Actual position and research subject

Assistant Profesor at INSA Toulouse Department of Chemical Engineering : Water Energy and Environment – Deputy Director of the GP3E Department

My research activities are focused on microbial engineering and more precisely on the interactions between biological activities and environmental constraints in complex three-phase environments. My objectives are to understand and to quantify the interactions between microorganisms and their biological activity and the physicochemical evolution of their environment (liquid and gas phases) in order to identify the phenomena that limit microbial performance. My activities are declined on pure or mixed cultures by using or developing specific tools (flow cytometry, confocal microscopy, Q RT PCR methods…) in order to quantify the microbial dynamics and to propose culture strategies or innovative process configurations to maximize the conversion of substrates into products with more or less high added value.

My research projects deal with (i) the intensification of microbial reactions by integrating environmental assessments for eco-designed bioproduction strategies as well as the development of hybrid bioprocesses (extractive fermentation) or immobilized cells by (II) quantifying the reversibility or irreversibility of the biological activity (link between medium properties and cellular activity or death) in order to manage the microbial reaction at its optimal potential and improve the robustness of the strains.

Education and Diploma


(200 h /year)

Bachelor Level :

Chemistry (LabWorks) and Analytical Methods (C, Tutorials, Labworks)

Master Level :

Environmental Metrology (FR/EN) (C, Tutorials, Labworks) ; Envionmental Management  and Environment Law (FR/EN) (C, Tutorials) ; Research and Calculation Projects ; Green Chemistry, Sustanaibility and Coroprate Social Responsability (FR/EN) (C, Tutorials)


  • Supervised or co-supervised: 9 PhD students, 4 post-doctoral position, 19 Master students and 6 contractual Engineers
  • Contribution to research projects:
    • I was involved in 3 European Projects (PAI (2005-2009), PHC Procope (2016-2018) and H2020 BABET REAL 5 (2016-2020), 5 French projects funding by OSEO FUTUROL (2008-2015), 3BCAR Carnot network (3 : 1 as coordinator, 1 as Scientific leader, 1 as participants) and FUI (Kefistab project as Coordinator), 6 ANR projects (as participants between 2006 – 2015) including one International (SPECTRE 2012-2015 as WP Leader).
      Currently, I am participating to 1 National project “Make Our Planet Great Again” Program (Cambioscop) and to EcoCTs Project (LIA France-Singapore CNRS@Create) ; I am coordinating 1 ANR project (“New Eco-Routes” 2022-2005) and I am leader of 2 workpackages in ANR-PIA3 project named EUR BIOECO (2020-2028).
  • Other:
    • Deputy Director of INSA GP3E Department (Since 2020)
    • International Coordinator for Bachelor program INSA Toulouse (since 2007).
    • WP Leader for Education program for Masters, PhD and Industrial public in PIA3 ANR program EUR BioECO (Since 2019)
    • Member of Editorial Board de Acta Innovations (Since 2018)
    • Rewiew Editor pour Frontiers in Biotechnology (Since 2019)
    • Member of the French Society for Chemical Eng. (SFGP) and Co-organizer of “thematic scientific webinars” for SFGP “section grand sud-ouest”
    • Member of French Association of Cytometry (Biosecurity Group)

