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UMR Procédés Alimentaires et Microbiologiques

Microbiological and Biotechnological Processes (PMB)


Keywords: Microorganisms, food, fermentation processes, enzymes, aromas, environmental stress, kinetics, membrane, genomic and cell response, preservation, decontamination

Main research objectives and topics: 

The PMB team comprises lecturer-researchers and other staff specialising in various disciplines: biology, microbiology, virology, enzymology, genetics, molecular and cell biology, biophysics, microbiological process engineering, IT, automation, and applied mathematics. These skills are used to improve food quality through the development of new products and/or processes implementing selected microorganisms and/or innovative processes for destroying pathogenic or spoilage flora.

Consequently, our research concerns all sectors of the food industry and aims to optimise the production and preservation of useful microorganisms (starters, probiotics, biotechnological flora) as well as their implementation in fermentation or biotechnological processes, or, on the contrary, to destroy unwanted spoilage and/or pathogenic microorganisms (bacteria, yeasts, viruses, microbial spores).

To attain these objectives, the research focuses on controlling the activity and the functionality of microorganisms (bacteria, probiotics, yeasts, filamentous fungi, spores) subjected to various types of physico-chemical and biological stress of varying magnitude and kinetics encountered in media, atmospheres, food matrices and processes, or in superior hosts (animal and human microbiota).

Industrial benefits: 

For the industrial applications targeted by and resulting from this fundamental research, the PMB laboratory has numerous research agreements with companies (confidential) in partnership with Welience, a transfer subsidiary of Burgundy University SATT - Grand EST.

The medium-term objectives of the applications of the research topics addressed by the PMB team will be:

to condition cell physiology and improve the quality of fermented products (sensory, preservation…);
• to improve the functionality and preservation of different types of dried, freeze-dried or frozen microorganisms, as well as to develop new, more sustainable processes (decrease in energy consumption);
• to optimise the destruction of microorganisms during technological processing (drying, pasteurisation, sterilisation, high pressure) whilst preserving the nutritional and sensory properties of the food products (combined soft technologies); this involves improving existing processes but also designing new processes.

This research is grounded on baseline studies on microbial behaviour:

Cell response mechanisms (passive, biophysical, and adaptive genomic responses) of microorganisms subjected to controlled changes in chemical (redox potential, pH, phenolic acids or other chemicals…) or physical parameters with varying kinetics and methods of implementation (isostatic pressure, temperature, osmotic pressure…), alone or in combination.

Response mechanisms to 'extreme' stress inducing only a passive response (mass and/or heat transfer) but also stress of intermediate intensity causing simultaneously adaptive (gene expression) and passive (plasma membrane, flow…) responses.

The research conducted by the PMB team implements high-performance tools and strategies adapted to a multi-disciplinary approach

  • Confocal, spectral, and two-photon microscopy (DImaCell facility)

  • Spectrophotometry (FTIR, Fluorescence), flow cytometry

  • Molecular and cell biology equipment, inverse genetics, transposon mutagenesis, gene deletion and expression, development and screening of a genomic DNA bank and random transposon or chemical mutant banks

  • Biochemistry of regulation mechanisms, microbial physiology, and interactions between microorganisms

  • Controlled fermentation equipment from laboratory to pilot phase (Welience)

  • P2 laboratory for handling class 2 pathogenic microorganisms (Listeria, Salmonella...)  

  • Laboratory for handling norovirus and other viruses (Faculty of medicine)

  • Culture rooms and obligate anaerobic laboratory

  • System for applying extremely high pressure to microbial cultures

For its research, the PMB team draws on the technical resources of the DImaCell facility (Regional Cell Imaging Facility), a support structure for the team and the JRClocated on the Agrosup site, as well as the pilot liquid and solid fermentation equipment of Welience - SATT Grand-Est.

