CV Erwan GUEGUEN

CURRENT POSITION

Assistant-Professor (Maître de Conférences hors-classe), HDR, at Claude Bernard University Lyon I since September 1, 2012.

Head of microbial genetics teaching team (13 faculty members) since September 2020. Head of the Life Sciences Bachelor's Microbiology program since 2022

Professional Contact: Erwan GUEGUEN, PhD MAP Laboratory Claude Bernard University Lyon 1 10 rue Raphaël Dubois Lwoff building 69622 Villeurbanne Cedex France

Profile: Molecular bacteriology and bacterial genetics. Affiliated with the "Microbiology, Adaptation and Pathogenicity" laboratory CNRS UMR5240

erwan.gueguen@univ-lyon1 http://map.univ-lyon1.fr

EDUCATION AND DEGREES

• 2021. Habilitation to Direct Research. Claude Bernard University, Lyon, France.

• 2002-2006. PhD in Genetics and Microbiology, 2006. Paul Sabatier University, Toulouse, France.

• 2001-2002. Master's degree in Microbiology, 2002. Université Paul Sabatier, Toulouse, France. 

ACADEMIC CAREER

• Since 2015: Associate Professor in the "Membrane Traffic and Bacterial Signaling (MTSB)" team, CNRS-MAP, Villeurbanne. Study of pathogenicity mechanisms in phytopathogenic bacteria of the Pectobacteriacea family.

• 2012 to 2015: Assistant Professor in the "bacteria and metals" team, CNRS-MAP, Villeurbanne (team leader Agnès Rodrigue). Study of bacterial resistance mechanisms to heavy metals.

• 2010-2012: Post-doctoral researcher in Eric Cascales' team "Assembly of trans-membrane systems", CNRS-LISM, Marseille. Characterization of type VI secretion systems in Yersinia pseudotuberculosis and Citrobacter rodentium.

• 2007-2010: Post-doctoral researcher. Dr. Andrew Darwin's Laboratory, New York University, USA. Study of the Phage Shock Protein system in the pathogenic bacterium Yersinia enterocolitica.

• 2002-2006: PhD student. Chandler Team, CNRS-LMGM, Toulouse. Study of transposition of the bacterial mobile element IS911.

RESEARCH ACTIVITIES

RESEARCH KEYWORDS : Molecular bacteriology, Bacterial pathogenesis, Dickeya, Pectobacteriaceae, Plant-pathogen interactions, Bacterial physiology, Bacterial genetics, Gene expression, Bacterial secretion systems (e.g. type VI), Virulence factors, Environmental adaptation.

CURRENT RESEARCH: My laboratory studies the virulence mechanisms and genomic diversity of plant pathogens in the Pectobacteriaceae family. We investigate how these bacteria use virulence factors and secretion systems to deliver essential proteins for infection. We also study how these bacteria produce and regulate secondary metabolites like antibiotics and siderophores, which are crucial for survival, competition, and environmental adaptation. Our research focuses on clarifying scientific questions such as how bacterial pathogens coordinate virulence strategies, which genes and metabolic pathways allow survival in plant hosts compared to aquatic environments, how secondary metabolites contribute to pathogen survival, spread, and competitiveness, and how genomic and phenotypic diversity facilitates evolutionary adaptation and ecological specialisation within Pectobacteriaceae. By integrating genomic, metabolic, and ecological studies, we aim to better understand the molecular basis of pathogenicity and the adaptive strategies that enable these bacteria to persist in complex environments. 

My expertise extends to the genetic manipulation of a wide range of bacteria to elucidate fundamental mechanisms of virulence and adaptation. Although my present research primarily targets plant-pathogen interactions in Dickeya, my versatility is demonstrated by significant work on plasmid biology, regulation by sRNAs, and stress responses in various organisms. My ability to transfer genetic skills between different bacterial systems is a central strength of my research program.

