Joseph Nesme Environmental Microbial Genomics Group

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

Education | Research Interests | Publications | Curriculum Vitae | More...

  Joseph Nesme

Laboratoire Ampère, UMR CNRS 5005
Ecole Centrale de Lyon
Université de Lyon
36 avenue Guy de Collongue
69134 Ecully cedex
  Phone: (33) 4 72 18 61 05
Fax: (33) 4 78 43 37 17




2008 - Microbiology B. Sc. (Licence de microbiologie) – Université Claude Bernard Lyon 1, University of Lyon.

2010 – Microbiology and Ecology M. Sc. (Master de Microbiologie et Ecologie) – Université Claude Bernard Lyon 1, University of Lyon

2010, Oct. – May 2014 Ph. D. in the Environmental Microbial Genomics Group, Laboratoire Ampère, Ecole Centrale de Lyon, University of Lyon under the supervision of Dr. Pascal Simonet : « Prevalence, diversity and dissemination potential of antibiotic resistance genes in soils between two contrasted situations regarding antibiotics exposure »


Interested in every aspects of the evolution theory, I’m particularly interested by the mechanics leading to the selection process and their ecological significance. Bacterial adaptation is a perfect field of study due to 1) the incredible diversity harboured by bacterial communities 2) their formidable capabilities of adaptation through a wide range of processes going from vertical inheritance to « genetic infection » of some mobile genetic elements 3) the relative ease of working on big populations with microbes.

Currently working on the ecological role of antibiotic resistances in the environment with a special focus on soil, the lab’s favorite ecosystem, I’m using metagenomic WGS sequence datasets and bioinformatic tools as well as a wide range of molecular techniques from quantitative PCR to gene cloning in order to achieve my research objectives.


Articles (peer reviewed) :

Nesme, J., Cécillon, S., Delmont, T.O., Monier, J-M., Vogel, T.M., Simonet, P. 2014. Large-Scale Metagenomic-Based Study of Antibiotic Resistance in the Environment Current Biology 24, 1–5,

Delmont, T.O., Francioli, D., Jacquesson, S., Laoudi, S., Mathieu, A., Nesme, J., Ceccherini, M.T., Nannipieri, P., Simonet, P., Vogel, T.M. 2014. Microbial community and unseen diversity development in inoculated sterile soil, Biology and Fertility of Soil, DOI: 10.1007/s00374-014-0925-8

Zhang, X., Nesme, J., Simonet, P. & Frostegård, Å. (2012). Fate of invading bacteria in soil and survival of transformants after simulated uptake of transgenes, as evaluated by a model system based on lindane degradation. Res Microbiol 1–39. Elsevier Ltd.

Oral presentations :
Nesme, J., Cécillon, S., Delmont, T. O., Vogel, T. M., Simonet, P. & Monier, J.-M. (june 2011). Characterization of the diversity and prevalence of Antibiotic Resistance Gene Determinants in the environment using a metagenomic approach. FEMS 2011, Geneva, Switzerland (J. Martinez & G. Wright, Eds.).

Nesme, J., Cécillon, S., Delmont, T. O., Vogel, T. M., Simonet, P. & Monier, J.-M. (october 2011). “Metaplasmidomics” investigation of soil bacteria in a reference soil. 1st International Conference on Soil Omics. Nanjing Agricultural University, Nanjing, China (Q. Shen & R. Zhang, Eds).





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