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3. PeakForest: a multi-platform digital infrastructure for interoperable metabolite spectral data and metadata management

Author

Paulhe, Nils, Canlet, Cécile, Damont, Annelaure, Peyriga, Lindsay, Durand, Stéphanie, Deborde, Catherine, Alves, Sandra, Bernillon, Stephane, Berton, Thierry, Bir, Raphael, Bouville, Alyssa, Cahoreau, Edern, Centeno, Delphine, Costantino, Robin, Debrauwer, Laurent, Delabrière, Alexis, Duperier, Christophe, Emery, Sylvain, Flandin, Amelie, Hohenester, Ulli, Jacob, Daniel, Joly, Charlotte, Jousse, Cyril, Lagree, Marie, Lamari, Nadia, Lefebvre, Marie, Lopez-Piffet, Claire, Lyan, Bernard, Maucourt, Mickael, Migne, Carole, Olivier, Marie-Francoise, Rathahao-Paris, Estelle, Petriacq, Pierre, Pinelli, Julie, Roch, Léa, Roger, Pierrick, Roques, Simon, Tabet, Jean-Claude, Tremblay-Franco, Marie, Traïkia, Mounir, Warnet, Anna, Zhendre, Vanessa, Rolin, Dominique, Jourdan, Fabien, Thévenot, Etienne, Moing, Annick, Jamin, Emilien, Fenaille, François, Junot, Christophe, Pujos-Guillot, Estelle, and Giacomoni, Franck

Published
2022
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6. New alternative ingredients and genetic selection are the next game changers in rainbow trout nutrition: a metabolomics appraisal

Author

Roques, Simon, primary, Deborde, Catherine, additional, Skiba-Cassy, Sandrine, additional, Médale, Françoise, additional, Dupont-Nivet, Mathilde, additional, Lefevre, Florence, additional, Bugeon, Jérome, additional, Labbé, Laurent, additional, Marchand, Yann, additional, Moing, Annick, additional, and Fauconneau, Benoit, additional

Published
2023
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8. Influence of agroecology practices on rumen microbiota associated with methane emission in dairy cattle

Author

Roques, Simon, Koning, Lisanne, van Riel, Johan, Bossers, Alex, Schokker, Dirkjan, Kar, Soumya Kanti, Sebek, Léon, Roques, Simon, Koning, Lisanne, van Riel, Johan, Bossers, Alex, Schokker, Dirkjan, Kar, Soumya Kanti, and Sebek, Léon

Abstract

Agroecology is a way to manage agroecosystems through the application of ecological principles. In dairy farming, implementation of agroecology aims to sustainable yet productive farms. A core principle is to incorporate diversity in farm components such as feed and animal. It is unclear, however, whether this diversity modifies the rumen microbiota and its environmentally threatening association with methane emission. The objective of this study was to decipher how the increase of botanical diversity in silage and late mowing of grasslands to produce silage, another principle of agroecology, modified the rumen microbiota of diverse dairy cattle breeds. Three groups of cows of different breeds, namely Holstein Friesian, Groninger Blaarkop and Jersey, were fed experimental silage-based diets with increasing levels of botanical diversity from late mowed grasslands compared to a reference silage-based diet with low botanical diversity and mowed earlier. Methane intensity was measured individually through GreenFeed stations. Rumen microbiota was characterized through 16S rRNA gene amplicon sequencing., Agroecology is a way to manage agroecosystems through the application of ecological principles. In dairy farming, implementation of agroecology aims to sustainable yet productive farms. A core principle is to incorporate diversity in farm components such as feed and animal. It is unclear, however, whether this diversity modifies the rumen microbiota and its environmentally threatening association with methane emission. The objective of this study was to decipher how the increase of botanical diversity in silage and late mowing of grasslands to produce silage, another principle of agroecology, modified the rumen microbiota of diverse dairy cattle breeds. Three groups of cows of different breeds, namely Holstein Friesian, Groninger Blaarkop and Jersey, were fed experimental silage-based diets with increasing levels of botanical diversity from late mowed grasslands compared to a reference silage-based diet with low botanical diversity and mowed earlier. Methane intensity was measured individually through GreenFeed stations. Rumen microbiota was characterized through 16S rRNA gene amplicon sequencing.