NATIONAL AND INTERNATIONAL COLLABORATIONS: R. Czajkowski (Intercollegiate Faculty of Biotechnology, Gdańsk, Pologne), D. Faure (I2BC, Gif-sur-Yvette, France), C. Ahrens (Agroscope, Suisse), J. Cigna (Inov3PT), L. Attaiech (CIRI, Lyon), S. Bigot (MMSB, Lyon), I. Chauvot de Beauchene (LORIA, Nancy), A. Boulanger (INRAE, Castanet), K. Papenfort (Jena University, Germany), M-A Barny (Sorbonne Université, Paris).

PUBLICATIONS

1. Lorang C, Canto P-Y, Gueguen E, Pédron J, Barny M-A. Pectobacterium versatile β-Lactamase Contributes to Soft Rot Pectobacteriaceae (SRP) Community Diversity During Potato Infection. Environmental Microbiology Reports. 2025;17: e70111.

2. Baffert Y, Fraikin N, Makhloufi Y, Baltenneck J, Val M-E, Dedieu-Berne A, Degosserie J, Iorga BI, Bogaerts P, Gueguen E, Lesterlin C, Bigot S. Genetic determinants of pOXA-48 plasmid maintenance and propagation in Escherichia coli. Nat Commun. 2025;16: 7734.

3. Royet K, Kergoat L, Lutz S, Oriol C, Parisot N, Schori C, et al. High-Throughput Tn-Seq Screens Identify Both Known and Novel KT2440 Genes Involved in Metal Tolerance. Environmental Microbiology. 2025;27: e70095. ($ Corresponding author)

4. Dubois Q, Brual T, Oriol C, Mandin P, Condemine G, Gueguen E$ . *Function and mechanism of action of the small regulatory RNA ArcZ in Enterobacterales.* RNA. 2024 Jun 5:rna.080010.124. doi: 10.1261/rna.080010.124. PMID: 38839110. ($ Corresponding author)

5. Brual T, Effantin G, Baltenneck J, Attaiech L, Grosbois C, Royer M, Cigna J, Faure D, Hugouvieux-Cotte-Pattat N, Gueguen E$. A natural single nucleotide mutation in the small regulatory RNA ArcZ of Dickeya solani switches off the antimicrobial activities against yeast and bacteria. PLoS Genet. 2023 Apr 27;19(4):e1010725. doi: 10.1371/journal.pgen.1010725. ($ Corresponding author)

6. Robic K, Munier E, Effantin G, Lachat J, Naquin D, Gueguen E, Faure D. 2023. Dissimilar gene repertoires of Dickeya solani involved in the colonization of lesions and roots of Solanum tuberosum. Front Plant Sci 14:1154110.

7. Job V, Gomez-Valero L, Renier A, Rusniok C, Bouillot S, Chenal-Francisque V, Gueguen E, Adrait A, Robert-Genthon M, Jeannot K, Panchev P, Elsen S, Fauvarque MO, Couté Y, Buchrieser C, Attrée I. Genomic erosion and horizontal gene transfer shape functional differences of the ExlA toxin in Pseudomonas spp. iScience. 2022 Jun 14;25(7):104596. 

8. Morinière L, Mirabel L, Gueguen E, Bertolla F. A Comprehensive Overview of the Genes and Functions Required for Lettuce Infection by the Hemibiotrophic Phytopathogen Xanthomonas hortorum pv. vitians. mSystems. 2022 Mar 21:e0129021. doi: 10.1128/msystems.01290-21

9. Hugouvieux-Cotte-Pattat N, Royer M, Gueguen E, Le Guen P, Süssmuth RD, Reverchon S, Cociancich S. Specificity and genetic polymorphism in the Vfm quorum sensing system of plant pathogenic bacteria of the genus Dickeya. Environ Microbiol. 2022 Jan 10. doi: 10.1111/1462-2920.15889.

10. Morinière L, Lecomte S, Gueguen E, Bertolla F. In-depth exploration of Xanthomonas hortorum pv. vitians essential genome in vitro using transposon insertion sequencing and comparative genomics discriminated between core and contextual essential genes. Microb Genom. 2021 Mar 24. doi: 10.1099/mgen.0.000546

11. Reuter A, Hilpert C, Berne AD, Lematre S, Gueguen E, Launay G, Bigot S, Lesterlin C. Targeted-Antibacterial-Plasmids (TAPs) combining conjugation and CRISPR/Cas systems achieve strain-specific antibacterial activity. Nucleic Acids Res. 2021 Apr 6;49(6):3584-3598. doi: 10.1093/nar/gkab126.

