Metabolomics and Natural Products Chemistry

Presentation

L'chemical ecology is a multidisciplinary field of research that studies interactions between organisms, as well as organism-environment interactions. These interactions are mediated mainly by specialised metabolites that play essential roles in the survival of an organism in its natural environment. They are the main mediators in chemical communication processes (pheromones, allelochemicals, volatile organic compounds) and thus make a significant contribution to the structuring of biodiversity and the functioning of ecosystems. They also help to protect organisms from environmental stresses. The study of the biosynthesis and function of these molecules is therefore essential in the context of environmental issues, functional ecology and evolutionary ecology.

La metabolomics by mass spectrometry is an analysis method mainly used to understand qualitative and quantitative metabolic variations in organisms (marine and terrestrial), studied in particular in the context of global change.

La chemistry of natural substances associated with the purification and structural characterisation of metabolites reinforces the results of metabolomic analyses by confirming the structures of marker metabolites and offering the possibility of quantifying them in absolute terms in samples.

The Metabolomics and Chemistry of Natural Substances department brings together a range of complementary instruments distributed across 4 IMBE sites to carry out these analyses.

The contacts for each site are:
  • Saint-Jerôme: Caroline Lecareux
  • Endoume: Stéphane Greff
  • Timone : Fathi Mabrouki
  • Avignon: Céline Joliot
 
This joint service offers members of the unit :
  • tools for preparing and conditioning samples prior to chemical analysis,
  • methods for analysing organic compounds resulting from specialised metabolism, 
  • training in routine analysis methods and interpretation of results,
  • Training in health and safety instructions for chemical analysis laboratories,
  • support for the development and introduction of new methods

The Team

Scientific manager of the MSN service
PR-Professor
Scientific manager of the MSN service
CR-Research charge
Technical manager of the MSN service
ITA-Engineer Administrative Technician
Technical manager of the MSN service
ITA-Engineer Administrative Technician
Search for a team member
Myriam Bertolotti
ITA-Engineer Administrative Technician
Stephane Greff
ITA-Engineer Administrative Technician
Celine Joliot
ITA-Engineer Administrative Technician
Emie Le Bonhomme
ITA-Engineer Administrative Technician
Caroline Lecareux
ITA-Engineer Administrative Technician
Fathi Mabrouki
ITA-Engineer Administrative Technician
Sacha Molinari
ITA-Engineer Administrative Technician
Cassandra Saignol
ITA-Engineer Administrative Technician
Serigne Seck
ITA-Engineer Administrative Technician
Charlotte Simmler
CR-Research charge

Instruments and Techniques

Photo gallery

The Gas chromatography coupled with low-resolution mass spectrometry (GC/MS) are used to analyse non-polar and volatile organic compounds (VOCs).

The system GCMS 7890/5977A (Agilent) combined with Thermodesorber TD-100 (Markes) is used to analyse the metabolites emitted by marine and terrestrial organisms in their environment. Various media are available, such as adsorbent tubes and Hisorb.

The system GCMS 7890/ 5977 A associated with an ALS 7693 (Agilent) is used to analyse non-polar compounds (terpenes, fatty acids) produced by marine and terrestrial organisms. They are extracted by solid/liquid extraction. Certain biomarkers of microorganisms present in soil, litter or on the surface of plants can also be characterised in order to understand the functions of the metabolites produced.

La Liquid chromatography coupled with high-resolution mass spectrometry (UHPLC/HRMS) is used to analyse non-volatile polar compounds in marine and terrestrial organisms. The non-targeted metabolomics is favoured in order to describe the metabolic variations of these organisms in relation to certain global change factors (i.e. water stress for plants, global warming, invasions, pollution, etc.).

We also have the option ofisolate and characterise major metabolites of these extracts by Centrifugal Partition Chromatography (CPC) or (Semi-)Preparative Chromatography (structure confirmation / absolute quantification).

L'solid phase extraction instrument (AutoTrace, Thermo) enables us to concentrate metabolites contained in large volumes of seawater (exometabolites) prior to analysis by UHPLC/HRMS.

The MSN Timone site is equipped with eco-extraction systems (MARS 5 microwave extractor, REUS ultrasonic extractor) which reduce the time and energy required to extract the compounds.

Analytical systems include 3 liquid chromatography systems (UHPLC-DAD-HRMS Agilent 1290, HPLC-DAD-ELSD Agilent 1260, HPLC-DAD/VIS 1200) and a Multi-well UV-VIS spectrophotometer which enables UV-VIS absorbance measurements to be taken on 96 samples at the same time. It can be used in analytical applications for general assays of compounds of interest, as well as for assessing the biological activity of molecules and extracts, such as anti-radical (DPPH), antioxidant (ABTS) or cytotoxic (on cancer cells) activity.

Two purification units complete the analytical park:

  • a flash chromatography purification system (CombiFlash RF200) compatible with normal and reversed phase purification conditions. The TLC to Gradient calculator automatically determines the optimum separation parameters while minimising operating time.
  • a Purification System using flash chromatography and a Preparative HPLC-DAD (Gilson PLC 2020)

The MSN department in Avignon specialises in the study of heritage samples and plant species, and more specifically species that produce natural resins and dyes, found around the Mediterranean, in Central America and Asia and used for heritage purposes.

Initial analyses can be carried out routinely by Fourier Transform infrared microscopy (IR-TF iN10/iZ10,Thermo Scientific) to determine the families of chemical compounds present in the matrices analysed.

The use of gas chromatography-mass spectrometry (GC-MS, GC Thermo Trace 1300 + MS detector Thermo ITQ 700), enabling the identification of volatile and semi-volatile organic compounds, as well as a better understanding of their degradation mechanisms and their ancestral uses in the field of cultural heritage.

Using a liquid chromatography chain coupled to a diode array detector (HPLC-DAD), we can characterise and/or purify certain organic compounds of interest.

All of our work is carried out using a variety of chemometric tools, in particular targeted and non-targeted metabolomics approaches.