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INRAE Research Director
BLADE Team leader

Actual position and research subject

I am a scientist in the “Microbiology and Food Chain” division of the French National Institute for Agricultural, Food and Environmental Research, currently working at the Toulouse Biotechnology Institute as head of the research group BLADE (Bacterial Adaptation Diversity and Engineering).

I am interested in the study of Bacterial Physiology and Metabolism to better understand mechanisms of adaptation of bacteria to their environment and to engineer bacteria for applications in biotechnology.

My major area of study is RNA dynamics in bacteria to better understand genome-wide post-transcriptional regulations, their role in the regulation of gene expression and their potential for engineering bacteria. More recently, I have also initiated studies on bacterial diversity and heterogeneity, working on various bacteria strains alone, in consortia or in interaction with non-equivalent monoclonal subpopulations.

My research concerns predominantly two model bacteria, Lactococcus lactis and Escherichia coli, using a systems biology approach to elucidate the different levels of metabolic regulation and notably genome wide omic regulations. I initiated collaborations with mathematicians to rationalise the use of large-scale genomic data-sets to investigate bacterial physiology. I am currently an associated member of the group Microcosm at INRIA Grenoble to combine computational and experimental approaches.

Education and Diploma


  • Supervised or co-supervised: 22 PhD students and 9 post-docs
  • Contribution to research projects: Coordination of 28 regional, national or international research projects
  • Major ongoing projects:
    • 2018-2023-ANR-18-CE43-0010, RIBECO, RNA life cycle engineering for an economic approach to microbial energetics: application to the bioconversion of biomass-derived carbon sources. Coordination

    • 2019-2024-ANR-19-CE43-0004-01, JANUS, Control and Optimization of Metabolic Transitions.  Work package leader

    • 2018-2024-Toulouse Tech Transfert maturation program and collaboration project with Lesaffre, health properties of L. lactis. Co-coordination