12. Hugouvieux‐Cotte‐Pattat N, Condemine G, Gueguen, E and Shevchik VE. (2020). Dickeya Plant Pathogens. In eLS, John Wiley & Sons, Ltd (Ed.).

13. Royet K, Parisot N, Rodrigue A, Condemine G*, Gueguen E$*. Identification by Tn-seq of Dickeya dadantii genes required for survival in chicory plants. Mol Plant Pathol. 2019 Feb;20(2):287-306. doi: 10.1111/mpp.12754. Epub 2018 Nov 15. PubMed PMID: 30267562. (Co-last authorship $ Corresponding author)

14. Rome K, Borde C, Taher R, Cayron J, Lesterlin C, Gueguen E, De Rosny E, Rodrigue A. The Two-Component System ZraPSR Is a Novel ESR that Contributes to Intrinsic Antibiotic Tolerance in Escherichia coli. J Mol Biol. 2018 Dec 7;430(24):4971-4985. doi: 10.1016/j.jmb.2018.10.021. Epub 2018 Oct 30. PubMed PMID: 30389436.

15. Cayron J, Prudent E, Escoffier C, Gueguen E, Mandrand-Berthelot MA, Pignol D, Garcia D, Rodrigue A. Pushing the limits of nickel detection to nanomolar range using a set of engineered bioluminescent Escherichia coli. Environ Sci Pollut Res Int. 2017 Jan;24(1):4-14. doi:10.1007/s11356-015-5580-6. Epub 2015 Oct 24. PubMed PMID: 26498802.

16. Petit-Härtlein I, Rome K, de Rosny E, Molton F, Duboc C, Gueguen E, Rodrigue A, Covès J. Biophysical and physiological characterization of ZraP from Escherichia coli, the periplasmic accessory protein of the atypical ZraSR two-component system. Biochem J. 2015 Dec 1;472(2):205-16. doi:10.1042/BJ20150827. Epub 2015 Oct 5. PubMed PMID: 26438879.

17. Gueguen E$, Wills NM, Atkins JF, Cascales E$. Transcriptional frameshifting rescues Citrobacter rodentium type VI secretion by the production of two length variants from the prematurely interrupted tssM gene. PLoS Genet. 2014 Dec 4;10(12):e1004869. doi: 10.1371/journal.pgen.1004869. eCollection 2014 Dec. PubMed PMID: 25474156. ($ Co-corresponding author)

18. Blériot C, Gault M, Gueguen E, Arnoux P, Pignol D, Mandrand-Berthelot MA,Rodrigue A. Cu binding by the Escherichia coli metal-efflux accessory protein RcnB. Metallomics. 2014 Aug;6(8):1400-9. doi: 10.1039/c4mt00036f. PubMed PMID: 24658095.

19. Gueguen E$, Durand E, Zhang XY, d'Amalric Q, Journet L, Cascales E$. Expression of a Yersinia pseudotuberculosis Type VI Secretion System Is Responsive to Envelope Stresses through the OmpR Transcriptional Activator. PLoS One. 2013 Jun 19;8(6):e66615. doi:0.1371/journal.pone.0066615. Print 2013. PubMed PMID: 23840509. ($ Co-corresponding author)

20. Gueguen E$, Cascales E. Promoter swapping unveils the role of the Citrobacter rodentium CTS1 type VI secretion system in interbacterial competition. Appl Environ Microbiol. 2013 Jan;79(1):32-8. doi: 10.1128/AEM.02504-12. Epub 2012 Oct 12. PubMed PMID: 23064344. ($ Corresponding author)

21. Gueguen E, Flores-Kim J, Darwin AJ. The Yersinia enterocolitica phage shock proteins B and C can form homodimers and heterodimers in vivo with the possibility of close association between multiple domains. J Bacteriol. 2011 Oct;193(20):5747-58. doi: 10.1128/JB.05080-11. Epub 2011 Aug 19. PubMed PMID: 21856846.

