade portion

Author

Brit, Guillaume, Bugeon, Jérôme, Goardon, Lionel, Kerneis, Thierry, Caudal, Erwan, Cardinal, Mireille, Marchand, Yann, Skiba-Cassy, Sandrine, Dupont-Nivet, Mathilde, Labbé, Laurent, Lefèvre, Florence, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Recherche Agronomique (INRA), Pisciculture Expérimentale INRA des Monts d'Arrée (PEIMA), Institut National de la Recherche Agronomique (INRA), LEMMMB, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Le Gouessant Aquaculture, Nutrition, Métabolisme, Aquaculture (NuMéA), Institut National de la Recherche Agronomique (INRA)-Université de Pau et des Pays de l'Adour (UPPA), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), FUI NINAQUA [Lesaffre / Copalis], Institut National de la Recherche Agronomique (INRA)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, and Institut Technique de l'Aviculture et des Elevages de Petits Animaux (ITAVI). FRA.

Subjects
fish, analyse sensorielle, alimentation, food intake, [SDV]Life Sciences [q-bio], fish fillets, qualité de la chair, sensory analysis, poisson, novelty foods, croissance animale, filet de poisson, chair de poisson, animal growth, aliment nouveau
Abstract

Session : Nutrition et qualité; NINAQUA : nouveaux ingrédients pour de nouveaux aliments aquacoles – effets sur la qualité des truitesau stade portion. 6. Journées de la Recherche Filière Piscicole

Published
2019

11. Exploring the adaptation of rainbow trout metabolome to novel aquafeeds by H-NMR metabolomics

Author

Roques, Simon, Deborde, Catherine, Richard, Nadege, Skiba-Cassy, Sandrine, Moing, Annick, Fauconneau, Benoit, Nutrition, Métabolisme, Aquaculture (NuMéA), Institut National de la Recherche Agronomique (INRA)-Université de Pau et des Pays de l'Adour (UPPA), Phileo Lesaffre Animal Care, Biologie du fruit et pathologie (BFP), Université Sciences et Technologies - Bordeaux 1-Institut National de la Recherche Agronomique (INRA)-Université Bordeaux Segalen - Bordeaux 2, FUI 2014 (NINAQUA with le Gouessant, COPALIS, Algae Natural food, Phileo-Lesaffre Animal Care), ANRT (CIFRE 2016/0775) and MetaboHUB (ANR-11-INBS-0010), ProdInra, Archive Ouverte, Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), and Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1

Subjects
trout, métabolome, [SDV.BA] Life Sciences [q-bio]/Animal biology, rainbow, animal nutrition, [SDV.BA]Life Sciences [q-bio]/Animal biology, novelty foods, nutrition animale, métabolomique, truite arc en ciel, aliment nouveau
Abstract

Résumé; Exploring the adaptation of rainbow trout metabolome to novel aquafeeds by H-NMR metabolomics. Metabolomics 2019. 15. Annual Conference of the Metabolomics Society

Published
2019

12. Integrative 1H-NMR metabolomic investigation of the effect of alternative diets on rainbow trout plasma

Author

Roques, Simon, Deborde, Catherine, Richard, Nadège, Skiba-Cassy, Sandrine, Moing, Annick, Fauconneau, Benoit, Nutrition, Métabolisme, Aquaculture (NuMéA), Institut National de la Recherche Agronomique (INRA)-Université de Pau et des Pays de l'Adour (UPPA), Biologie du fruit et pathologie (BFP), Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Phileo Lesaffre Animal Care, This research was funded by FUI 2014 (NINAQUA with Le Gouessant, COPALIS, Algae Natural Food and Phileo Lesaffre Animal Care), ANRT (CIFRE 2016/0775) and MetaboHUB (ANR-11-INBS-0010), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Université Sciences et Technologies - Bordeaux 1-Institut National de la Recherche Agronomique (INRA)-Université Bordeaux Segalen - Bordeaux 2, and ProdInra, Archive Ouverte

Subjects
endocrine system, trout, animal structures, métabolome, [SDV.BA] Life Sciences [q-bio]/Animal biology, urogenital system, alimentation animale, animal diseases, [SDV.BA]Life Sciences [q-bio]/Animal biology, education, [SDV.AEN] Life Sciences [q-bio]/Food and Nutrition, rainbow, animal nutrition, animal feeding, nutrition animale, micromass, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, plasma, métabolomique, truite arc en ciel
Abstract

