Pascal SIMONET Environmental Microbial Genomics Group

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Laboratoire Ampere
Ecole Centrale de Lyon . France
(33) 472 18 65 14

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Research Director at CNRS


Environmental Microbial Genomics Group
Laboratoire Ampère, UMR CNRS 5005
Ecole Centrale de Lyon
Université de Lyon
36 avenue Guy de Collongue
69134 Ecully cedex
  Phone: 33 (0)4 72 18 60 92
Fax: 33 (0)4 78 43 37 17


Explains the group's general approach


2005:                  Promotion to the grade : « Directeur de Recherche de 1ère classe »
1993:                  Promotion to the grade : « Directeur de Recherche de 2ème classe ».
1990:                  Habilitation à diriger les recherches (HDR). University of Lyon.
1988:                  Promotion to the grade: « Chargé de Recherche 1ère classe »
1984                   Integration at CNRS as a Scientist.
1983:                  PhD in microbiology. University of Lyon.


Dr. Pascal Simonet obtained his PhD in 1983. Currently his research group investigates the evolution potential of bacteria in environments such as the soil and plants. For more than 15 years the research group entitled « Gene Transfer and Bacterial Adaptation » that he led at the University of Lyon has had the general objectives of determining the involvement of horizontal gene transfers (HGT) in the adaptation and evolution of bacteria to new environments. Studies of the group focused mainly on natural genetic transformation and also, but at a lesser extent, on conjugation. These objectives lead the group to develop soil DNA extraction methods and it was among the first to investigate environmental bacteria with metagenomic approaches. Several of the studies were devoted to investigate the fate of DNA released by genetically engineered organisms including the possibility that recombinant DNA, and particularly antibiotic resistance genes transforms indigenous bacteria. The group also demonstrated a transforming effect on soil bacteria of lightning-generated electrical conditions that motivated the move to the “Laboratoire Ampère” (UMR CNRS 5005) at Ecole Centrale de Lyon (ECL) for developing the “Environmental Microbial Genomics” group (département Bioingéniérie). Dr. Pascal Simonet has co-authored more than 100 scientific papers.

top PUBLICATIONS (for a complete list of publications click here)


  • Habtom H, Demanèche S, Dawson L, Azulay C, Matan O, Robe P, Gafny R, Simonet P, Jurkevitch E and Z Pasternak. 2017. Soil characterisation by bacterial community analysis for forensic application: a quantitative comparison of environmental technologies. Forensic Sci. Int. 26:21-29.
  • Demanèche S, Schauser L, Dawson L, Franqueville L, Simonet P. 2017. Microbial soil community analyses for forensic science: Application to a blind test. Forensic Science International 270 (2017) 153–158.
  • Blanchard LS, Monin A, Ouertani H, Touaibia L, Michel E, Buret F, Simonet P, Morris CE and Demanèche S. 2017. Survival and electrotransformation of Pseudomonas syringae exposed to simulated lightning. The ISME J (submitted). 
  • Hily JM, Demanèche S, Poulicard N, Tannières M, Djennane S, Beuve M, Vigne E, Demangeat G, Komar V, Marmonier A, Hemmer C, Vigneron S, Marais A, Candresse T, Simonet P and Lemaire O. 2017. Metagenomic-based impact study of transgenic grapevine rootstock on its associated virome and soil bacteriome. PLoS Biology (submitted).