Some recent contract-based research projects:

- DOPEOS: Development and Optimization of a Production process of Extremely Oxygen Sensitive bacteria for their industrial exploitation (ANR funded project)

- BlacHP: Lactic acid bacteria combined with high pressure for a sustainable stabilisation process of refrigerated meat products (ANR funded project)
Probiotics: Selection and integration of a functional probiotic strain in a dry matrix (FUI – government funded project)
Neotok: Development of a method of drying and preservation of a live protozoan with antigenic action for use in vaccines (FUI - government funded project)
SpiceClean: Destruction of resistant microbial forms present in food powders using high-pressure gases (nitrogen, 4 000 bars) (ANR funded project)
Homeoepith: Exploration of the mechanisms of homoeostasis and rupture of the intestinal epithelium in the presence of commensals and pathogens. Creation of a mutant bank using signature-tagged transposon mutagenesis (STM) of Lactobacillus casei and phenotypic screening to identify genes required to colonise the digestive tract (ERC programme)
Transaronat: Development of microbial and enzymatic processes for the production of natural flavour compounds to foster technology transfer to small business (ANR funded project)
Food-Redox: Control of pathogenic and spoilage flora in food products through the rational use of oxidoreduction potential (ANR funded project)

More information

Team members

The PMB team comprises 23 lecturer-researchers, 5 engineers, and 2 technicians specialising in various fields including microbiology, cell and molecular biology, biophysics, process engineering, IT, and mathematics, as well as 16 PhD students. This versatility allows the scientists to address and improve understanding of phenomena combining physics and biology.  

University Lecturer

Associate biologist practitioner


PMB Team Manager 

Post-doctoral student


PMB Assistant Team Manager


University Lecturer

Researcher Associate

Assistant Engineer

PhD student

Temporary Teaching and Research Assistant

Research Engineer

Research Scientist

Research topics

The research undertaken by the PMB team addresses the mechanisms of resistance and adaptation of different types of cells to various physical and chemical environmental stresses.

These environments pertain to food and can be natural (plant surfaces, ground, intestine...) or technological (food, workshops, work surfaces...). Our research focuses both on microorganisms of interest (starters, , probiotics, symbiotics) and spoilage and pathogenic flora including yeasts and fungi, bacterial spores, and noroviruses. Our work facilitates the identification of mechanisms with strong potential for use in future applications (screnning, production, preservation and use of microbial flora for the food chain and biotcdehnology, new technology for microbial decontamination of raw material, ingredients and food products ...).

Notable accomplishments

PMB Team > Research topic > notable accomplishments > Use of fibrolytic bacteria

Use of fibrolytic bacteria as useful microorganisms in horses

Fibrolytic bacteria involved in the breakdown of polysaccharides in plant cell walls (cellulose, hemicellulose, and pectins) play a key role in the large intestine of the horse (Julliand and Grimm, 2016). The breakdown and fermentation of polysaccharides into short-chain amino acids (SCAA) provides energy for the host and plays a central role in the biochemical and physiological processes that affect the health of the host. We have shown that these bacteria are very sensitive to environmental stress, especially diet-related (Medina et al, 2002; Respondek et al, 2008; Philippeau et al, 2015). However, the mechanisms explaining this sensitivity at cell and molecular level are not yet understood. Despite their key role in nutrition, wellbeing, and health of the horse (Destrez et al, 2015), these fibrolytic bacteria have been studied very little to date, above all because they are very sensitive to oxygen making them very difficult to study as well as to produce and use on a large scale. Two new celluloytic bacterial strains have just been isolated and are being studied.

PMB team > Research topic > notable accomplishments > Gene identification

Identification of genes involved in the commensalism and colonisation of the intestine by Lactobacillus casei

The adaptation of microorganisms to external stresses generally involves a gene response specific to the environmental stress that induced the response.

In order to identify, in as much detail as possible, the genetic factors involved in stress response, we have developed a global reverse genetics strategy (Licandro-Seraut et al, 2012) which has been used to explore the initial stages of colonisation of Lactobacillus casei in the intestine.
So far, 47 genes with various functions (metabolism, wall, regulation, unknown...) have been identified (
Licandro-Seraut et al, 2014), most of which are new components as yet unidentified using other universal approaches (transcriptomic...). This is, therefore, a major breakthrough in the understanding of interactions between the intestine and microorganisms. In the near future, it will be possible to select bacterial strains capable of establishing themselves in the intestine.

