The French National Research Institute for Agriculture, Food, and the Environment (INRAE) is a public research establishment. It is a community of 12,000 people with more than 200 research units and 42 experimental units located throughout France. The institute is among the world leaders in agricultural and food sciences, in plant and animal sciences, and is 11th in the world in ecology and environment. INRAE’s main goal is to be a key player in the transitions necessary to address major global challenges. In the face of the increase in population, climate change, scarcity of resources and decline in biodiversity, the institute develops solutions for multiperformance agriculture, high quality food and sustainable management of resources and ecosystems.

WORKING ENVIRONMENT AND ACTIVITIES

Postdoctoral Position in Metabolomics and Microbiology at INRAE

A postdoctoral position is available at INRAE (the French National Research Institute for Agriculture, Food, and the Environment) as part of the TARGET project. The project is funded by the ‘INRAE’s ‘EXPLOR’AE « high-risk research » programme and brings together expertise in microbiology, culturomics, genetic engineering, systems biology, and computational modelling to develop a new approach to cultivate non-cultivated bacteria using Phytoplasma as a model. The project spans four years, and the postdoctoral position is initially offered for a 23-month term, with the possibility of renewal for an additional two years (24 months).

Project Context

Since the late 19th century, microbiologists have developed culture media and techniques to study microorganisms such as bacteria, archaea, yeasts, and filamentous fungi. However, only a small fraction of bacterial species can currently be cultivated in the laboratory, posing a significant challenge to their study. While advances in metagenomics have provided insights into microbial diversity, genome sequencing alone has not explained why many bacteria remain unculturable. This gap limits progress in various fields, including disease control, antibiotic discovery, biomolecule production, microbiome management, and bioremediation.

For bacteria that associate with eukaryotic hosts, understanding their metabolic interactions with these hosts opens new avenues for designing tailored culture media. The TARGET project aims to address bacterial non-cultivability using Flavescence Dorée phytoplasma, a plant-pathogenic bacterium, as a proof of concept. By integrating systems biology, genome engineering, and culturomics, this project seeks to develop innovative strategies for bacterial cultivation.

Role and Responsibilities

The recruited postdoctoral researcher will contribute to Work Package 2 (WP2) of the TARGET project, which focuses on understanding the metabolic response of phytoplasma in relation to its insect and plant hosts. Using both targeted and untargeted transcriptomics and metabolomics approaches, the researcher will analyze the metabolism of phytoplasma in its ‘hosts’ intracellular environments. This work will involve close collaboration between computational modelers and experimental microbiologists, bridging data-driven and laboratory-based research. More specifically, the researcher will:

• Develop and validate methodological approaches to distinguish bacterial metabolic responses from those of its hosts.
• Conduct transcriptomic analyses to examine bacterial gene expression changes within different hosts’ intracellular environments.
• Perform metabolomics studies using targeted and untargeted LC-MS-based approaches to identify key metabolites in infected and healthy host tissues.
• Develop and utilize metabolic imaging techniques (MALDI, DESI-MS) to spatially map metabolite distributions within the host environments.
• Integrate transcriptomic and metabolomic data to infer metabolic interactions between phytoplasma and its hosts.
• Support metabolic modeling efforts by contributing data that will help refine a metabolic model (WP1) and guide the formulation of a suitable culture medium (WP3).
• Participate in targeted biochemical studies, including RT-qPCR quantification of key enzymes, metabolic reaction analysis, and heterologous protein expression for enzyme characterization.
• Collaborate with bioinformaticians to refine models.
• Write scientific articles and communicate results (lab meetings, seminars, symposia).

Research Environment

The successful candidate will work within the Mollicutes and Metabolism teams, both part of the UMR INRAE BFP (Fruit Biology and Pathology) unit in Villenave d’Ornon, France. The position will be co-supervised by Dr. Pierre Pétriacq (Metabolism) and Dr. Bessem Chouaia (Mollicutes), ensuring a multidisciplinary research experience.

UMR 1332 BFP is a leading research unit in plant biology, formed as a partnership between INRAE (Divisions of Biology and Plant Breeding and Plant Health and Environment) and the University of Bordeaux. With over 150 staff members, including researchers, engineers, and PhD students, BFP plays a crucial role in research and training in plant sciences, microbiology, and biochemistry. The unit has strong international collaborations, participating in multiple EU-funded projects and coordinating an International Associated Laboratory (LIA FReQUenCE) with the University of Tsukuba in Japan. It also maintains active industry partnerships and connections with grower organizations.

The Metabolism team (MéTA), specializing in Systems Biology approaches, applies analytical chemistry, biochemistry, molecular biology, physiology, statistics, and bioinformatics to study metabolism. The team generates large datasets to develop predictive models for understanding metabolic control and its impact on plant development and stress adaptation. While traditionally focused on central metabolism, its recent interests extend to redox and secondary metabolic pathways. The team also hosts the Bordeaux Metabolome facility, member of the national infrastructure MetaboHUB, which offers a comprehensive range of metabolomics capabilities.

The Mollicutes team (Molli) focuses on pathogenic bacteria affecting animals (mycoplasmas) and plants (phytoplasmas, spiroplasmas). These bacteria, classified as Mollicutes, are characterized by their minimal genomes and lack of a cell wall. The team’s research aims to unravel the molecular mechanisms governing host interactions and pathogen evolution with applications in disease control. Specifically, it investigates Flavescence Dorée phytoplasma in grapevines and mycoplasmas affecting ruminants. Comprising 13 permanent researchers, lecturers, and engineers, along with 9 technicians and 9 PhD/postdoctoral researchers, the Mollicutes team provides a rich environment for collaborative and innovative research.

Join us in tackling one of ‘microbiology’s greatest challenges and contributing to groundbreaking research at INRAE!

 TRAINING AND SKILLS REQUIRED

Qualifications and Requirements

The profile we are looking for:

• PhD in microbiology, metabolomics, systems biology, molecular biology, biochemistry or a related field
• Experience in transcriptomics and/or metabolomics, particularly in LC-MS-based metabolomics approaches
• Knowledge of metabolic modeling and biochemical pathway analysis is a plus
• Strong background in microbiology, molecular biology, or bioinformatics
• Experience with RT-qPCR, metabolic imaging, or protein expression/purification is desirable
• Ability to work collaboratively in an interdisciplinary team
• Excellent analytical, organizational, and communication skills