  • Nesme J,  Achouak W, Agathos SN, Bailey M, Baldrian P, Brunel D, Frostegård Å, Heulin T, Jansson JK, Jurkevitch E, Kruus KL, Kowalchuk GA, Lagares A, Lappin-Scott HM, Lemanceau P, LePaslier D, Mandic-Mulec I, Murrell JC, Myrold DD, Nalin R, Nannipieri P, Neufeld JD, O’Gara F, Parnell JJ, Pühler A, Pylro V, Ramos JL, Roesch LFW, Schloter M, Schleper C, Sczyrba A, Sessitsch A, Sjöling S, Sørensen J, Sørensen SJ, Tebbe CC, Topp E, Tsiamis G, van Elsas JD, van Keulen G, Widmer F, Wagner M, Zhang T, Zhang X, Zhao L, Zhu Y-G, Vogel TM and P Simonet. 2016. Back to the Future of Soil Metagenomics. Front. Microbiol : 7:73. doi: 10.3389/fmicb.2016.00073 published: 10 February 2016
  • Ufarte, L, S Bozonnet, E Laville, D A Cecchini, S Pizzut-Serin, S Jacquiod, S Demaneche, P Simonet, L Franqueville and G Potocki-Veronese. 2016. Functional Metagenomics: Construction and High- Throughput Screening of Fosmid Libraries for Discovery of Novel Carbohydrate-Active Enzymes. In Martin, F and S Uroz (ed.), Microbial Environmental Genomics (MEG). Springer Science + Business Media, New York.
  • Subirats J, A Sànchez-Melsió, CM Borrego, JL Balcázar and P Simonet. 2016. Metagenomic analysis reveals bacteriophages are reservoirs for antibiotic resistance genes. Int. J. Antimicrob. Agents:  48:163-167.
  • Pylro VS, Mui TS, Rodrigues JLM, Andreote FD, Roesch LFW and the Working Group supporting the INCT Microbiome (P Simonet, member of the working group). 2016. A step forward to empower global microbiome research through local leaderships. Trends Microbiol. 24:767-771.
  • Smalla K, P Simonet, J Tiedje and E Topp. 2016. Opinion Paper/Editorial. Co-editors, Special section of FEMS Microbiology Ecology on the environmental dimension of antibiotic resistance. FEMS Microbiol. Ecol. 92: fiw17.
  • Alizon S, F Angelier, G Bécard, L Bézin, F Courchamp, S. Dutreuil, L Guidi, U Hibner, M Jebbar, O Klatz, F Heullier, O Loudet, P Simonet, J Tost, N Vergnolle. 2016. L’être vivant dans son environnement.  Livre blanc pour les sciences de la vie du XXIème siècle (eds T Gaude, C Jessus, Y Levy). CNRS Editions. (in press).
  • Simonet P and A Maître. 2016. De la santé de l’environnement à la santé humaine. Les Big Data à découvert (eds S Abiteboul, G Baldacci, P Besse, O Cappé, A Cappy, C Jeandel, D Joly, B Jouve, S Laugier, Y Maday, C Nédellec, J-N Patillon, M-C Rousset et H Touzet). CNRS Editions. (in press).
  • Royet  D, Hériveaux Y, Marchalot J, Scorretti  R, Dias A, Dempsey NM, Bonfim M, Simonet  P and Frénéa-Robin M. Using injection molding and reversible bonding for easy fabrication of magnetic cell trapping and sorting devices. J. Magn. Magn. Mater. (in press). 


  • Nesme J and P. Simonet. 2015. The soil resistome: a critical review on antibiotic resistance origins, ecology and dissemination potential in telluric bacteria. Environ. Microbiol. 17: 913-930.  (doi: 10.1111/1462-2920.12631).
  • Delmont, T. O., A. M. Eren, L. MacCario, E. Prestat, O. C. Esen, E. Pelletier, D. Le Paslier, P. Simonet and T. M. Vogel. 2015. Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics. Front. Microbiol. 6:358.
  • Pivetal J, D. Royet, G. Ciuta, M. Frenéa-Robin, N. Haddour, N.M. Dempsey, F. Dumas-Bouchiat and P. Simonet. 2015. Micro-magnet arrays for specific single bacterial cell positioning. J. Magn. Magn. Mater. 380: 72-77.
  • Navarro E, O Fabrègue, R Scorretti, J Reboulet, P Simonet, L Dawson and S Demanèche. 2015. RisaAligner: a software to align fluorescent data between Agilent 2100 Bioanalyzer arrayschips; Application to soil microbial community analysis. BioTechniques 59: 347-358.
  • Pivetal J, M Frenea-Robin, N Haddour, C Vezy, LF Zanini, G Ciuta, NM Dempsey, F Dumas-Bouchiat, G Reyne, S Begin-Colin, D Felder-Flesh, C Ghobril, G. Pourroy  and P Simonet. 2015. Development and application of a DNA labeling method with magnetic nanoparticles to study the role of horizontal gene transfer between bacteria in soil pollutant bioremediation processes. Environ Sci Pollut Res. 22: 20322-20327. DOI 10.1007/s11356-015-5614-0


  • Delmont TO, Francioli D, Jacquesson S, Laoudi S, Mathieu A, Nesme J, Ceccherini M-T, Nannipieri P, Simonet P and Vogel TM. 2014. Microbial Community Development in Inoculated Sterile Soil. Biol. Fertil. Soils (in press).
  • Pivetal J, Ciuta G, Frenéa-Robin M, Haddour N, Dempsey NM, Dumas-Bouchiat F and Simonet P. 2014. Magnetic nanoparticle DNA labeling for individual bacterial cell detection and recovery.  J. Microbiol. Methods (in press). doi: 10.1016/j.mimet.2014.09.006.
  • Pivetal J, Royet D, Ciuta G, Frenéa-Robin M, Haddour N, Dempsey NM, Dumas-Bouchiat F and Simonet P. 2014. Selective micro-patterning of microbial cells upon micro-magnet arrays for single cell analysis. J. Magn. Magn. Mater. (in press).
  • Nesme J and Simonet P 2014. The soil resistome: a critical review on antibiotic resistance origins, ecology and dissemination potential in telluric bacteria. Environ. Microbiol. (in press). doi: 10.1111/1462-2920.12631
  • Pivetal J, Toru S, Frénéa-Robin M, Haddour N, Cecillon S, Dempsey NM, Dumas-Bouchiat F and Simonet P. 2014. Selective isolation of bacterial cells within a microfluidic device using magnetic probe-based cell fishing. Sensors and Actuators B: Chemical 195: 581–589.
  • Mathieu A, Vogel TM and Simonet P. 2014. The Future of Skin Metagenomics. Res Mic. 165:69-76. doi: 10.1016/j.resmic.2013.12.002.
  • Nesme J, Cécillon S, Delmont TO, Monier J-M, Vogel T.M and Simonet P. 2014. Large scale metagenomic-based study of antibiotic resistance in the environment. Current Biol. 24: 1096-1100.
  • Jacquiod S, Demanèche S, Delmont TO, Ausec L, Dunon V, Franqueville L, Mandic-Mulec I, Springael D, Vogel TM and Simonet P. 2014. Genetic screening of a fosmid metagenomic soil library using radio-labeled oligonucleotide probes. J. Biotechnol. (in press).  doi: 10.1016/j.jbiotec.2014.03.036.


