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Nathalie GORRET

Nathalie Gorret FAME

Nathalie GORRET

INRAE Research Scientist

Actual position and research subject

I’m an INRAE Research Scientist in the Fermentation Advances and Microbial Engineering Group (FAME Group) at Toulouse Biotechnology Institute (TBI) since 2007. My pHD followed by a 3 years post-doctorate at Massachussets Institute of Technology (Cambridge –USA) in the laboratory of Pr Sinskey (Biology Department) have contributed to develop expertise on Microbiology/Microbial Physiology and Biochemical Engineering skills with both Bacteria and Yeast.

I joined the Toulouse Biotechnology Institute in 2005 as a post-doctorate to investigate the dynamics of the interaction between biological and physical phenomena observed in large-scale bioreactor. Since then, my researches focus on the understanding of the impact of the heterogeneities (substrates/products/pH/dissolved oxygen gradients/sub-populations) on the microbial behavior and strain robustness at both population and sub-population level (physiological states / morphological states / genetic stability) using Wild Type (WT) and genetically engineered strains in order to optimize microbial processes. I develop skills on methodologies and tools to characterize and quantify the transient microbial responses to environmental stresses using offline and online biosensors at both global population and single-cell levels.

In addition, I develop projects focusing more specifically on biochemical engineering and bioprocess development and optimization implanting unconventional microorganisms (extremophile microorganism for example) or for specific bioproduction such as Single Cell Proteins.

Education and Diploma


Microbial Physiology, Biochemical Engineering, Microbial Metabolism   at INSA Toulouse (M1 and M2 levels)


  • Scientific supervision of PhD students (7), post-doctoral fellow (4), Master (3) since 2007
  • Elected Member of the scientific board of the axis Microbiology & Enzyme Engineering in the SEVAB Doctoral School (2016-2020 / 2021-2024)
  • Elected Member of the scientific board of CEPIA department of INRA (2011-2016)         
  • Member of PhD Defense Jury (4), PhD thesis Committee (3), PhD mentors (4)
  • Expert for national and international funding agencies (EraIB, FNRS, ANR-PRC, IBISBA 1.0)
  • Reviewer for international scientific journals (Applied Microbiology and Biotechnology, Bioprocess and Biosystems Engineering, Bioprocess Engineering, Journal of Biotechnology, Microbial Cell Factories, Advances in Bioscience and Biotechnology, Process Biochemistry, Journal of Fungi, Biotechnology and Bioengineering, Yeast….)
  • Participation (proposal writing/scientific responsibility and coordination) to several academic national and international projects
    • National Projects: ANR-IDYBioPBio (2005-2008) / ANR-OSEO DEINOL-Lot1.6 (2009-2013) / ANR-OSEO FUTUROL-Action F2A3 (2011-2013) / 3BCAR-BIMECOMB (2012-2014) / TWB-Précompétitif-CARBOYEAST (2012-2014) / ANR-OSEO-IA Probio3 (2013-2016) / 3BCAR-HME (2017-2019) / ANR PRC-JANUS (2020-2024) / 3BCAR – Cytomate (2020-2021) / 3BCAR-OptiPOU (2020-2022) / 3BCAR-NutriPOU (2021-2023) / CNES-AstroPOU I et II (2020-2023)
    • European Projects : PHC-PAI Tournesol (2008/2009) / PHC-PAI PROCOPE (2016/2017) / ITN- ConCO2rde (2021-2025)
    • International Projects: France-MIT Energy Forum (2012-2015) / France-MSTI Seed Fund (2014) / LIA-Singapour ECOCTS