Résumé; Integrative 1H-NMR metabolomic investigation of the effect of alternative diets on rainbow trout plasma. 18. ISFNF International Symposium on Fish Nutrition and Feeding "40 years of research in fish nutrition"

Published
2018

13. 1H-NMR metabolomic investigation of the effect of alternative diets on rainbow trout plasma profiles

Author

Roques, Simon, Deborde, Catherine, Richard, Nadège, Skiba-Cassy, Sandrine, Moing, Annick, Fauconneau, Benoit, Nutrition, Métabolisme, Aquaculture (NuMéA), Institut National de la Recherche Agronomique (INRA)-Université de Pau et des Pays de l'Adour (UPPA), Biologie du fruit et pathologie (BFP), Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Phileo Lesaffre Animal Care, This research was funded by FUI 2014 (NINAQUA with Le Gouessant, COPALIS, Algae Natural Food and Phileo Lesaffre Animal Care), ANRT (CIFRE 2016/0775) and MetaboHUB (ANR-11-INBS-0010), European Aquaculture Society (EAS)., Université Sciences et Technologies - Bordeaux 1-Institut National de la Recherche Agronomique (INRA)-Université Bordeaux Segalen - Bordeaux 2, and Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1

Subjects
Animal biology, oncorhynchus mykiss, alimentation animale, [SDV.BA]Life Sciences [q-bio]/Animal biology, Biologie animale, animal feeding, rainbow trout, micromass, plasma, métabolomique, alimentation alternative, analyse métabolomique
Abstract

Résumé; Fish farming needs high quality feeds to support the growing global demand for fish. Over the last two decades, the development of sustainable feeds based on plant feedstuffs has strongly reduced the use of marine resources. However, full plant-based feeds still reduce growth performances in carnivorous species such as salmonids. Thus, active research programmes are conducted on alternative feedstuffs in order to provide sustainable feeds for aquaculture especially trout farming. Our project aims at establishing a link between feed composition and plasma metabolome of rainbow trout (Oncorhynchus mykiss) through i) the characterization of plant-based diets devoid of marine resources complemented with insect, microalgae or yeast products, and ii) the analysis of trout plasma metabolome fed these alternative diets. Fish were fed ad libitum for three months with nine, iso-proteic and iso-energetic experimental diets: a control plant-based diet (PB) and eight diets containing 5%, 10% and 15% of either insects (INS), micro-algae (SPI) or yeast (YST). Ethanolic extracts of diets were prepared and analysed. Fish blood was collected 48 h after feeding and centrifuged to obtain plasma. The 1D 1 H-NMR profiles of both diet extracts and plasmas were acquired on a 500 MHz NMR spectrometer. Spectra were processed to select and integrate spectral regions with NMRProcFlow (nmrprocflow.org) and statistical analyses were realised with BioStatFlow webtool (biostatflow.org). Diet extract 1 H-NMR spectra showed specific compounds for INS and SPI diets compared to PB. These signals were related to triglyceride residues and organic acids and account for the origin of feedstuff and the effect of process. Multivariate analysis of plasma spectral data showed a classification of individuals based on diets according to highly discriminant signals variables. Several specific signals showed an increasing trend with graduate incorporation of alternative feedstuffs. Integrative metabolomics combining diet and trout plasma characterization highlights the significance of the soluble fraction of alternative diets and their extended impact on plasma metabolome.

Published
2018

14. Evaluation of alternative diets for farmed rainbow trout (Oncorhynchus mykiss) by H-NMR metabolomics

Author

Roques, Simon, Deborde, Catherine, Moing, Annick, Richard, N., Marchand, Y., BUREL, Christine, Skiba, Sandrine, Fauconneau, Benoit, Nutrition, Métabolisme, Aquaculture (NuMéA), Institut National de la Recherche Agronomique (INRA)-Université de Pau et des Pays de l'Adour (UPPA), Phileo Lesaffre Animal Care, Biologie du fruit et pathologie (BFP), Université Sciences et Technologies - Bordeaux 1-Institut National de la Recherche Agronomique (INRA)-Université Bordeaux Segalen - Bordeaux 2, Le Gouessant Aquaculture, Projet Fonds Unique Interministériel - Région Nouvelle Aquitaine Nouveaux Ingrédients pour de Nouveaux Aliments aQUAcoles (FUI NINAqua), ANRT (S.R.), INRA and the French MetaboHUB project (ANR-11-INBS-0010), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, ProdInra, Archive Ouverte, and Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)

