Key Research Interests
We are Molecular Microbiologists and our primary research interests relate to the evolution of microbial genomes through the acquisition of prophage genes. We are particular interested in dissecting the interconnexions between prophages and bacterial genomes from evolutionary as well as mechanistic point of views. The contribution of prophages to their bacterial hosts encompasses a wide range of traits adaptive to bacterial pathogens, way beyond the well-studied provision of deadly toxins. The study of lysogenic conversion, notably in terms of the integration of the prophage genes in the host gene repertoire and genetic network, constitute the central aspect of our research and is highly valuable to understand genome dynamics in the perspective of the fight against infectious diseases.
Current Research Projects
Interactions phage-bacterial host :
- Temperate phage infection and lysogenic conversion influence bacterial genome evolution and physiology, several bacterial models are studied in the lab, such as E. coli, Salmonella enterica and Xyllela fastidiosa. In particular, we aim at elucidating the regulatory interplays between prophage and host genes and decipher how the regulatory network influence prophage gene expression and prophage maintenance (Menouni et al., 2013, 2015). Current work details the mechanisms of genetic interactions between bacteria and prophages that have important consequences on the understanding of bacterial adaptation and regulation.
- Early infection steps of T5 lytic infection are studied in collaboration with P. Boulanger IB2C (Orsay). T5 DNA is injected by a 2 step mechanism that allows the highjacking of the host cellular machineries before complete injection. Early events and host factors requirement are under study.
Phages as biotechnology tools :
- Phages are used for their specificity of infection as biosensors to detect Enterobacteria in complex environmental water. Several prototypes able to detect various E. coli strains and Salmonella enterica using gfp or different luciferase genes as reporter systems were designed and characterized (Vinay et al., 2015 ; Franche et al., 2016).
- Phage-antibiotic synergism (PAS) has been characterized in the lab with a variety of antibiotics and phages, both used at sub-inhibitory concentrations. The molecular mechanisms underlying the PAS effect is studied using T5 as a model system. This project is performed in collaboration with the Georgian State University (Tbilisi, Georgia).
- Phage cocktails development for the biocontrol of phytopathogens. This project is supported by the BIOTOP company.
Life in our research group
Our research group uses a powerful combination of genetics, functional genomics, basic biochemistry and phage infection models to understand the mechanisms of prophage driven bacterial genome evolution. We use the excellent facilities available at the Mediterranean Institute of Microbiology (IMM) that include biophotonic and electronic microscopy, transcriptomic analysis, proteomic and fermentation and NMR.
We meet on a regular basis for lab meetings and journal presentations and we make sure that each group member goes to conferences relevant to our work.
In recent years, all group members presented ongoing work at the Viruses of Microbes International conference (Brussels 2012 and Zurich 2014), the Phage and bacteria meeting (Cold Spring Harbor Laboratory 2012 ; Madison 2013), the Bacteriophage 2015 meeting (London, 2015). Members of the group are fully involved in the organization of the Molecular Microbiology School (CNRS-INRA-I. Pasteur-AVIESAN-CEA-INSERM).
D. Pignol (CEA Cadarache), A. Rodrigue (INSA Lyon), I. Bazin (ARMINES Alès), P. Cholet (AP2E) "COMBITOX : conception d’un outil analytique multiparamètre en ligne" ANR ECOTECH 2011-2015
F. Pouillot (Chief R&D. PHERECYDES-PHARMA) Development of phage-based biosensors.
P. Boulanger (Orsay University) Transcriptomics of T5 phage early infection.
T. Mdzinarashvili (Tbilisi State University, Georgia) "Bacterial development in biologically active materials : a turbidity approach" Franco-Georgian Program CNRS-GNSF.
E. Talla (LCB Marseille) Phage genome annotation, tools and applicationsto RDF genes.
Postdocs & Fellows
Feel free to email me to discuss projects and alternative sources of funding. Possible funding routes include applying for fellowships, e.g. EU Marie Curie, with me acting as sponsor, or grant applications with you as a named post-doc.