22. Yamaguchi S, Gueguen E, Horstman NK, Darwin AJ. Membrane association of PspA depends on activation of the phage-shock-protein response in Yersinia enterocolitica. Mol Microbiol. 2010 Oct;78(2):429-43. PubMed PMID: 20979344.

23. Bernard CS, Brunet YR, Gueguen E, Cascales E. Nooks and crannies in type VI secretion regulation. J Bacteriol. 2010 Aug;192(15):3850-60. doi:10.1128/JB.00370-10. Epub 2010 May 28. Review. PubMed PMID: 20511495.

24. Gueguen E, Savitzky DC, Darwin AJ. Analysis of the Yersinia enterocolitica PspBC proteins defines functional domains, essential amino acids and new roles within the phage-shock-protein response. Mol Microbiol. 2009 Nov;74(3):619-33. doi: 10.1111/j.1365-2958.2009.06885.x. Epub 2009 Sep 22. PubMed PMID: 19775245.

25. Gueguen E, Rousseau P, Duval-Valentin G, Chandler M. Truncated forms of IS911 transposase downregulate transposition. Mol Microbiol. 2006 Nov;62(4):1102-16. PubMed PMID: 17078817.

26. Gueguen E, Rousseau P, Duval-Valentin G, Chandler M. The transpososome: control of transposition at the level of catalysis. Trends Microbiol. 2005 Nov;13(11):543-9. Epub 2005 Sep 21. Review. PubMed PMID: 16181782.

27. Rousseau P, Gueguen E, Duval-Valentin G, Chandler M. The helix-turn-helix motif of bacterial insertion sequence IS911 transposase is required for DNA binding. Nucleic Acids Res. 2004 Feb 23;32(4):1335-44. Print 2004. PubMed PMID: 14981152.

ORAL COMMUNICATIONS: Between 2004 and 2025, I delivered 23 oral communications, including 15 invited presentations and 8 contributions to workshops or conferences. About 70% were held in France and 30% abroad (Poland, Italy, USA). Between 2019 and 2024, I delivered 8 oral communications, including 6 invited presentations (seminars or professorships) and 2 participations in scientific meetings. Among these, 5 took place in France (Marseille, Castanet, Lyon, Gif-sur-Yvette) and 3 abroad (Poland and Italy).

Oral communications include an invited professorship at the Erasmus+ BIP programme “Biotechnology for Society” in Gdansk, Poland (30 June–4 July 2025), an invited seminar at LIPME INRAE Castanet (30 September 2024), a presentation at Bactolyon Day (11 April 2024), participation in the international symposium “Pectinolytic Bacteria” at ICPP, Lyon (19–20 August 2023), an invited seminar at the Laboratory of Bacterial Chemistry in Marseille (7 July 2023), an invited seminar by Robert Czajkowski at the University of Gdansk, Poland (14 October 2022), a presentation at the 4th “IEW Workshop” in Assisi, Italy (3 July 2022), another contribution to Bactolyon Day (8 April 2022), an invited seminar at I2BC Gif/Yvette (5 November 2021), a keynote lecture at Bactogre Day (23 June 2020), an invited professorship with a course on Tn-seq in planta during the 3rd thematic school “Tracking Bacteria in Planta” (COST action EuroXanth, Toulouse, 9–13 March 2020), invited seminars at IMM Marseille (2019), IBENS ENS Paris (2018), and INRA Castanet (2018), a presentation at the Meeting of the Regional Research Group in Microbiology of Interactions, Villeurbanne (2017), an invited seminar at Lycée du Parc, Lyon (2016), an invited seminar at LMGM Toulouse (2014), an invited seminar at IBS Grenoble (2013), a presentation at the Meeting of the Regional Research Group in Microbiology of Interactions, Villeurbanne (2013), participation in the Thematic School of Microbiology, Hyères, France (2010), an invited seminar at LMGM Toulouse (2010), a contribution to the conference “Molecular Genetics of Phages and Bacteria”, Madison, USA (2009), and presentations at the French conferences “Mobile Genetic Elements” held in Tours (2004) and Orsay (2005).