Subjects
oncorhynchus mykiss, [SDV.BA] Life Sciences [q-bio]/Animal biology, aquaculture, [SDV.BA]Life Sciences [q-bio]/Animal biology, rainbow trout, alimentation alternative, métabolomique
Abstract

Résumé; Evaluation of alternative diets for farmed rainbow trout (Oncorhynchus mykiss) by H-NMR metabolomics. Aquaculture Europe 2017

Published
2017

15. Antimicrobial usage - impact on human and animal health and reduction

Author

Chauvin, Claire, Bertin, Joel, Guillot, Jean François, Dunoyer, Charlotte, Boudergue, Caroline, Giraud, Etienne, Laboratoire de Ploufragan - Plouzané, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Coopérative Le Gouessant [Lamballe], Université Francois Rabelais [Tours], Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), Institut National de la Recherche Agronomique (INRA). FRA. Institut Technique de l'Aviculture et des Elevages de Petits Animaux (ITAVI). Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), FRA. Centre Technique de la Conservation des Produits Agricoles (CTCPA), FRA., and Institut National de la Recherche Agronomique (INRA)-Université de Tours

Subjects
[SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2015

16. Genetic diversity and population structure of Mycobacterium marinum: new insights into host and environmental specificities

Author

Cédric Libert, Dominique Terru, Claudine Belon, Sylvain Godreuil, Antoine Barnaud, Christian Michel, Jean-Christophe Raymond, Anne-Laure Bañuls, Philippe Van de Perre, Maria-Laura Boschiroli, Vincent Broutin, Nicolas Keck, Pieter Stragier, Jean-François Bernardet, Alexandra Aubry, Cristina Gutierrez, Françoise Portaels, Marc Choisy, Emmanuelle Cambau, Olivier Dereure, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Universitaire de Montpellier (CHU Montpellier ), Université Montpellier 1 (UM1), Centre National de Références des Mycobactéries et de la Résistance aux Antituberculeux, Partenaires INRAE, Laboratoire Départemental Vétérinaire de l'Hérault, Conseil Général de l'Hérault, Unité de recherche Virologie et Immunologie Moléculaires (VIM (UR 0892)), Institut National de la Recherche Agronomique (INRA), Comité National des Pêches Maritimes et des Elevages Marins (CNPMEM), Parc Zoologique Darwin, Coopérative Le Gouessant [Lamballe], Institut de Médecine Tropicale Prince Léopold (IMT), Foundation for Innovative New Diagnostics (FIND), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Centre National de Référence des Mycobactéries et de la Résistance aux Antituberculeux [CHU Pitié-Salpêtrière], CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), ProdInra, Migration, Centre National de Référence des Mycobactéries et de la Résistance aux Antituberculeux [CHU Pitié-Salpêtrière] (CNR-MyRMA), and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)

Subjects
Male, [SDV]Life Sciences [q-bio], Strains, Population structure, Genetic diversity, Environmental impact, Fish Diseases, Genotype, Child, Genetics, 0303 health sciences, education.field_of_study, biology, Fishes, Osteomyelitis, Middle Aged, Biota, [SDV] Life Sciences [q-bio], Animal diseases, Skin infections, Child, Preschool, Female, Adult, DNA, Bacterial, Microbiology (medical), animal structures, Adolescent, Population, Mycobacterium Infections, Nontuberculous, Bacterial genetics, Young Adult, 03 medical and health sciences, Genetic variation, Animals, Humans, Typing, Polymorphism, education, Cutaneous reactions, Mycobacterium marinum, Ecosystem, Aged, 030304 developmental biology, 030306 microbiology, Arthritis, Genetic Variation, Mycobacteriology and Aerobic Actinomycetes, Tenosynovitis, biology.organism_classification, bacterial infections and mycoses, Interspersed Repetitive Sequences, Molecular Typing, Fish, Immunology, Tissue tropism, bacteria, Aquaria
Abstract

