Besides their major role in many infectious diseases, bacteria also serve as models to understand fundamental biological mechanisms. The research performed in the Department of Microbiology mainly focuses on the molecular characterization of functions that enable bacteria to interact with their environment and, in some cases, to cause diseases.

The scientists of the Department of Microbiology study various bacteria and Archaea (and their viruses) as model systems to analyze fundamental biological processes at the population, cellular and molecular levels. They also focus on mechanisms rendering some of these microorganisms virulent and enabling them to evade the host immune system, or to develop resistance to antibiotics. For these studies,the scientists of the Department of Microbiology possess a wide range of expertise and use diverse integrative approaches to improve our understanding of the biology of these microorganisms. These  studies also constitute a prerequisite for the development of new therapies or new diagnostic tools that can be used to treat or prevent bacterial infections.

The Department of Microbiology includes 20 teams: 14 research teams, 1 Institut Pasteur/Paris University laboratory, 1 laboratory, and 4 collections. Three entities also host a National Reference Center and 2 are WHO Collaborating Centers. In addition, several research teams from other departments (Genomes & Genetics, Structural Biology and Chemistry and Infection & Epidemiology) are affiliated to the Department of Microbiology. The Department also hosts a joint research entity with the CNRS (French National Center for Scientific Research) – UMR2001.


El Mortaji L, Tejada-Arranz A, Rifflet A, Boneca IG, Pehau-Arnaudet G, Radicella JP, Marsin S, De Reuse H. (2020) A peptide of a type I toxin-antitoxin system induces Helicobacter pylori morphological transformation from spiral shape to coccoids. Proc Natl Acad Sci U S A. Nov 23:202016195. doi: 10.1073/pnas.2016195117.

• Nguyen TQN, Tooh YW, Sugiyama R, Nguyen TPD, Purushothaman M, Leow LC, Hanif K, Yong RHS, Agatha I, Winnerdy FR, Gugger M, Phan AT, Morinaka BI (2020) Post-translational formation of strained cyclophanes in bacteria. Nat Chem Aug 17. . doi:10.1038/s41557-020-0519-z

• Lourenço M, Chaffringeon L, Lamy-Besnier Q, Pédron T, Campagne P, Eberl C, Bérard M, Stecher B, Debarbieux L, De Sordi L (2020) The spatial heterogeneity of the gut limits predation and fosters coexistence of bacteria and bacteriophages. Cell Host Microbe Jun 29:S1931-3128(20)30341-3;gutjnl-2019-318640. doi:10.1016/j.chom.2020.06.002

Stressmann F#, Bernal-Bayard J#, Pérez-Pascual D, Audrain B, Rendueles O, Briolat V, Bruchmann S, Volant S, Ghozlane A, Haussler S, Duchaud E, Levraud JP, Ghigo JM* (2020) Mining zebrafish microbiota reveals key community-level resistance against fish pathogen infection. The ISME Journal, Oct 19. doi: 10.1038/s41396-020-00807-8.

• Pérez-Cobas AE, Ginevra C, Rusniok C, Jarraud S, Buchrieser C. (2020) Persistent legionnaires’ disease and associated antibiotic treatment engender a highly disturbed pulmonary microbiome enriched in opportunistic microorganisms. mBio Apr 22. May19;11(3):e00889-20. doi:10.1128/mbio.00889-20

• Baquero DP, Contursi P, Piochi M, Bartolucci S, Liu Y, Cvirkaite-Krupovic V, Prangishvili D, Krupovic M. (2020) New virus isolates from italian hydrothermal environments underscore the biogeographic pattern in archeal virus communities. ISME J Apr 22. . doi:10.1038/s41396-020-0653-z

• Williams AH, Wheeler R, Deghmane AE, Santecchia I, Schaub RE, Hicham S, Moya Nilges M, Malosse C, Chamot-Rooke J, Haouz A, Dillard JP, Robins WP, Taha MK, Gomperts Boneca I. (2020)Feb 5;9:e51247.  eLife doi:10.7554/eLife.51247

• Patino-Navarrete R, Rosinski-Chupin I, Cabanel N, Gauthier L, Takissian J, Madec JY, Hamze M, Bonnin RA, *Naas T, *Glaser P. (2020) Stepwise evolution and convergent recombination underlie the global dissemination of carbapenemase-producing Escherichia coli. Genome Med Jan 20;12(1)/10. doi:10.1186/s3073-019-0699-6



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