Technology unit
Microbiology and molecular engineering

Design and develop original scientific and technological solutions to accelerate microbiological research for the benefit of animal and human health.

Microbiology and molecular engineering

Our mission is to design and develop original scientific and technological solutions to accelerate microbiological research for the benefit of animal and human health.

We provide cutting-edge scientific and technological expertise, from the conception to the conclusion of a project, in the fields of microbial genetics, protein engineering, bacteriology (aerobic and anaerobic), and virology.
The Microbiology Unit brings together experts in bacteriology, virology, genetics, and protein engineering to facilitate microbiological research.



  • Biofilms are complex, multi-species bacterial communities that live on biotic and abiotic surfaces.
  • In the medical setting, biofilms are associated with the serious problem of nosocomial infection, especially when they contaminate medical devices.
  • Biofilm-related infections are difficult to treat, because of a high prevalence of antibiotic tolerance/resistance.
  • It is necessary to design new strategies for biofilm control, involving the prevention of biofilm formation on the surfaces of medical devices and biofilm eradication strategies.
  • It is difficult to undertake drug screening using relevant conditions.
  • To identify the modes of action of anti-biofilm drugs.
  • The optimization of anti-biofilm strategies using combinations of modalities; for example, phages, antibiotics, and enzymes.

We can evaluate new anti-biofilm strategies using fully customized in vitro and/or in vivo approaches.


  • To design new strategies for the prevention of biofilm formation on surfaces.
  • To develop effective new strategies for biofilm eradication.
  • To design and develop novel biofilm infection models for use in vitro.
  • To design novel screening approaches and technologies to permit the use of anti-biofilm solutions in patients.
  • To test new anti-biofilm approaches using fully customized in vitro and/or in vivo approaches.


  • We use an integrated biofilm platform (BIOFILM-ID),
  • We perform biofilm analysis using well-established and standardized methods,
  • We work with both static and dynamic models,
  • We design tailored screening approaches, according to your needs,
  • We can develop physiologically relevant models,
  • We can work with BSL-3 pathogens,
  • We have access to a collection of microorganisms of various origins; for example, clinical samples, gut microbiota, and antibiotic-resistant strains.


We have developed:

  • BiofilmCare,
  • A multi-OMIC approach to the investigation of anti-biofilm Mode of Action (MoA),
  • In vivo models

Watch the Biofilm video here.



  • The gut microbiota plays an important role in the maintenance of human health, but it is also involved in the development of disease.
  • Imbalances in the microbiome, or dysbiosis, have been linked to a range of diseases, including certain types of cancer (e.g. colon cancer), autoimmune diseases (e.g. multiple sclerosis and type 1 diabetes), inflammatory bowel disease, and even depression.

Today, there is increasing interest in the study of the microbiota, with the intention of identifying or developing new probiotics.


  • The culture and identification of the bacteria that inhabit the guts of humans and animals.
  • The reawakening of culture techniques for microbiology, for example using anaerobic-specific media dedicated to difficult-to-culture gut bacteria (e.g. F. prausnitzii and C. minuta).
  • The identification of new antimicrobials, obtained from the microbiota.
  • The identification of biomarkers of the gut microbiota that indicate health status and predict future pathologies.


We use the ANOXIC Platform:

This is an integrated platform for the isolation and cultivation of microorganisms in a controlled environment (aerobic or anaerobic conditions) and their characterization.

  • It combines the use of a new-generation high-precision flow cytometer, the molecular selection of microorganisms (e.g. antibodies or molecular labeling), the molecular identification and characterization of microorganisms (NGS, full 16S, or shotgun sequencing), and their phenotypic characterization (e.g. bacteriocin, anti-inflammatory compounds, or short-chain fatty acid production).
  • We have access to a collection of microorganisms of various origins, including clinical samples, the gut microbiota, and antibiotic-resistant strains.

Protein Engineering


  • The need for complex molecules in the development of new clinical strategies, such as novel vaccines, diagnostic tools, and drug delivery systems.
  • The need for customized workflows to be compatible with your downstream applications.
  • The need for functional assays, including of enzyme activity.
  • The need for expert support and customizable options (e.g. for codon optimization and protein purification procedures).


  • Integrated solutions for the expression, extraction, and purification of complex molecules of appropriate quality and quantity that are suitable for pharmaceutical discovery.
  • An experienced team that responds to the expectations of partners from protein design to product characterization.
  • A series of vectors for various purposes and specific applications (e.g. lipoproteins, VLPs, secretion).


We have an integrated platform and appropriate expertise in:

  • expression System Optimization (genetically optimized strains and transposon sequencing library generation);
  • protein Engineering (protein design and vectorization systems, codon harmonization, combinational cloning and screening, and the optimization of expression and purification);
  • development of analytical tools (de novo binder generation, biophysical and biochemical characterization, preclinical batch characterization, and protein-ligand characterization).
Jérémy WelschHead of Microbiology and Preclinical research unitIcon email