Published
2022

9. Effect of Feeding 0.8% Dried Powdered Chlorella vulgaris Biomass on Growth Performance, Immune Response, and Intestinal Morphology during Grower Phase in Broiler Chickens

Author

Roques, Simon, Koopmans, Sietse Jan, Mens, Annemarie, van Harn, Jan, van Krimpen, Marinus, Kar, Soumya Kanti, Roques, Simon, Koopmans, Sietse Jan, Mens, Annemarie, van Harn, Jan, van Krimpen, Marinus, and Kar, Soumya Kanti

Abstract

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.

Published
2022

11. RMN métabolomique, aliments & nutrition : quelques exemples de la plateforme Métabolome-MetaboHUB -Bordeaux

Author

Deborde, Catherine, Hounoum, Blandine, Roques, Simon, Jacob, Daniel, Maucourt, Mickaël, Moing, Annick, Fauconneau, Benoît, 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, Biologie du fruit et pathologie (BFP), Université de Bordeaux (UB)-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), Phileo Lesaffre Animal Care, FUI NINAquaANRT Convention Cifre (S Roques), UR370 QuaPA et PF AgroResonance, INRAE, ANR-11-INBS-0010,METABOHUB,Développement d'une infrastructure française distribuée pour la métabolomique dédiée à l'innovation(2011), and European Project: 288925,EC:FP7:KBBE,FP7-KBBE-2011-5,ARRAINA(2012)

Subjects
[SDV]Life Sciences [q-bio], [SDV.SA.SPA]Life Sciences [q-bio]/Agricultural sciences/Animal production studies, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition
Abstract

International audience

Published
2021

12. Metabolic effect of chronic exposure to airborne endotoxins in weaned piglet along with acute heat stress

Author

Roques, Simon, Soumya, Kar, Kluivers-Poodt, Marion, Schokker, Dirkjan, Stockhofe, Norbert, and Rebel, Johanna M

Subjects
Host Pathogen Interaction & Diagnostics, Epidemiologie, Animal Nutrition, Epidemiology, Bioinformatica & Diermodellen, animal diseases, Bacteriologie, Bacteriology, Diervoeding, Host Pathogen Interactie & Diagnostiek, Dierenwelzijn en gezondheid, Bio-informatics & Animal models, WIAS, Dierecologie, Animal Ecology, Animal Health & Welfare
Abstract

This dataset contains the raw data used for the article "Metabolic effect of chronic exposure to airborne endotoxins in weaned piglet along with acute heat stress".

Published
2021
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14. Métabolomique intégrative de l’adaptation du métabolisme de la truite arc-en-ciel (Oncorhynchus mykiss) à de nouveaux aliments à base de matières premières végétales et alternatives

Author

Roques, Simon, Nutrition, Métabolisme, Aquaculture (NuMéA), Institut National de la Recherche Agronomique (INRA)-Université de Pau et des Pays de l'Adour (UPPA), Université de Pau et des Pays de l'Adour, and Benoît Fauconneau, Annick Moing

Subjects
[SDV.BA]Life Sciences [q-bio]/Animal biology, these, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition
Abstract

UMR BFP - Equipe Métabolisme

Published
2019

15. Apport de la métabolomique par 1H-RMN pour le développement de nouveaux aliments chez la truite arc en ciel

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), Phileo Lesaffre Animal Care, Plateforme Metabolome MetaboHUB INRA Nouvelle Aquitaine, Institut National de la Recherche Agronomique (INRA), Biologie du fruit et pathologie (BFP), Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Institut Technique de l'Aviculture et des Elevages de Petits Animaux (ITAVI). FRA., Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, and ProdInra, Archive Ouverte

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

Session : Nutrition et Qualité; Apport de la métabolomique par 1H-RMN pour le développement de nouveaux aliments chez la truite arc en ciel. 6. Journées de la Recherche Filière Piscicole

