Missions

The ANR POPS project (ANR-24-CE44-1190) aims to elucidate the fundamental mechanisms linking polyamine metabolism to bacterial virulence, leveraging multi-omics experimental and computational approaches.

As part of this project, the HolobiomicsLab, led by Dr. Louis-Félix Nothias at the Institut de Chimie de Nice (ICN), will develop advanced metabolomics methods to understand how polyamines influence the physiology of Staphylococcus aureus. This research will be conducted in close collaboration with other project partners.

The recruited postdoctoral researcher (M/F) will work on the development and application of new analytical methods in mass spectrometry-based metabolomics, with the objective of improving metabolite annotation and multi-omics data analysis.

This will involve establishing and optimizing advanced analytical protocols, combining high-resolution multi-level mass spectrometry and liquid chromatography, to enhance the detection and annotation of metabolites derived from microbial cultures.

A particular focus will be placed on the evaluation of innovative analytical strategies, including:
• Semi-automated sample preparation to improve the reproducibility and sensitivity of analyses.
• Development of online chromatographic pre-enrichment methods to enhance the detection of specific classes of metabolites.
• Optimization of chromatographic separations to broaden metabolomic coverage and improve compound characterization.

The postdoctoral researcher (M/F) will also be responsible for processing, annotating, and interpreting metabolomics data, as well as integrating these data with proteomics and transcriptomics analyses, to characterize the response of Staphylococcus aureus to polyamines.

This work will be carried out in synergy with the Franco-Swiss MetaboLinkAI project, which is developing an artificial intelligence-based system dedicated to metabolomics data analysis.

This position offers a high-level research environment, with access to cutting-edge infrastructure, and direct collaboration with researchers in mass spectrometry, analytical chemistry, microbiology, and artificial intelligence.

Activities

1. Methodological Development in Analytical Metabolomics
• Design and implement semi-automated protocols for sample extraction and pre-treatment from microbial cultures to improve reproducibility and analytical sensitivity.
• Develop and optimize advanced chromatographic protocols to enhance separation efficiency and metabolomic coverage, integrating:
• Size exclusion chromatography (SEC)
• Mixed-mode polarity chromatography (MMPC)
• Reverse-phase liquid chromatography (RP-LC)
• Develop online chromatographic pre-enrichment methods (solid-phase extraction) to increase the detection and quantification of microbial metabolites.
• Perform high-resolution, multi-level mass spectrometry acquisitions (MS/MS and MSn) on study samples.

2. Experimental Deployment and Validation
• Apply and validate the developed methodologies on microbial samples in alignment with the objectives of the ANR POPS project.
• Optimize high-resolution and multi-level mass spectrometry data acquisition to improve metabolite detection, annotation, and quantification.

3. Data Analysis and Multi-Omics Integration
• Process and annotate mass spectrometry data using appropriate computational tools.
• Integrate metabolomics results with proteomics and transcriptomics data to analyze the metabolic interactions of Staphylococcus aureus and its response to polyamines.

4. Scientific Dissemination and Collaborations
• Publish findings in peer-reviewed scientific journals and present research progress at international conferences.
• Collaborate with partners from the ANR POPS project as well as with other initiatives within the lab, particularly MetaboLinkAI and other projects at the intersection of experimental metabolomics, computational metabolomics, and artificial intelligence.
• Ensure adherence to F.A.I.R. principles, making developed methodologies openly accessible and standardizing analytical workflows.
• Contribute to the training and supervision of students and early-career researchers in analytical metabolomics techniques.

Skills

• PhD in Analytical Chemistry, Metabolomics, Proteomics, or Analytical Sciences Applied to Biology.
• Expertise in the development and optimization of chromatographic methods (SEC, MMPC, RP-LC).
• Expertise in high-resolution mass spectrometry applied to microbial metabolite analysis.
• Experience in optimizing analytical protocols and/or automating extraction methods is desirable.
• Ability to integrate metabolomics data with proteomics and transcriptomics analyses for a multi-omics approach.
• Proficiency in Python or R for data processing and analysis is an asset.

Transversal Skills
• Ability to work in an interdisciplinary team (analytical chemists, bioinformaticians, microbiologists).
• Excellent scientific writing and communication skills (publications, conferences).
• Autonomy and proactiveness in developing and optimizing analytical methods.
• Strong command of scientific English (written and spoken).

Work Context

The Institut de Chimie de Nice (ICN), located on the Parc Valrose campus, offers a dynamic and interdisciplinary research environment, with access to state-of-the-art mass spectrometry facilities, including an Orbitrap IQ-X dedicated to advanced metabolomics analyses.

The postdoctoral researcher will join the HolobiomicsLab, led by Dr. L.-F. Nothias, and will work within the ANR POPS project, in close collaboration with other initiatives in the laboratory, including MetaboLinkAI and other projects integrating experimental and computational metabolomics as well as artificial intelligence.

The ANR POPS project presents a unique opportunity for the postdoctoral researcher to work within a multidisciplinary scientific consortium, bringing together experts in analytical chemistry, microbiology, infectious disease biology, and bioinformatics. Integration into this research network will enable collaborations with specialists in multi-omics analysis and contribute to the development of innovative analytical approaches applied to understanding bacterial interactions and virulence mechanisms.

Additionally, the HolobiomicsLab will provide a stimulating research environment, combining methodological advancements in chromatography/mass spectrometry with cutting-edge computational approaches. This position will offer a unique opportunity to develop skills in bioinformatics and artificial intelligence applied to metabolomics, particularly through the analysis and integration of large multi-omics datasets. The postdoctoral researcher will also have the opportunity to gain expertise in machine learning tools and advanced modeling techniques to optimize data interpretation and accelerate scientific discoveries.

Constraints and risks

• Work on complex analytical protocols: The postdoctoral researcher (M/F) will develop and optimize advanced methods in mass spectrometry and chromatography, requiring strong experimental rigor, precise management of analytical parameters, and the ability to quickly troubleshoot technical issues.
• Exposure to chemical hazards: The use of organic solvents (methanol, acetonitrile, formic acid, etc.) and chemical reagents for sample preparation and chromatographic analyses requires strict adherence to laboratory safety standards. The strict application of chemical management protocols and the use of personal protective equipment (PPE) will be mandatory.
• Handling of microbial samples: The analyses will involve cultures of Staphylococcus aureus and other microorganisms, requiring strict compliance with biosafety protocols and handling in controlled conditions to prevent cross-contamination and minimize exposure risks.
• Meeting deadlines and project management: The ANR POPS project is structured into multiple work packages with specific deliverables. The postdoctoral researcher will need to manage their time efficiently, ensure rigorous tracking of results, and coordinate work with other project partners.
• Potential travel requirements: Occasional travel within France and Europe will be required for project meetings, collaborations, and scientific conferences.