Mycobacterium marinum causes a systemic tuberculosis-like disease in fish and skin infections in humans that can spread to deeper structures, resulting in tenosynovitis, arthritis, and osteomyelitis. However, little information is available concerning (i) the intraspecific genetic diversity of M. marinum isolated from humans and animals; (ii) M. marinum genotype circulation in the different ecosystems, and (iii) the link between M. marinum genetic diversity and hosts (humans and fish). Here, we conducted a genetic study on 89 M. marinum isolates from humans ( n = 68) and fish ( n = 21) by using mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) typing. The results show that the M. marinum population is genetically structured not only according to the host but also according to the ecosystem as well as to tissue tropism in humans. This suggests the existence of different genetic pools in the function of the biological and ecological compartments. Moreover, the presence of only certain M. marinum genotypes in humans suggests a different zoonotic potential of the M. marinum genotypes. Considering that the infection is linked to aquarium activity, a significant genetic difference was also detected when the human tissue tropism of M. marinum was taken into consideration, with a higher genetic polymorphism in strains isolated from patients with cutaneous forms than from individuals with deeper-structure infection. It appears that only few genotypes can produce deeper infections in humans, suggesting that the immune system might play a filtering role.

Published
2012
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17. First full-length sequences of the S gene of European isolates reveal further diversity among turkey coronaviruses

Author

J. Bertin, D. Toquin, S. Maurel, François-Xavier Briand, Chantal Allée, M. Queguiner, Nicolas Eterradossi, C. Retaux, H. Morvan, L. Ravillion, V. Turblin, Avian and Rabbit Virology Immmunology and Parasitology Reserach Unit (VIPAC), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Coopérative Le Gouessant [Lamballe], MC Vet Conseil, present adress: Ceva Animal Health, and Laboratoire de Développement et d'analyse des Côtes d'Armor

Subjects
Turkeys, 040301 veterinary sciences, Sequence analysis, Molecular Sequence Data, Biology, medicine.disease_cause, Sensitivity and Specificity, Conserved sequence, 0403 veterinary science, 03 medical and health sciences, Viral Proteins, Food Animals, Viral Envelope Proteins, Phylogenetics, Genetic variation, medicine, Coronavirus, Turkey, Animals, Amino Acid Sequence, Gene, Conserved Sequence, Phylogeny, 030304 developmental biology, Coronavirus, Genetics, 0303 health sciences, Membrane Glycoproteins, General Immunology and Microbiology, Phylogenetic tree, Base Sequence, Reverse Transcriptase Polymerase Chain Reaction, [SDV.BA]Life Sciences [q-bio]/Animal biology, Life Sciences, Genetic Variation, 04 agricultural and veterinary sciences, Sequence Analysis, DNA, Nucleocapsid Proteins, RNA-Dependent RNA Polymerase, Virology, 3. Good health, Turkey coronavirus, Spike Glycoprotein, Coronavirus, Enteritis, Transmissible, of Turkeys, RNA, Viral, Animal Science and Zoology, France, Sequence Alignment
Abstract

An increasing incidence of enteric disorders clinically suggestive of the poult enteritis complex has been observed in turkeys in France since 2003. Using a newly designed real-time reverse transcriptase-polymerase chain reaction assay specific for the nucleocapsid (N) gene of infectious bronchitis virus (IBV) and turkey coronaviruses (TCoV), coronaviruses were identified in 37% of the intestinal samples collected from diseased turkey flocks. The full-length spike (S) gene of these viruses was amplified, cloned and sequenced from three samples. The French S sequences shared 98% identity at both the nucleotide and amino acid levels, whereas they were at most 65% and 60% identical with North American (NA) TCoV and at most 50% and 37% identical with IBV at the nucleotide and amino acid levels, respectively. Higher divergence with NA TCoV was observed in the S1-encoding domain. Phylogenetic analysis based on the S gene revealed that the newly detected viruses form a sublineage genetically related with, but significantly different from, NA TCoV. Additionally, the RNA-dependent RNA polymerase gene and the N gene, located on the 5' and 3' sides of the S gene in the coronavirus genome, were partially sequenced. Phylogenetic analysis revealed that both the NA TCoV and French TCoV (Fr TCoV) lineages included some IBV relatives, which were however different in the two lineages. This suggested that different recombination events could have played a role in the evolution of the NA and Fr TCoV. The present results provide the first S sequence for a European TCoV. They reveal extensive genetic variation in TCoV and suggest different evolutionary pathways in North America and Europe.

Published
2011
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18. Prospective pisciculture 2021 : quels scénarios ?