POSTER PRESENTATION: Poster presentations include the “Microbes & RNA Meeting” (1–4 September 2025, Strasbourg, France), the “Plant/Bacteria” Conference (2025, Aussois, France), the Bacnet Conference (16–20 September 2024, Sant Feliu de Guíxols, Spain), the ICPPB Conference (3–8 July 2022, Assisi, Italy; awarded Best Poster), the “Plant/Bacteria” Conference (2020, Aussois, France), the Thematic School of Molecular Microbiology (2018, Carry-Le-Rouet, France), the EMBO Conference: “New Approaches and Concepts in Microbiology” (2017, Heidelberg, Germany), the ASM Conference: “Mobile DNA” (2006, Banff, Canada), the Conference: “Recombination, Replication and Repair” (2005, Giens, France), the Conference: “Transposition and Site-specific Recombination” (2004, Woods Hole, USA), and the French Conference: “Mobile Genetic Elements” (2003, 2004, 2005, 2006).

TEACHING

Assistant Professor in Microbiology and Bacterial Genetics at Claude Bernard University Lyon I. Approximately 220 teaching hours per year.

• An average of 211 EqTD teaching hours from 2012 to 2022, including 10% lectures, 10% tutorials, 72% practical sessions, and 8% HRS. In 2020 and 2021, approximately 100 teaching hours due to receiving a half CNRS delegation for two consecutive years, then a return to a full teaching load in 2022.

• Responsibilities include director of the “Molecular Genetics of Microbes” course unit in the Lyon I Master’s in Microbiology since 2016, co-director of the “Microbial Engineering” course unit in the Lyon I Master’s in Microbiology since 2016, director of the “Methods and Techniques in Molecular Microbiology” course unit in the Microbiology Bachelor’s program since 2022, co-director of the “Molecular Microbiology” course unit in the ENS Lyon Bachelor’s program since 2022, director of the E2M2 doctoral school module “Genetic Tools and Mutant Construction in Microorganisms”, and director of three bacterial genetics practical courses from L3 to M2 level in the Master’s in Microbiology.

FUNDING OBTAINED

"C" if coordinator, and "P" if partner.

2020–2025:

• ANR DeCa-P (P, 2023–2026, 110 k€) – Deciphering the mechanisms of Carbapenem resistance propagation by studying conjugative plasmid transfer.

• Inov3PT Contracts (C, 2022–2023, €2×15k) – Obtaining and monitoring bioluminescent strains of Dickeya solani in potato tissues.

• Bienvis – GEGARAT (P, 2022, 5 k€) – Essential genome and rhizosphere adaptation genes in Azospirillum (Tn-Seq approach).

• PHC Polonium (C, 2021–2022, 5 k€) – Analysis of the physical barriers encountered by Dickeya solani during its propagation in the host plant (collaboration avec Univ. Gdansk, Pologne).

• CNRS prematurity – Chitibact (C, 2020, €89k) – Production of a molecule of industrial interest by bacteria.

• UCBL Large Equipment Call for Proposals (C, 2020, €150k) – Acquisition of an in vivo imaging system for plants (NightShade LB 985, Berthold), installed in the future BSL2 of the Doua campus.

• ANR Tn-Phyto (P, 2019–2024, €516k, including €205k for the MTSB team) – Tn-Seq identification of new genetic determinants of phytopathogenic bacteria, involved in infection and persistence; scientific leader of 2 tasks.

Before 2020 :

• AAP FR Bienvis : LumiSerre (C, 2019); CrispRi-Lego (C, 2018); Novel adaptive genes in Agrobacterium (P, 2017); BluePippin and Tn-Seq libraries (C, 2016).

• BQR UCBL (C, 2013, 10 k€) – Metal resistance determinants in Pseudomonas putida (Tn-Seq).

• Foundation for Medical Research (C, 2010, 110 k€) – 2-year postdoctoral fellowship (E. Cascales team, Marseille).

