Société Française de Bioinformatique

Mots-Clés

mobile genetic element genomics phages plasmids Acinetobacter baumannii

Description

Open shared PhD position in team NutriPhage (MICALIS, Jouy-en-Josas) and HORIGENE (CIRI, Lyon).
The project focuses on how mobile genetic elements drive gene flow in Acinetobacter baumannii. Though once thought to be confined to hospitals, Acinetobacter bacteria have now also been found in soil and associated with plants, making environmental strains potential reservoirs for resistance genes. Understanding how resistance genes mobilize in agricultural and natural settings is, therefore, key to sustainable farming and veterinary practices.
The project is on the interface between comparative phage genomics (70-80%) and experimental, molecular biology (20-30%).
We are seeking a motivated PhD candidate with:
• A Master’s degree (or equivalent) in microbiology, bioinformatics, or a related field
• Strong interest in phage genomics, mobile genetic elements, and bacterial genome evolution
• Experience with bioinformatics and comparative genomics (e.g. genome assembly, phylogenetics, pangenome analysis); familiarity with tools such as R, or command-line/Unix environments
• Willingness to combine dry-lab (computational) and wet-lab (microbiology/molecular biology)
• Good written and spoken English (B2), as the project involves international collaboration and scientific communication
• Strong organizational skills and autonomy
• A collaborative, team-player mindset, as the project involves close cooperation between two research teams (NutriPhage and HORIGENE)
• Curiosity about One Health, antimicrobial resistance, and environmental microbiology
• Prior lab experience in microbiology or molecular biology is an asset, but not mandatory