Author

Barnaud, A., Joseph Bonnemaire, Olivier Clément, Forraz, M., Alexis Fostier, Gerard, A., Stéphane Girard, Yann Jouan, Jérôme Lazard, Pierre-Yves Le Bail, Marine Levadoux, Françoise Médale, Tocqueville, A., Coopérative Le Gouessant [Lamballe], Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD), Nutrition, Aquaculture et Génomique (NUAGE), Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Viviers de France SA, Partenaires INRAE, Station commune de Recherches en Ichtyophysiologie, Biodiversité et Environnement (SCRIBE), Institut National de la Recherche Agronomique (INRA), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Filière Lorraine d'Aquaculture Continentale, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Comité Interprofessionnel des Produits de l'Aquaculture (CIPA), ITAVI, and ProdInra, Migration

Subjects
[SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], [INFO]Computer Science [cs], [INFO] Computer Science [cs], ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2007

19. New alternative ingredients and genetic selection are the next game changers in rainbow trout nutrition: a metabolomics appraisal.

Author

Roques S, Deborde C, Skiba-Cassy S, Médale F, Dupont-Nivet M, Lefevre F, Bugeon J, Labbé L, Marchand Y, Moing A, and Fauconneau B

Subjects
Animals, Saccharomyces cerevisiae, Diet, Dietary Supplements, Selection, Genetic, Animal Feed analysis, Oncorhynchus mykiss metabolism
Abstract

The formulation of sustainable fish feeds based on plant ingredients supplemented by alternative ingredients to plant (insect, micro-algae, yeast) and genetic selection of fish for plant-based diets were tested on rainbow trout in two separate experiments. Plant-based diets and corresponding diets supplemented with an ingredient mix: insect, micro-algae and yeast in Experiment A, and insect and yeast in Experiment B were compared to commercial-like diets. In experiment A, the mix-supplemented diet was successful in compensating the altered growth performance of fish fed their respective plant-based diet compared to those fed the commercial diet, by restoring feed conversion. In experiment B, the selected line demonstrated improved growth performances of fish fed mix-supplemented and plant-based diets compared to the non-selected line. Metabolomics demonstrated a plasma compositional stability in fish fed mix-supplemented and basal plant-based diets comprising an amino acid accumulation and a glucose depletion, compared to those fed commercial diets. The selected line fed mix-supplemented and commercial diets showed changes in inositol, ethanol and methanol compared to the non-selected line, suggesting an involvement of microbiota. Changes in plasma glycine-betaine content in fish fed the mix-supplemented diet suggest the ability of the selected line to adapt to alternative ingredients., (© 2023. The Author(s).)

Published
2023
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20. Sustainable plant-based diets promote rainbow trout gut microbiota richness and do not alter resistance to bacterial infection.

Author

Pérez-Pascual D, Pérez-Cobas AE, Rigaudeau D, Rochat T, Bernardet JF, Skiba-Cassy S, Marchand Y, Duchaud E, and Ghigo JM

Abstract

Background: Farmed fish food with reduced fish-derived products are gaining growing interest due to the ecological impact of fish-derived protein utilization and the necessity to increase aquaculture sustainability. Although different terrestrial plant proteins could replace fishmeal proteins, their use is associated with adverse effects. Here, we investigated how diets composed of terrestrial vegetal sources supplemented with proteins originating from insect, yeast or terrestrial animal by-products affect rainbow trout (Onchorynchus mykiss) gut microbiota composition, growth performance and resistance to bacterial infection by the fish pathogen Flavobacterium psychrophilum responsible for frequent outbreaks in aquaculture settings., Results: We showed that the tested regimes significantly increased gut bacterial richness compared to full vegetal or commercial-like diets, and that vegetal diet supplemented with insect and yeast proteins improves growth performance compared to full vegetal diet without altering rainbow trout susceptibility to F. psychrophilum infection., Conclusion: Our results demonstrate that the use of insect and yeast protein complements to vegetal fish feeds maintain microbiota functions, growth performance and fish health, therefore identifying promising alternative diets to improve aquaculture's sustainability.

Published
2021
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21. Growth Performance and Adaptability of European Sea Bass ( Dicentrarchus labrax ) Gut Microbiota to Alternative Diets Free of Fish Products.

