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24, chemin de Borde Rouge -Auzeville - CS52627 31326 Castanet Tolosan cedex - France

Last update: May 2021

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Marie-Agnès Petit

Marie-Agnès Petit
Director of Research

Present position

Leader of the Phage team in the  Micalis institute


Key words

Bacteriophage evolution, DNA recombination,Comparative genomics and phage genome annotations
Intestinal phages, viromes, mice models with controlled microbiota
Phages infecting Escherichia coli,Enterococcus faecalis, Enterococcus faecium, Roseburia intestinalis, Faecalibacterium prausnitzii

Scientific goals of the team

The Phage team is part of the INRA institute, a french institute financed by the government aiming at developing researches in the fields of agriculture, food and environment. It is located in the Micalis department, grouping over 350 experts in the field of microbiology for food and health, and sharing platforms and facilities for growing pathogens, anaerobes, high through put analyses, electron microscopy, axenic mice, among others. The team itself has 9 members at present, including 4 permanent researchers and 2 permanent technicians. Its goals are to understand the behavior of temperate phages in the gut using both global and reconstruction approaches, to understand how phages evolve and acquire new genes, and to develop new bio-informatic tools to facilitate phage genome annotations. It has long standing expertise in growing phages on various Gram positive and negative bacteria, including anaerobes.

Scientific career

2011    Hired as Research director for INRA

2010    Creation of the ‘phage genomes dynamics’  team, within the Micalis department

2004    Research associate at INRA, Jouy en Josas, Lactic Bacteria unit, comparative genomics of bacteria, structural DNA motifs analysis

2001    Sabbatical year at INSERM, Necker, unit  U571, Mosaïcism of bacteriophage genomes

1992    Research associate  at INRA, Génétique Microbienne unit of Jouy en Josas, Transposition, DNA helicases and genome stability

1990    Post-doctoral period : 2 years at UC Berkeley, H. Echols laboratory, Large genome rearrangements in E. coli, heat shock proteins and PolV of E. coli

1984    PhD at INRA, laboratoire de Génétique Microbienne, mechanism of DNA amplification in Bacillus subtilis



2001    HDR Université Paris XI       

1988    Doctorate in Microbiology (INAPG school)

1984    Engineer diploma from the agronomic school INAPG

Five typical publications

Phages infecting Faecalibacterium prausnitzii belong to novel viral genera that help decipher intestinal viromes (2018) Cornuault, J., Petit, M.A., Mariadassou, M., Benevides, L., Moncaut, E., Langella, P., Sokol, H., De Paepe. Microbiome

Phages rarely encode antibiotic resistance genes : a cautionary tale for virome analysis (2016) François Enault, Arnaud Briet, Léa Bouteille, Simon Roux, Matthew B. Sullivan, Marie-Agnès Petit. ISME Journal (doi: 10.1038/ismej.2016.90)

Phagonaute: A web-based interface for phage synteny browsing and protein function prediction (2016). Hadrien Delattre , Oussema Souiai, Khema Fagoonee, Raphaël Guerois,Marie-Agnès Petit. Virology 496, 42-50.

Carriage of lambda latent virus is costly for its bacterial host due to frequent reactivation in monoxenic mouse intestine (2016) De Paepe M., Tournier L., Moncaut E., Son O., Langella Ph., Petit M.-A. PLoS Genet. 12(2): e1005861.doi:10.1371/journal.pgen.1005861

Temperate phages acquire DNA from defective prophages by relaxed homologous recombination: the role of Rad52-like recombinases De Paepe M, Hutinet G, Son O., Amarir-Bouhram J., Schbath S., Petit M-A.  (2014). PLoS Genet. 10(3):e1004181. doi: 10.1371/journal.pgen.1004181