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24, chemin de Borde Rouge -Auzeville - CS52627 31326 Castanet Tolosan cedex - France

Last update: May 2021

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UMR 1332 Biologie du Fruit et Pathologie

Bordeaux Metabolome Facility

 Labeled IBISA platform, a member of the French Network of Metabolomics and Fluxomics 

Logo Bordeaux Metabolome

Contacts :

Metabolomics : Pierre PétriacqTel. +33 
Lipidomics : Laetitia FouillenTel. +33 
Polyphenols : Josep Valls Tel. +33  Tristan Richard Tel. +33
Biochemical phenotyping : Yves GibonTel. +33

Web :
Adress : INRA bât. IBVM - 71 avenue E. Bourlaux - CS 20032 - 33882 Villenave d'Ornon Cedex - France

Brief history of the facility

The Bordeaux Metabolome facility, a recognised leader site in plant metabolomics in France and in Europe, was created in 2003 in response to the emerging development of metabolomics and with the aim of federating and sharing the tools and know-how present in different institutes and teams studying metabolism in Bordeaux. It then expanded to become a Platform currently supported by three institutions (University of Bordeaux, INRAE and CNRS) via three research units: UMR1332 Fruit Biology and Pathology, Oenology (EA 4577, USC INRAE 1366) and UMR5200 Laboratory of Membrane Biogenesis.

In 2006, Bordeaux Metabolome was integrated into the Centre for Functional Genomics of Bordeaux (CGFB) which was restructured into a Federation of Research Platforms in 2019, in connection with the new research departments of the University of Bordeaux. During this period, Bordeaux Métabolome consolidated its position as a reference entity in plant metabolomics in France: it was labelled by IBiSA as a Research Platform in Life Sciences in 2008, recognized by INRA as a Strategic Platform in 2008 and as National Strategic Platform in 2013. It is the only Plant Metabolomics Platform to be labelled by INRA as a Common Scientific Infrastructure (ISC) in 2018. It was recently labelled Research Platform by the University of Bordeaux (July 2019) because it mainly contributes to the research of the Department of Environmental Sciences. It is also involved in major research projects at the University of Bordeaux (Bordeaux Plant Science, Tackling, and Frontiers of Life).

Bordeaux Metabolome participates in five large ANR projects (PIA) including two National Infrastructures in Biology and Health (INBS) projects: PHENOME-EMPHASIS and its European version EPPN2020, and MetaboHUB which is coordinated locally (PHENOME and MetaboHUB having been renewed by the ANR until 2025), as well as three ANR PIA BioTechnologies and BioRessources (BTBR) projects: AMAIZING, BreedWheat and SUNRISE. Its members include researchers, (associate)-professors, engineers and technicians from the University and Research Institutes. The Platform is also associated with two start-ups (Polyphénols Biotech and LEB Aquitaine transfert) that ensure the relationship with industry at regional and national level regarding lipidomics and polyphenols. This ensemble of skills, networks and activities promotes the Platform's catalytic role in identifying and enhancing synergies between fields of research, scientific innovation, the transfer of knowledge to society through teaching activities, technology transfer, provision of services and availability to meet industrial and societal needs.

Activities of the facility

The facility specialises in the metabolomics of plants and their derivatives. It carries out technological adaptations and developments, designs and implements analytical strategies and bioinformatic tools in the fields of metabolomics, lipidomics, metabolic phenotyping and fluxomics. These activities correspond to the following objectives:

  • scientific: develop innovative research activities to improve knowledge of plant metabolism
  • transfer: connecting new knowledge to the challenges of climate change, in particular for variety selection, adaptation to drought and/or heat and reduction of inputs in agriculture
  • teaching: train our university students competently and competitively in advanced analytical techniques and metabolomic data analysis

The Platform provides both access to high-performance equipment and cutting-edge analytical skills, responding to requests for metabolomic analyses, hosting and training of students and scientists. It enables the generation of high-level knowledge in biology and serves as a support for research mainly in ecophysiology, plant-microorganism relationships, functional genomics, genetics and integrative biology of plants, analysis of products derived from plants (including wine) and pharmacological approaches (effect of plant metabolites on plant and human health). The offer brings together techniques and know-how that cover the fields of high-throughput biochemical phenotyping (robotic measurements of metabolites and enzymatic activities), metabolomics by LC-MS and NMR (targeted or non-targeted analysis of sugars, organic acids, amino acids, lipids, polyphenols, redox compounds, etc.)


Robotised extractions coupled to UHPLC-LTQ-Orbitrap-MS for high-throughput metabolic profiling

In conjunction with the French Institute of Bioinformatics, the facility also develops bioinformatics and web tools that (i) help capture and manage data and metadata, based on FAIR principles, as with ODAM and LINDA at the regional level (CBIB - UBdx labelled platform) and national / international (PHENOME-EMPHASIS), (ii) facilitate NMR processing and annotation (NMRProcFlow), and (iii) allow statistical processing of omics data (BioStatFlow).

Each year, the facility hosts between 120 and 140 projects for around fifty different teams. These projects are formulated within the framework of regional (in particular the Department of Environmental Sciences), national (in particular several ANR BTBR projects) and international (H2020 and ERC projects) collaborations. The Platform also works in close collaboration with other national platforms (the MetaboHUB network and the INRAE BAP department) and European metabolomics platforms.


NMR spectra of green tomato fruit


Typical LCMS-based metabolomics workflow from a phytopathological study (A) to perform targeted (B) and untargeted (C) metabolomics. From Williams et al. (in press,


Selected MRM chromatograms of main grapevine leaf polyphenols (stilbenoids, flavanols, flavonols)