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. 
• Lamy-Besnier Q, Chaffringeon L, Lourenço M, Payne RB, Trinh JT, Schwartz JA, Sulakvelidze A, Debarbieux. (2021)Prophylactic Administration of a Bacteriophage Cocktail Is Safe and Effective in Reducing Salmonella enterica Serovar Typhimurium Burden in Vivo. Microbiol Spectr 2021 Sep; 9(1): e0049721. doi: 10.1128/Spectrum.00497-21
• Tremblay YDN, Durand BAR, Hamiot A, Martin-Verstraete I, Oberkampf M, Monot M, Dupuy B. (2021) Metabolic adaption to extracellular pyruvate triggers biofilm formation in Clostridioides difficile. ISME J. 2021 Jun 21. doi: 10.1038/s41396-021-01042-5
• Pernitzsch SR, Alzheimer M, Bremer BU, Robbe-Saule M, De Reuse H, Sharma CM. (2021) Small RNA mediated gradual control of lipopolysaccharide biosynthesis affects antibiotic resistance in Helicobacter pylori. Nat Commun. 2021 Jul 21;12(1):4433. doi: 10.1038/s41467-021-24689-2.
• Salas-Ambrosio P, Tronnet A, Since M, Bourgeade-Delmas S, Stigliani JL, Vax A, Lecommandoux S, Dupuy S, Verhaeghe P, Bonduelle C. (2021) Cyclic-Poly(α-peptoid)s by Lithium bis(trimethylsilyl)amide (LiHMDS)-Mediated Ring-Expansion Polymerization: Simple Access to Bioactive Backbones. J Am Chem Soc.143(10):3697-3702. doi: 10.1021/jacs.0c13231.
• Liu J, Cvirkaite-Krupovic M, Baquero DP, Yang Y, Zhang Q, Shen Y, Krupovic M (2021) Virus-induced cell gigantism and asymmetric cell division in archaea. Proc Natl Acad Sci USA Apr;118(15):e2022578118. doi: 10.1073/pnas.2022578118
• Rousset F, Cabezas-Caballero J, Piastra-Facon F, Fernandez-Rodriguez J, Clermont O, Denamur E, Rocha EPC, Bikard D (2021) The impact of genetic diversity on gene essentiality within the Escherichia coli species. Nat Microbiol Mar;6(3):301-312. doi: 10.1038/s41564-020-00839-y
• Henry C, Loiseau L, Vergnes A, Vertommen D, Mérida-Floriano A, Chitteni-Pattu S, Wood EA, Casadesus J, Cox M, Barras F, Ezraty B (2021) Redox controls RecA protein activity via reversible oxidation of its methionine residues. eLife Feb 19;10:e63747. doi: 10.7554/eLife.63747
•Purushothaman M, Sarkar S, Morita M, Gugger M, Schmidt EW, Morinaka BI (2021) Genome-mining-based discovery of the cyclic peptide tolypamide and Tolf, a Ser/Thr forward O-Prenyltransferase. Angew Chem Int Ed Engl Feb 14. doi: 10.1002/anie.202015975
• Orgeur M, Frigui W, Pawlik A, Clark S, Williams A, Ates LS, Ma L, Bouchier C, Parkhill J, Brodin P, Brosch R (2021) Pathogenomic analyses of Mycobacterium microti, an ESX-1-deleted member of the Mycobacterium tuberculosis complex causing disease in various hosts. Microb Genom Feb;7(2). doi: 10.1099/mgen.0.000505
• Pérez-Pascual D, Vendrell-Fernandez S, Audrain B, Bernal-Bayard J, Patiño-Navarrete D, Petit V, Rigaudeau D, Ghigo JM (2021) Gnotobiotic rainbow trout (Oncorhynchus. Mykiss) model reveals endogenous bacteria that protect against Flavobacterium columnare infection. PLoS Pathogens, Jan 29;17(1):e1009302. doi: 10.1371/journal.ppat.1009302