• Association for Research on Cancer (ARC) (C, 2005, 7.5 k€) – End of thesis (6 months).

PARTICIPATION IN THE THESIS STEERING COMMITTEE, JURIES, MCU SELECTION COMMITTEE

Thesis jury:

• Reviewer: Fanny Nazaret (Univ. Côte d'Azur, 2024), Tomas Quiroz Monnens (Univ. Toulouse, 2024), Minjia Shen (Univ. Paris-Saclay, 2023), Victor Simon (Univ. Grenoble, 2023).

• Examiner: Corentin Blanchais (Univ. Lyon I, 2024), Raphaël Rachedi (Univ. Aix-Marseille, 2023), Thibault Chautrand (Univ. Rouen, 2022), Sushovam Dam (Univ. Aix-Marseille, 2018).

HDR jury:

• Examiner: Franck Bertolla, Université Claude Bernard Lyon I (defended on 23/06/2023)

Member of the MCU selection committee: University of Aix-Marseille (2024, position n°0123), University of Rouen (2023, position n°4645), University of Lyon I (2022, positions n°4630 and n°4655), Université Saint-Étienne (2021, position n°0774), and University of Aix-Marseille (2020, position n°0894).

Member of the selection committee for the ATER position of the UFR Biosciences from 2018 to 2021.

Member of the thesis steering committee since 2017: Marie Tillet (BF2I, Villeurbanne); Marvin Navarro (INRAE, Castanet); Sylvain Vicente (INRAE, Castanet); Laura Valery (MAP, Lyon); Corentin Arthaud (LCB, Marseille); Prunelle Carcassonne (LCB, Marseille); Quentin Collet (CIRI, Lyon); Léa Bednarczuk (CIRI, Lyon); Xanthe Adams-Ward (CIRI, Lyon); Florence Deschèvre (LEM, Villeurbanne); Théophile Franzino (LEM, Villeurbanne); Mathieu Blandenet (Bayer UCBL, Lyon); Audrey Reuter (MMSB, Lyon); Kevin Picq (CIRI, Lyon); Léo Hardy (CIRI, Lyon); Corentin Jaboulay (CIRI, Lyon); Laura Camus (CIRI, Lyon); Julien Luneau (INRA, Castanet); Léo Hardy (CIRI, Lyon); Joy Lachat (I2BC, Gif-sur-Yvette); Julien Cayron (MMSB, Lyon); William Galand (LEM, Villeurbanne).

Participation in the jury for the allocation of doctoral grants at the BSB doctoral school in Toulouse in 2014, and E2M2 in 2024

FUNCTIONS OF COLLECTIVE INTEREST

Present

• Laboratory UMR5240: Member of the laboratory council (since 2021); Ecological transition and sustainable development correspondent.

• University of Lyon 1: evaluation referent for the Masters of the UFR Biosciences (since 2016); head of the microbial genetics teaching team (13 teachers, since 2020); head of the Microbiology course of the Life Sciences Bachelor's degree (since 2022); invited member of the Teaching Commission nd the UFR Biosciences.

• International: Reviewer for several journals (mSystems, PLoS Pathogens, BMC, Journal of Microbiology, Environmental Microbiology, PLoS One, Frontiers, Virulence, MPMI, Molecular Microbiology).

Past

• Laboratory UMR5240: responsible for scientific animation (seminars) from 2012 to 2016, co-director from 2017 to 2020.

• University of Lyon 1: elected member of the Department of Biology/UFR Biosciences (2018–2021); member of the Human Resources and Training WG of the UFR (2018–2021, ATER evaluation and grade advancements).

• Expert evaluator for the NSERC (Canada) and the Marsden Fund (New Zealand) in 2020

MEDIA APPEARANCES ON SCIENCE AND SOCIETY ISSUES

• Interview with L'Express in 2019 for the article: "Science: The New Obscurantists" (https://www.lexpress.fr/actualite/sciences/sciences-les-nouveaux-obscurantistes_2087668.html)

• Interview with Arrêt sur Images about the peer review process in 2020 (https://www.arretsurimages.net/articles/les-revues-scientifiques-des-medias-comme-les-autres)