PMB team > Research topic > notable accomplishments > Key role of the plasma membrane

Key role of the plasma membrane in microbial resistance to environmental stress

The plasma membrane is considered as the first interface between the environment and the cell and is often presented as the primary target of physical or chemical alterations in the extracellular medium. As a result, it is likely to play a role of sensor and to participate in stress signalling. When its integrity is affected, it participates in the initiation of cell death (Guyot et al., 2014; Dupont et al., 2014; Martin-Desjardin et al., 2013; Moussa et al., 2013; Ta et al., 2012). The search for destabilisation mechanisms is consequently an essential aim for the team. For the first time, our work has shown that the dehydration kinetics have a direct influence on the spatial reorganisation of the membrane constituents. This reorganisation, which occurs during slow dehydration of yeast, is a key factor in surviving drying (Lemetais et al., 2012). Our work also deals with the effects of transient plasma membrane permeabilization. Durable permeabilization is described as deadly, but we have shown that osmotic stress can lead to temporary plasma membrane permeabilization (that we have called osmoporation) compatible with survival (Da Silva Pedrini, 2014). Similar phenomena result in cell death during cell freezing protocols (Simonin et al., 2015)

PMB team > Research topic > notable accomplishments > Deadly effects of dehydration

Deadly effects of dehydration and fluctuations in water on yeasts, bacteria, and viruses

Dehydration is a major natural and technological stress that threatens the survival and integrity of biological systems. Controlling the effects on cells is necessary for the development of preservation techniques that do not require the use of cold. Through our work, we have identified the causes of cell death induced by drying. The transition from a liquid to a gaseous environment is destructive for cells as it simultaneously causes structural stress (linked to the loss of cell water) and intense oxidative stress (due to the dysfunction of intracellular enzymes and reactive oxygen species) (Lemetais et al., 2012; Dupont et al., 2014). We have also shown that some biological molecules are essential to anhydrobiosis (resistance of some organisms to drying). For Saccharomyces cerevisiae, the progression along the ergosterol biosynthetic pathway increases the resistance of the yeast to drying. This phenomenon can be explained by the biochemical maturation of sterols, which provides yeast membranes with mechanical resistance and resistance to oxidation (Dupont et al., 2012). Other research has addressed the effects of fluctuations in the humidity of the environment on the persistence of norovirus (responsible for viral gastroenteritis), and has highlighted, for the first time, a correlation between the absolute air humidity and the infectivity of this virus (Colas de la Noue et al., 2014).

PMB team > Research topic > notable accomplishments > Internal spore membrane

The internal spore membrane, an essential element of bacterial spore resistance

Bacterial spores are one of the most resistant forms in the living world. In extreme external conditions, the unique, characteristic structure of the spore enables the bacterium that produces it to preserve the molecules essential to its revivification (DNA, proteins, enzymes). Despite the development of numerous analytical techniques, the conditions necessary for this preservation of the biological material remain poorly understood. Our recent work has helped improve our understanding of the state and the properties of the internal membrane, a key component of spore permeability (Loison et al., 2013). This global understanding will enable the development of a "model" structure mimicking the spore and constituting the basis of an "encapsulation" process of sensitive molecules to protect them effectively from external conditions. Knowledge of the spore structure will also help make progress in terms of their destruction and to propose new sterilisation techniques (Colas de la Noue et al., 2012, Moussa et al., 2013).

PMB Team > Research topic > notable accomplishments > Use of microorganisms

Use of microorganisms as natural vectors of useful molecules

The aim is to optimise the culture conditions to integrate molecules of nutritional importance into microorganisms such as yeasts S. cerevisiae and Y. lipolytica and Bacillus subtilis spores (Pham-Hoang, et al., 2013). Work has been conducted on carotenoids, polyphenols, anthocyanins, and aromatic compounds providing insights into the factors affecting molecules entering yeasts used as carrier cells (Da Silva Pedrini et al., 2014). As a result of this work, a researcher at PMB (Y Waché) has created a start-up, Natencaps.

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