Author

Pérez-Pascual D, Estellé J, Dutto G, Rodde C, Bernardet JF, Marchand Y, Duchaud E, Przybyla C, and Ghigo JM

Abstract

Innovative fish diets made of terrestrial plants supplemented with sustainable protein sources free of fish-derived proteins could contribute to reducing the environmental impact of the farmed fish industry. However, such alternative diets may influence fish gut microbial community, health, and, ultimately, growth performance. Here, we developed five fish feed formulas composed of terrestrial plant-based nutrients, in which fish-derived proteins were substituted with sustainable protein sources, including insect larvae, cyanobacteria, yeast, or recycled processed poultry protein. We then analyzed the growth performance of European sea bass ( Dicentrarchus labrax L.) and the evolution of gut microbiota of fish fed the five formulations. We showed that replacement of 15% protein of a vegetal formulation by insect or yeast proteins led to a significantly higher fish growth performance and feed intake when compared with the full vegetal formulation, with feed conversion ratio similar to a commercial diet. 16S rRNA gene sequencing monitoring of the sea bass gut microbial community showed a predominance of Proteobacteria , Firmicutes , Actinobacteria, and Bacteroidetes phyla. The partial replacement of protein source in fish diets was not associated with significant differences on gut microbial richness. Overall, our study highlights the adaptability of European sea bass gut microbiota composition to changes in fish diet and identifies promising alternative protein sources for sustainable aquafeeds with terrestrial vegetal complements.

Published
2020
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22. Proton-NMR Metabolomics of Rainbow Trout Fed a Plant-Based Diet Supplemented with Graded Levels of a Protein-Rich Yeast Fraction Reveal Several Metabolic Processes Involved in Growth.

Author

Roques S, Deborde C, Richard N, Marchand Y, Larroquet L, Prigent S, Skiba-Cassy S, Moing A, and Fauconneau B

Subjects
Animal Feed analysis, Animals, Body Weight drug effects, Diet veterinary, Dietary Supplements analysis, Dose-Response Relationship, Drug, Female, Fungal Proteins, Liver metabolism, Muscle, Skeletal drug effects, Muscle, Skeletal metabolism, Saccharomyces cerevisiae, Dietary Proteins administration & dosage, Magnetic Resonance Spectroscopy methods, Metabolomics methods, Oncorhynchus mykiss growth & development, Plants chemistry
Abstract

Background: Plant raw materials are commonly used in aquafeeds, as marine resources are unsustainable. However, full plant-based diets lead to poorer fish growth performance., Objective: We aimed to understand the metabolic effects of a yeast fraction as a protein supplement in a plant-based diet and to integrate such effects with phenotypic traits as a new approach to assess the interest of this raw material., Methods: Juvenile (49 g) rainbow trout (Oncorhynchus mykiss) were fed graded levels of a yeast protein-rich fraction (5% YST05, 10% YST10, 15% YST15) in a plant-based diet (PB) for 84 d. Final body weight, feed conversion ratio, and hepatosomatic and viscerosomatic indexes were measured. Plasma, liver, and muscle 1H-NMR fingerprints were analyzed with principal component analyses, and their metabolite patterns were clustered according to the yeast level to identify concomitant metabolic effects. A regression modeling approach was used to predict tissue metabolite changes from plasma fingerprints., Results: In tissues, the patterns of metabolite changes followed either linear trends with the gradual inclusion of a yeast fraction (2 patterns out of 6 in muscle, 1 in liver) or quadratic trends (4 patterns in muscle, 5 in liver). Muscle aspartate and glucose (395 and 138% maximum increase in relative content compared with PB, respectively) revealing modification in energy metabolism, as well as modification of liver betaine (163% maximum increase) and muscle histidine (57% maximum decrease) related functions, indicates that the yeast fraction could improve growth in several ways. The highest correlation between measured and predicted metabolite intensities in a tissue based on plasma fingerprints was observed for betaine in liver (r = 0.80)., Conclusions: These findings herald a new approach to assess the plurality of metabolic effects induced by diets and establish the optimal level of raw materials. They open the way for using plasma as a noninvasive matrix in trout nutrition studies., (Copyright © The Author(s) on behalf of the American Society for Nutrition 2020.)

Published
2020
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23. Integrative Metabolomics for Assessing the Effect of Insect ( Hermetia illucens ) Protein Extract on Rainbow Trout Metabolism.

Author

Roques S, Deborde C, Guimas L, Marchand Y, Richard N, Jacob D, Skiba-Cassy S, Moing A, and Fauconneau B

Abstract

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%). 1 H-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.

Published
2020
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