List of selected publications

  • Roux C., Etienne T.A., Hajnsdorf E., Ropers D., Carpousis A.J., Cocaign-Bousquet M.#, GIRBAL L.# 2022. The essential role of mRNA degradation in understanding and engineering E. coli metabolism. Biotechnol Adv. 2022 Jan-Feb;54: 107805, doi: 10.1016/j.biotechadv.2021.107805. hal-03325744v1.
  • Nguyen H.L., Duviau M.P., Laguerre S., Nouaille S., Cocaign-Bousquet M.#, GIRBAL L#. 2022. Synergistic regulation of transcription and translation in Escherichia coli revealed by co-directional increases in mRNA concentration and translation efficiency. Microbiol Spectr. 2022 Feb 9:e0204121. doi: 10.1128/spectrum.02041-21. hal-03546610v2.
  • Laroute V., Mazzoli R., Loubière P., Pessione E., Cocaign-Bousquet M. (2021) Environmental conditions affecting GABA production in Lactococcus lactis NCDO 2118. Microorganisms. Jan 7;9(1):122. doi: 10.3390/microorganisms9010122. hal-03277774v1
  • Etienne T., Cocaign-Bousquet M., Ropers D. (2020) Competitive effects in bacterial mRNA decay. J. Theor. Biol. 504(7)110333. hal-2967513v1.
  • Barthe M., Tchouanti J., Henrique-Gomes P., Bideaux C., Lestrade D., Graham C., Steyer J.-P., Meleard S., Harmand J., Gorret N., Cocaign-Bousquet M.#, Enjalbert B.# (2020) Availability of the molecular switch XylR controls phenotypic heterogeneity and lag duration during Escherichia coli adaptation from glucose to xylose, mBio. 2020 Dec 22;11(6), doi: 10.1128/mBio.02938-20. hal-03096881v1.
  • Morin M., Enjalbert B., Ropers D., GIRBAL L., Cocaign-Bousquet M. 2020. Genome-wide stabilization of mRNA during a ‘feast-to-famine’ growth transition in Escherichia coli. mSphere, doi: 10.1128/mSphere.00276-20. hal-02967494v1.
  • Patent n° WO 2020/157297 Extension PCT Cocaign-Bousquet M, ML Daveran Mingot, V Laroute, V Theodorou, MH Eutamene, M Mercier-Bonin. Lactococcus lactis strains for the prevention and/or the treatment of visceral pain.
  • Hadjeras L., Poljak L., Bouvier M., Morin-Ogier Q., Canal I., Cocaign-Bousquet M., Girbal L., Carpousis A-J. (2019) Detachment of the RNA degradosome from the inner membrane of Escherichia coli results in a global slowdown of mRNA degradation, proteolysis of RNase E and increased turnover of ribosome-free transcripts. Mol. Microbiol. 111(6):1715-1731. doi: 10.1111/mmi.14248. hal-02317164v1.
  • Dressaire C., Pobre V., Laguerre S., Girbal L., Arraiano C.M., Cocaign-Bousquet M. (2018) PNPase is involved in the coordination of mRNA degradation and expression in stationary phase cells of Escherichia coli. BMC Genomics 19(1):848. doi: 10.1186/s12864-018-5259-8. hal-01954725v1.
  • Nouaille S., Mondeil S., Finoux A-L., Moulis C., Girbal L., Cocaign-Bousquet M. (2017) The stability of an mRNA is influenced by its concentration: a potential physical mechanism to regulate gene expression. Nucleic Acids Res. 45(20):11711-11724. hal-01882991v1. doi: 10.1093/nar/gkx781. hal-01882991v1.
  • Morin M., Ropers D., Letisse F., Laguerre S., Portais J-C., Cocaign-Bousquet M.#, Enjalbert B# (2016) The post-transcriptional regulatory system CSR controls the balance of metabolic pools in upper glycolysis of Escherichia coli. Mol. Microbiol. 100(4):686-700; doi: 10.1111/mmi.13343. hal-02147255v1
  • EsquerrE T., Turlan C., Bouvier M., Carpousis A.J., Girbal L.#, Cocaign-Bousquet M.# (2016) The Csr system regulates genome-wide mRNA stability and transcription and thus gene expression in Escherichia coli. Sci Rep. 2016 Apr 26;6:25057. doi: 10.1038/srep25057.
  • Esquerre T., Laguerre S., Turland C., Carpousis A.J., Girbal L., Cocaign-Bousquet M. (2014) Dual role of transcription and transcript stability in the regulation of gene expression in Escherichia coli cells cultured on glucose at very different growth rates. Nucleic Acids Res. 42:2460-2472. ⟨10.1093/nar/gkt1150⟩. hal-02129879v1.
  • Dressaire C., Picard F., Redon E., Queinnec I., Loubière P., Girbal L., Cocaign-Bousquet M. (2013) Role of mRNA stability during bacterial adaptation, PLoS One. 8(3):e59059.       
  • Racle J., Picard F., Girbal L., Cocaign-Bousquet M., Hatzimanikatis V. (2013) A genome-scale integration and analysis of Lactococcus lactis translation data. PLoS Comput. Biol. 2013 Oct;9(10):e1003240.
  • DRESSAIRE C., GITTON C., LOUBIERE P., MONNET V.  QUEINNEC I., COCAIGN-BOUSQUET M. (2009) Transcriptome and Proteome Exploration to Model Translation Efficiency and Protein Stability in Lactococcus lactis, PLoS Comput. Biol. Dec;5(12):e1000606.
  • Nouaille S., Even S., Charlier C., Le Loir Y., Cocaign-Bousquet M., Loubière P. (2009) Transcriptomic response of Lactococcus lactis in mixed culture with Staphylococcus aureus. App. Environ. Microbiol., 75: 4473-82.
  • MALIGOY M., MERCADE M., Cocaign-Bousquet M., Loubiere P. (2008) Transcriptome analysis in mixed culture: the response of Lactococcus lactis faced to Saccharomyces cerevisiae. App. Environ. Microbiol., 74: 485-494.
  • REDON E., LOUBIERE P., COCAIGN-BOUSQUET M. (2005) Role of mRNA stability during the genome-wide adaptation of Lactococcus lactis to carbon starvation. J. Biol. Chem., 280:36380-36385.
  • REDON E., LOUBIERE P., COCAIGN-BOUSQUET M., (2005) Transcriptome analysis of the progressive adaptation of Lactococcus lactis to carbon starvation. J. Bacteriol., 187:3589-3592
  • Even S., Lindley N. D., Loubiere P., Cocaign-Bousquet M. (2002) Dynamic response of catabolic pathways to auto-acidification in Lactococcus lactis: transcript profiling in relation to metabolic and energetic constraints. Mol. Microbiol., 45:1143-1152.
  • DOMINGUEZ H., ROLLIN C., GUYONVARCH A., GUERQUIN-KERN J-L., COCAIGN-BOUSQUET M., LINDLEY N.D. (1998) Carbon-flux distribution in the central metabolic pathways of Corynebacterium glutamicum during growth on fructose. Eur. J. Biochem., 254:96-102.
  • Garrigues C., Loubiere P., Lindley N.D., Cocaign-Bousquet M. (1997) Control of the shift from homolactic to mixed acid fermentation in Lactococcus lactis: predominant role of the NADH:NAD+ ratio. J. Bacteriol., 179:5282-5287.
  • Cocaign-Bousquet M., Guyonvarch A., Lindley N.D. (1996) Growth rate dependent modulation of carbon flux through central metabolism and the kinetic consequences for glucose-limited chemostat cultures of Corynebacterium glutamicum. App. Environ. Microbiol., 62:429-436.