The postodoctoral position is offered as part of a partnership between INRAE (the French National Research Institute for Agriculture, Food, and the Environment) and Inria (the French National Institute for Research in Digital Science and Technology). It is funded by the TARGET project, promoted by INRAE’s EXPLOR’AE « high-risk research » programme. The TARGET project is an interdisciplinary initiative combining microbiology, culturomics, genetic engineering, systems biology, and modelling. It is a four-year research project. The postdoctoral position offered within this project is for an initial two-year period, with the possibility of renewal for an additional two years.

Context of the project. Since the late 19th century, microbiologists have been developing culture media and techniques to study microorganisms such as bacteria, archaea, yeasts, and filamentous fungi. However, only a small fraction of bacterial species are currently cultivable, severely limiting their study. While advances in metagenomics have highlighted this limitation, genome sequencing alone has not provided sufficient explanations for why many bacterial species remain unculturable. This lack of cultivability remains a scientific enigma and a major barrier to applications in fields such as disease control, antibiotic discovery, biomolecule production, microbiome management, and bioremediation. In bacteria that live in association with eukaryotic hosts, understanding metabolic interactions with their partners opens new possibilities for developing tailored culture media, thereby facilitating their study. Using grapevine Flavescence Dorée phytoplasma as a proof of concept, the TARGET project aims to demonstrate that integrating systems biology, genome engineering, and culturomics can help overcome the challenge of bacterial non-cultivability.

This postdoctoral position is part of the project’s metabolic modelling work package, with objectives including the development of numerical models for the metabolism of minimal bacteria and Flavescence Dorée phytoplasma. These models will be used to predict suitable culture media. The project involves close collaboration between modellers and microbiologists to bridge computational and experimental approaches.

The recruited researcher will work in collaboration between Inria Pleiade team in Talence and INRAE BFP (Fruit biology and Pathology) unit at Villenave d’Ornon. At Inria, the work will be carried under the supervision of Clémence Frioux. Pleiade hosts researchers in mathematics, computer science and computational biology working on developing approaches for microbial community characterisation. Two teams are involved at INRAE: MOLLI (Pascal Sirand Pugnet) where most of the experimentations will be carried out, and META specialised in metabolic modelling. The co-supervisor of the position is Sylvain Prigent, researcher in the META team.