List of selected publications

  • Boy C, Lesage J, Alfenore S, Guillouet SE, Gorret N. 2022. Study of plasmid-based expression level heterogeneity under plasmid-curing like conditions in Cupriavidus necator. Journal of Biotechnology 345:17-29 doi:
  • 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
  • Boy, J. Lesage, S. Alfenore, N. Gorret, S. Guillouet. 2020. Plasmid expression level heterogeneity monitoring via heterologous eGFP production at the single-cell level in Cupriavidus necator. Applied Microbiology and Biotechnology, ⟨10.1007/s00253-020-10616-w⟩.
  • Alfenore S, Molina-Jouve C. 2016. Current status and future prospects of conversion of lignocellulosic resources to biofuels using yeasts and bacteria. Process Biochemistry; 51:1747-1756.
  • Bideaux C, Montheard J, Cameleyre X, Molina-Jouve C, Alfenore S. 2016. Metabolic flux analysis model for optimizing xylose conversion into ethanol by the natural C5-fermenting yeast Candida shehatae. Applied microbiology and biotechnology; 100:1489-1499.
  • Pagliardini J, Hubmann G, Alfenore S, Nevoigt E, Bideaux C, Guillouet SE. 2013. The metabolic costs of improving ethanol yield by reducing glycerol formation capacity under anaerobic conditions in Saccharomyces cerevisiae. Microbial cell factories; 12:29.
  • Soussan L, Guigui C, Mathe C, Alfenore S, Cabassud C. 2013. Enzyme-labeled phages detected by amperometry: A new method to study inline virus retention in membrane processes. AIChE Journal, 59:68-78.
  • Soussan L, Alquier M, Guigui C, Alfenore S, Mathe S, Cabassud C. 2013. Characterization of the inline virus removal performances in hollow fibre modules by a new tracer electrochemically detected. Water Science and Technology-Water Supply; 13:507-514.
  • Amillastre E, Aceves-Lara C-A, Uribelarrea J-L, Alfenore S, Guillouet SE. 2012. Dynamic model of temperature impact on cell viability and major product formation during fed-batch and continuous ethanolic fermentation in Saccharomyces cerevisiae. Bioresource Technology; 117:242-250.
  • Montheard J, Garcier S, Lombard E, Cameleyre X, Guillouet S, Molina-Jouve C, Alfenore S. 2012. Assessment of Candida shehatae viability by flow cytometry and fluorescent probes. J Microbiol Methods; 91:8-13.
  • Beaufort S, Da Silva T, Lafforgue C, Alfenore S. 2012. Fluorescent proteins as in-vivo and in-situ reporters to study the development of a Saccharomyces cerevisiae yeast biofilm and its invasion by the bacteria Escherichia coli. FEMS microbiology ecology; 80:342-351.
  • Kerfai S, Mathe S, Alfenore S, Fernandez A. 2011. Intensive Ion Exchange Process for Soluble Proteins Recovery from Industrial Alfalfa Green Juice. In: J. J. Klemes, P. S. Varbanov,H. L. Lam editors. Chem Engineer Trans vol. 25; p. 1061-1066.
  • Hery M, Sanguin H, Perez Fabiel S, Lefebvre X, Vogel TM, Paul E, Alfenore S. 2010. Monitoring of bacterial communities during low temperature thermal treatment of activated sludge combining DNA phylochip and respirometry techniques. Water Res; 44:6133-6143.
  • Beaufort S, Alfenore S, Lafforgue C. 2009 Fluorescent microorganisms: a relevant tool to quantify the relationships between environmental conditions and 3D microbial organization in biological aggregates. New Biotechnology; 25, Supplement:S208-S209.
  • Sanchez-Gonzalez Y, Cameleyre X, Molina-Jouve C, Goma G, Alfenore S. 2009. Dynamic microbial response under ethanol stress to monitor Saccharomyces cerevisiae activity in different initial physiological states. Bioprocess and biosystems engineering; 32:459-466.
  • Ben Chaabane F, Aldiguier AS, Alfenore S, Cameleyre X, Blanc P, Bideaux C, Guillouet SE, Roux G, Molina-Jouve C. 2006 Very high ethanol productivity in an innovative continuous two-stage bioreactor with cell recycle. Bioprocess and biosystems engineering; 29:49-57.
  • Alfenore S, Bideaux C, Cameleyre X, Molina-Jouve C, Uribelarrea JL, Guillouet SE. 2006 Minimization of glycerol production during the high-performance fed-batch ethanolic fermentation process in Saccharomyces cerevisiae, using a metabolic model as a prediction tool. Applied and environmental microbiology; 72:2134-2140.
  • Aldiguier AS, Alfenore S, Cameleyre X, Goma G, Uribelarrea JL, Guillouet SE, Molina-Jouve C. 2004 Synergistic temperature and ethanol effect on Saccharomyces cerevisiae dynamic behaviour in ethanol bio-fuel production. Bioprocess and biosystems engineering; 26:217-222.
  • Alfenore S, Cameleyre X, Benbadis L, Bideaux C, Uribelarrea JL, Goma G, Molina-Jouve C, Guillouet SE. 2004 Aeration strategy: a need for very high ethanol performance in Saccharomyces cerevisiae fed-batch process. Applied microbiology and biotechnology; 63:537-542.
  • Alfenore S, Delia ML, Strehaiano P. 2003 Use of ATP measurements by bioluminescence to quantify yeast’s sensitivity against a killer toxin. Analytica Chimica Acta; 495:217-224.
  • Alfenore S, Molina-Jouve C, Guillouet SE, Uribelarrea JL, Goma G, Benbadis L. 2002 Improving ethanol production and viability of Saccharomyces cerevisiae by a vitamin feeding strategy during fed-batch process. Applied microbiology and biotechnology; 60:67-72.