Published
2019

16. 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

17. NMR-based metabolomics at Bordeaux Metabolome Facility: 4 short stories

Author

Deborde, Catherine, Jacob, Daniel, Roques, Simon, Roch, Léa, CLAVE, Anaïs, Batsale, Marguerite, Moing, Annick, ProdInra, Migration, Biologie du fruit et pathologie (BFP), Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), MetaboHUB, Nutrition, Métabolisme, Aquaculture (NuMéA), and Institut National de la Recherche Agronomique (INRA)-Université de Pau et des Pays de l'Adour (UPPA)

Subjects
[SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2019

18. Metabolomic application in fish nutrition: profiling novel aquaculture feeds and assessing their impact on rainbow trout plasma

Author

Roques, Simon, Deborde, Catherine, Richard, Nadège, Skiba, 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-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), ProdInra, Archive Ouverte, and Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1

Subjects
fish, trout, métabolome, [SDV.BA] Life Sciences [q-bio]/Animal biology, [SDV.BA]Life Sciences [q-bio]/Animal biology, fish feeding, nmr, aquaculture, poisson, rainbow, animal nutrition, nutrition animale, métabolisme, alimentation des poisson, truite arc en ciel
Abstract

UMR BFP - Equipe Métabolisme; Metabolomic application in fish nutrition: profiling novel aquaculture feeds and assessing their impact on rainbow trout plasma. EUROMAR - European Magnetic Resonance Meeting

Published
2018

19. NMR-based metabolomics workflow for characterization and effect assessment of alternative plant-based diets onplasma and microbiote in rainbow trout

Author

Deborde, Catherine, Madji Hounoum, Blandine, Jacob, Daniel, Maucourt, Mickael, Roques, Simon, Terrier, Frédéric, Gatesoupe, Francois Joël, Corraze, Geneviève, Médale, Françoise, Skiba-Cassy, Sandrine, Moing, Annick, Fauconneau, Benoit, Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, 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, Université Sciences et Technologies - Bordeaux 1-Institut National de la Recherche Agronomique (INRA)-Université Bordeaux Segalen - Bordeaux 2, ProdInra, Archive Ouverte, and Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)

Subjects
fish, approche métabolomique, trout, oncorhynchus mykiss, [SDV.BA] Life Sciences [q-bio]/Animal biology, [SDV.BA]Life Sciences [q-bio]/Animal biology, rmn métabolique, rainbow trout, fish feeding, poisson, aquaculture, rainbow, animal nutrition, nutrition animale, micromass, alimentation des poisson, métabolisme, plasma, métabolomique, truite arc en ciel
Abstract

UMR BFP - Equipe Métabolisme; NMR-based metabolomics workflow for characterization and effect assessment of alternative plant-based diets onplasma and microbiote in rainbow trout. EUROMAR - European Magnetic Resonance Meeting

Published
2018

20. 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

21. NMR-based metabolomics workflow for quality and effect assessment of alternative plant-based diets in rainbow trout

Author

DEBORDE, Catherine, MADJI HOUNOUM, Blandine, JACOB, Daniel, MAUCOURT, Mickael, ROQUES, Simon, TERRIER, Frédéric, CORRAZE, Geneviève, MÉDALE, Françoise, SKIBA-CASSY, Sandrine, MOING, Annick, FAUCONNEAU, Benoit, Biologie du fruit et pathologie (BFP), Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Platetorme Métabolome Bordeaux, Institut National de la Recherche Agronomique (INRA), Nutrition, Métabolisme, Aquaculture (NuMéA), and Institut National de la Recherche Agronomique (INRA)-Université de Pau et des Pays de l'Adour (UPPA)

Subjects
[CHIM.ANAL]Chemical Sciences/Analytical chemistry, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, ComputingMilieux_MISCELLANEOUS, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM]
Abstract

International audience

Published
2018

22. 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

23. 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

24. Metabolomics and fish nutrition: a review in the context of sustainable feed development.

Author

Roques, Simon, Deborde, Catherine, Richard, Nadège, Skiba‐Cassy, Sandrine, Moing, Annick, and Fauconneau, Benoit