  • Mathieu A, Delmont TO, Vogel TM, Robe P, Nalin R and Simonet P. 2013. Life on human surfaces: skin metagenomics. PLoS ONE 8(6): e65288. doi:10.1371/journal.pone.0065288.
  • Delmont TO, Simonet P, Vogel TM. 2013. Mastering methodological pitfalls for surviving the metagenomic jungle. BioEssays 35: 744–754.
  • Gaze WH, Krone SM, Larsson DGJ, Li X-Z, Robinson J, Simonet P, Smalla K, Timinouni M, Topp E, Wellington EM, Wright GD, Zhu Y-G. 2013. The impact of humans on the evolution and mobilization of the environmental antibiotic resistome. Environmental Health Perspectives 19 : doi: 10.3201/eid1907.120871.
  • Jacquiod S, Franqueville L, Cécillon S, Vogel TM and Simonet P. 2013. Soil bacterial community shift after chitin enrichment: An integrative metagenomic approach. PLoS ONE 8(11): e79699.
  • Simonet, P. 2013. Évolution de l’antibiorésistance dans le sol. ANSES: Les cahiers de la Recherche: Santé, Environnement, Travail. Octobre 2013 :42-44.

top Professional Experience
since 2006:         PI in the Working group “Environmental Microbial Genomics” at UMR CNRS 5005,                             Laboratoire Ampère, Ecole Centrale de Lyon.
1990- 2006:        PI in the Working group “Horizontal gene transfer and bacterial adaptation” at UMR                            CNRS 5557, Ecologie Microbienne du sol, Université de Lyon.
1983-1990:         Scientist in the Working group “Frankia symbiosis” at UMR CNRS 5557, Ecologie                            Microbienne du sol, Université de Lyon.          
1982 -1983:        Post-doctoral position at the department of forestry, University Laval, Québec, Canada.

American Society for Microbiology (ASM)
International Society for Microbial Ecology (ISME)

Reviewing appointments
Agence Nationale Recherche (ANR), France
Agence Evaluation Recherche (AERES), France

INRA : Recruitments, Promotions, Projects and Careers

F.R.S.-FNRS, Belgium
Israel Science Foundation (ISF), Israel
Chinese Academy of Sciences, Strategic Priority Research Program (Type-B), China
WO-Expertpanel Molecular and Cellular Biology (Bio1), Belgique
ECOS : Evaluation-orientation de la COopération Scientifique Programme de coopération et de partenariat universitaire technique et scientifique France-Amérique Latine

Progr. Hospitalier Recherche Clinique PHRC, France
INRA : Département SPE, France
CNRS : Programme GESSOL, France
>CNRS-INEE: Génom.  Environnement. (APEGE).
Conseil Région d’Aquitaine, France
Conseil Région Bretagne, France
Conseil Région Pays de la Loire, France
Conseil Région Ile de France, France
Ville de Paris: Médecine et Santé, France
Convergence-UPMC, France
Convergence-Sorbonne Universités, France

topMember of Editorial Boards

Research in Microbiology (full editor since 2007)
Annals of Microbiology (full editor 2008-2012)
ISME Journal (since 2007)                                               
Applied and Environmental Microbiology (until 2012)


since 2011                              Member of the Scientific Committee of Plant Health and Environment (SPE)                                                department of INRA.
since 2008                              Member of the French council (Scientific committee) “Haut Conseil des                                                Biotechnologies” (HCB)”
1990-2008                              Member of the French committee “Commission de Génie Génétique” (CGG)
2000-2008                              Member of the Biotechnology Committee at the French Food Security                                                Commission (AFSSA)
2005                                       President of the Organizing committee of the 8th Symposium on Bacterial                                                Genetics and Ecology. BAGECO-08. June 26-29 2005, Lyon
1995-2005                              Member of the former National Ecotoxicology Commission (PNETOX)
                                               Member of scientific committees of different conferences