Muriel Thomas, Research Director, INRA - PI of the group

Muriel Thomas

Muriel Thomas : Microbiota and digestive and respiratory health

We are studying the bi-directional cross-talk between microbiota and gut epithelium.

Our team is expert in studying the beneficial effects triggered by microbiota. The group combines approaches at the frontier between physiology, microbiology, and nutrition.

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Main results and activities:

1/ fundamental and academic research: microbiota and digestive health. By using gnototiotic rodents (Anaxem germ free facility, MICALIS), we have shown that the microbiota is a main actor shaping the structure, the proliferation and absorption and secretion functions of the intestinal epithelium. Our data reveal that certain microbes engage the functions of epithelial cells and actively shape digestion physiology of host. (Am J Physiol Gastrointest Liver Physiol., 2010 ; Faseb J., 2013 ; BMC Biol., 2013 ; Faseb J 2016 ; ISME J, 2015 ; Critical Reviews in Food Science and Nutrition, 2018).

2/ fundamental and academic research: microbiota and respiratory health.  We have recently shown that appropriate bacterial lung stimuli during early life are critical for susceptibility to allergic asthma in a preclinical model. (ISME J, 2017 ; Frontiers in physiol, 2018).

3/ applied projects with industrials.  We aim at isolating new probiotics or prebiotics and we also establish the mechanisms accounting for their beneficial effects observed in host (Int. J. Food Microbiol, 2010 ; J. Biol. Chem, 2011 ; PLoS One, 2011; Beneficial Microbes, 2013; Plos One, 2012 ; Plos One, 2013; Curr. Opin. Microbiol., 2013, gut microbes., 2014., Mbio, 2015 ; scientific reports, 2016 ; Frontiers in microbiology, 2017 ; Frontiers in physiology, 2018).

4/ translational research. In collaboration with clinicians, we study the intestinal physiology and microbiota of patients with major mal-absorption. (Am.J. Physiol. Gastro.liver, 2009 ; Biochimie, 2010 ; Plos One, 2013 ; Microorganism 2016 ; Scientific reports 2016 ; Frontiers in physiology, 2017).

5/ expertise and collective work. Our engagement in teaching at university, in public health agency (ANSES), specialized societies (SFNEP/SFNCM) and stakeholder (Vitaogora) is an asset to adapt our projects with the public health priorities, regulatory framework and food safety policy (Microbial cell factories, 2015).


Projects funded by ANR :


Project ANR SEVATSHMA (2019-2023) : Defining the severe paediatric asthma endotype: an integrated approach combining phenotypic analyses related to immune, metabolomic, and microbial features

Project ANR CIMMAP (2018-2020): To elucidate mechanisms linked to atopic diseases development using clinical and preclinical approaches and to develop an antenatal nutritional strategy to prevent allergy development in children using prebiotics.

Project ANR ACROBAT (2018-2020): Role of the lung/gut/bone marrow axis and of the microbiota during influenza A virus infection

Project ANR DOPEOS (2017-2019): Development and Optimization of a Production process of Extremely Oxygen Sensitive bacteria for their industrial exploitation.

They are currently working with us :


Aurélia Bruneau (Engeneer, INRA)

Claire Cherbuy. Research Ingeneer /

Claire Cherbuy (Engeneer, INRA)


Eugénie Huillet (researcher, INRA)

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Camille Mayeur (Engeneer, INRA)

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Marie-Louise Noordine (Technician, INRA)

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Véronique Robert (Assistant Engeneer, INRA)


Yohannes Seyoum (PhD)

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Elliot Mathieu (PhD)

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Cassandre Bedu-Ferrari (PhD)


Sophie Verstaeten (CDD, Engeneer)

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Alexandre David-Hachette (CDD, Engeneer)


Jennifer Palomo (Post-doc, CDD)

See also

They were working with us :


Unai Escribano-Vasquez (PhD student, 2015-2018)

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Laura Gillard (PhD student, in collaboration with INSERM, 2012-2015)

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Aude Remot (Post-doc, INRA- AgreenSkill) (2013-2016)


Joanna Radziwill-Bienkowska

Joanna Radziwill-Bienkowska- PhD student (IBB, Varsaw, Poland) - Visiting PhD for 1 year (2013-2014)

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Muriel Mercier-Bonin (Researcher, INRA) - Visiting scientist for 2 years (2012-2014)

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Julie Tomas - PhD student (2010-2013)

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Sylvie Miquel - Post-doc (2011-2013)


Laura Wrzosek - M2 and PhD student (2008-2012)

Modification date: 14 September 2023 | Publication date: 14 April 2011 | By: Muriel Thomas