Subjects
AQUAPONICS, METABOLOMICS, SUSTAINABLE development, FISH fillets, FISHES, NUTRITION, NUTRITIONAL genomics, FISH physiology
Abstract

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. [ABSTRACT FROM AUTHOR]

Published
2020
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26. Plant Metabolomics at Bordeaux Metabolome Facility, a member of MetaboHUB and PHENOME IA projects. Tools and Applications

Author

Deborde, Catherine, Ballias, Patricia, Bénard, Camille, Bernillon, Stéphane, Berton, Thierry, Cabasson, Cécile, Cocureau, Virginie, Diarrassouba, Salimata, Gibon, Yves, Jacob, Daniel, Lefebvre, Marie, Maucourt, Mickael, Rolin, Dominique, Roques, Simon, Fouillen, Laetitia, Mongrand, Sebastien, Bessoule, Jean-Jacques, Domergue, Frederic, Le Guedard, Marina, Testet, Eric, Moing, Annick, Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Laboratoire de biogenèse membranaire (LBM), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), ADERA, Université de Bordeaux (UB), Metabolomics Society., and ProdInra, Migration

Subjects
[SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2016

27. Preliminary results of the first NMR ring test inside MetaboHUB IA project on NMR acquisition and annotation of the NIST standard reference material of human plasma (SRM1950)

Author

Deborde, Catherine, Maucourt, Mickael, Roques, Simon, Rolin, Dominique, Moing, Annick, Lopez, Claire, Lagrée, Marie, Jousse, Cyril, Traïka, Mounir, PALAMA, Tony, Cahoreau, Edern, Peyriga, Lindsay, Portais, Jean-Charles, Bouville, Alyssa, Canlet, Cecile, Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Unité de Nutrition Humaine (UNH), Université d'Auvergne - Clermont-Ferrand I (UdA)-Clermont Université-Institut National de la Recherche Agronomique (INRA), Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Analyse de Xénobiotiques, Identification, Métabolisme (E20 Metatoul-AXIOM), ToxAlim (ToxAlim), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA)-MetaToul-MetaboHUB, Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Réseau Francophone de Métabolomique et Fluxomique (RFMF). FRA., Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1 (UB), Institut National de la Recherche Agronomique (INRA)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Clermont Université, Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), MetaToul FluxoMet (TBI-MetaToul), MetaboHUB-MetaToul, MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Toulouse Biotechnology Institute (TBI), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), MetaToul AXIOM (E20), Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Ecole d'Ingénieurs de Purpan (INP - PURPAN), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-MetaboHUB-MetaToul, Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Nutrition Humaine - Clermont Auvergne (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Université Clermont Auvergne (UCA), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA)

Subjects
[SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], NIST, metabolite, identification, santé humaine, human health, métabolisme, NMR, plasma, métabolomique
Abstract

Preliminary results of the first NMR ring test inside MetaboHUB IA project on NMR acquisition and annotation of the NIST standard reference material of human plasma (SRM1950). 10. journées scientifiques du Réseau Francophone de Métabolomique et Fluxomique RFMF 2016

Published
2016

28. Characterizing alternative feeds for rainbow trout (O. mykiss) by 1H NMR metabolomics.

Author

Roques, Simon, Deborde, Catherine, Richard, Nadège, Sergent, Luce, Kurz, Francis, Skiba-Cassy, Sandrine, Fauconneau, Benoît, and Moing, Annick

Subjects
FISH feeds, AQUACULTURE, RAINBOW trout, METABOLOMICS, NUCLEAR magnetic resonance
Abstract

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. [ABSTRACT FROM AUTHOR]

Published
2018
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29. Recent Advances in Enteric Methane Mitigation and the Long Road to Sustainable Ruminant Production.

Author

Roques S, Martinez-Fernandez G, Ramayo-Caldas Y, Popova M, Denman S, Meale SJ, and Morgavi DP

Subjects
Animals, Livestock, Diet, Animal Husbandry, Methane, Ruminants
Abstract

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.

Published
2024
Full Text
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