List of selected publications

  • Boy, C., Lesage, J., Alfenore, S., Guillouet, S.E. and Gorret, N. (2022) Study of plasmid-based expression level heterogeneity under plasmid-curing like conditions in Cupriavidus necator. J Biotechnol 345, 17-29.
  • Boy C, Lesage J, Alfenore S, Guillouet SE, Gorret N (2021) Investigation of the robustness of Cupriavidus necator engineered strains during fed-batch cultures. AMB Express 11(1):151 doi:10.1186/s13568-021-01307-4
  • Lesage J, Timoumi A, Cenard S, Lombard E, Lee HLT, Guillouet SE, Gorret N (2021) Accelerostat study in conventional and microfluidic bioreactors to assess the key role of residual glucose in the dimorphic transition of Yarrowia lipolytica in response to environmental stimuli. New Biotechnology 64:37-45 doi:
  • Barthe M, Tchouanti-Fotso J, Gomes P, Bideaux C, Lestrade D, Graham C, Steyer J-P, Meleard S, Harmand J, Gorret N, Cocaign-Bousquet M, Enjalbert B. (2021). Availability of the molecular switch XylR controls phenotypic heterogeneity and lag duration during Escherichia coli adaptation from glucose to xylose. mBio mBio02938-20.
  • Boy C, Lesage J, Alfenore S, Gorret N, Guillouet SE. (2020). Plasmid expression level heterogeneity monitoring via heterologous eGFP production at the single-cell level in Cupriavidus necator. Applied Microbiology and Biotechnology 104:5899-5914.
  • Timoumi A, Guillouet SE, Molina-Jouve C, Fillaudeau L, Gorret N. 2018. Impacts of environmental conditions on product formation and morphology of Yarrowia lipolytica. Appl Microbiol Biotechnol 102:3831-3848.. doi: 10.1007/s00253-018-8870-3
  • Camarasa C, Chiron H, Daboussi F, Della Valle G, Dumas C, Farines V, Floury J, Gagnaire V, Gorret N, Leonil J, Mouret J-R, O’Donohue MJ, Sablayrolles J-M, Salmon J-M, Saulnier L, Truan G. (2018). INRA’s research in industrial biotechnology: For food, chemicals, materials and fuels. Innovative Food Science & Emerging Technologies 46:140-152.
  • Timoumi A, Bideaux C, Guillouet SE, Allouche Y, Molina-Jouve C, Fillaudeau L, Gorret N. (2017). Influence of oxygen availability on the metabolism and morphology of Yarrowia lipolytica: insights into the impact of glucose levels on dimorphism. Appl Microbiol Biotechnol 101:7317-7333.
  • Marc, J., Grousseau, E., Lombard, E., Sinskey, A. J., Gorret, N., & Guillouet, S. E. (2017). Over expression of GroESL in Cupriavidus necator for heterotrophic and autotrophic isopropanol production. Metab Eng, 42, 74-84. doi: 10.1016/j.ymben.2017.05.007
  • Timoumi A, Cléret M, Bideaux C, Guillouet SE, Allouche Y, Molina-Jouve C, Fillaudeau L, Gorret N (2016). Dynamic behavior of Yarrowia lipolytica in response to pH perturbations: dependence of the stress response on the culture mode. Applied Microbiology and Biotechnology:1-16 doi:10.1007/s00253-016-7856-2
  • Grunwald S, Mottet A, Grousseau E, Plassmeier JK, Popovic MK, Uribelarrea JL, Gorret N, Guillouet SE, Sinskey A (2015). Kinetic and stoichiometric characterization of organoautotrophic growth of Ralstonia eutropha on formic acid in fed-batch and continuous cultures. Microbial Biotechnology 8(1):155-163 doi:10.1111/1751-7915.12149
  • Bornot J, Molina-Jouve C, Uribelarrea JL, Gorret N (2015). Quantitative Characterization of the Growth of Deinococcus geothermalis DSM-11302: Effect of Inoculum Size, Growth Medium and Culture Conditions. Microorganisms 3:441-463 doi:10.3390/microorganisms30x000x
  • Grousseau E, Lu JN, Gorret N, Guillouet SE, Sinskey AJ (2014). Isopropanol production with engineered Cupriavidus necator as bioproduction platform. Applied Microbiology and Biotechnology 98(9):4277-4290 doi:10.1007/s00253-014-5591-0
  • Bornot J, Molina-Jouve C, Uribelarrea JL, Gorret N (2014). Growth of the extremophilic Deinococcus geothermalis DSM 11302 using co-substrate fed-batch culture. Applied Microbiology and Biotechnology 98(3):1281-1290 doi:10.1007/s00253-013-5397-5
  • Bornot J, Aceves-Lara CA, Molina-Jouve C, Uribelarrea JL, Gorret N (2014). Experimental and statistical analysis of nutritional requirements for the growth of the extremophile Deinococcus geothermalis DSM 11300. Extremophiles 18(6):1009-1021 doi:10.1007/s00792-014-0671-8
  • Sunya S, Bideaux C, Molina-Jouve C, Gorret N (2013). Short-term dynamic behavior of Escherichia coli in response to successive glucose pulses on glucose-limited chemostat cultures. Journal of Biotechnology 164(4):531-542 doi:10.1016/j.jbiotec.2013.01.014
  • Brognaux A, Thonart P, Delvigne F, Neubauer P, Twizere JC, Francis F, Gorret N (2013). Direct and indirect use of GFP whole cell biosensors for the assessment of bioprocess performances: Design of milliliter scale-down bioreactors. Biotechnology Progress 29(1):48-59 doi:10.1002/btpr.1660
  • Bornot J, Molina-Jouve C, Uribelarrea J-L, Gorret N (2013). Growth of the extremophilic Deinococcus geothermalis DSM 11302 using co-substrate fed-batch culture. Applied Microbiology and Biotechnology:1-10 doi:10.1007/s00253-013-5397-5
  • Sunya S, Gorret N, Delvigne F, Uribelarrea JL, Molina-Jouve C (2012). Real-time monitoring of metabolic shift and transcriptional induction of yciG::luxCDABE E. coli reporter strain to a glucose pulse of different concentrations. Journal of Biotechnology 157(3):379-390 doi:10.1016/j.jbiotec.2011.12.009
  • Sunya S, Delvigne F, Uribelarrea JL, Molina-Jouve C, Gorret N (2012). Comparison of the transient responses of Escherichia coli to a glucose pulse of various intensities. Applied Microbiology and Biotechnology 95(4):1021-1034 doi:10.1007/s00253-012-3938-y