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24, chemin de Borde Rouge -Auzeville - CS52627 31326 Castanet Tolosan cedex - France

Last update: May 2021

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Microbiota and digestive and respiratory health

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


Muriel Thomas


From left to right: Muriel Thomas, Claire Cherbuy, Gerlando Natalello, Aurélia Bruneau, Marie-Louise Noordine, Claire Le Poupon, Mélanie Briard, Eugénie Huiller, Frédéric Pepke, Marine Polinacci, Paul Biscarrat, Vinciane Saint-Criq, Elsa Fissier

Major research activities and results:

1/ generic research and fundamental study of the effects of the intestinal microbiota on digestive health. Using gnotobiotic rodents (Anaxem platform, MICALIS), we have shown that the microbiota is an essential player in the major intestinal physiological functions by modifying the life cycle, structure and absorption, storage and barrier capacities of the digestive epithelium (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/ generic research and fundamental study of the effects of the lung microbiota on respiratory health. We recently isolated and cultured mouse lung strains after birth. These strains are able to modify the susceptibility of animals to develop asthma (ISME J, 2017; Frontiers in physiol, 2018).

3/ research with operational objectives. These projects are carried out in partnership with industrial partners and aim to isolate probiotics or prebiotics and describe their mechanisms of action. We are studying their mechanisms of action as part of the design of new functional foods. (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, intestinal microbes. , 2014., Mbio, 2015; scientific reports, 2016; Frontiers in microbiology, 2017; Frontiers in physiol, 2018).

4/ human clinical research. We are developing research projects with clinicians on the digestive physiology and microbiota of patients with short bowel syndrome who suffer from intestinal insufficiency. (Am.J. Physiol. Gastro.liver, 2009; Biochemistry, 2010; Plos One, 2013; Microorganism 2016; Scientific reports 2016; Frontiers in physiology, 2017). We collaborate with clinicians on the microbiota of cancer patients suffering from malabsorption.

5/ transversal activity and expertise. Our group contributes to the collective life of the laboratory (Quality, supervision activities), to university teaching, and to science/society interaction. We have published an opinion paper on the European regulation of novel foods and health claims (Microbial cell factory, 2015). M. Thomas is a member of the "Biorisk" expert committee at ANSES and of the scientific committee of the "Vitagora" competitiveness cluster.

Projects funded by the ANR:

ANR CIMMAP project (2018-2020): Characterization, in the perinatal period, of the maturation of the immune system and the composition of the intestinal microbiota and milk, in the presence or absence of maternal supplementation with prebiotics aimed at preventing childhood allergy. Coordinator: M. Bodinier

ANR ACROBAT project (2018-2020): Role of the lung/brain/bone marrow axis and of the microbiota during infection by the influenza A virus. Coordinator: F. Trottein

ANR DOPEOS project (2017-2019): Development and Optimization of a Process for the Production of Bacteria Extremely Sensitive to Oxygen for their Industrial Exploitation. Coordinator: L.Beney

ANR Sevasthma project (2019-2023): Defining the endotypes of severe pediatric asthma: an integrated approach combining phenotypic analyzes in relation to immune, metabolomic and microbial characteristics. Coordinator: M. Leite-de-Moraes

ANR GenoFood project (2020-2023): Exacerbation of the genotoxicity of the intestinal microbiota by a food contaminant. Coordinator: J.P Nougayrède

ANR AdMIR project (2023-2026):



Aurélia Bruneau


Claire Cherbuy. Research Ingeneer /

Claire Cherbuy

Research Engineer - Gastrointestinal physiologist


Eugénie Huillet

Senior Scientist - Microbiologist


Marie-Louise Noordine

Research technician

Claire LeP.4

Claire Le Poupon

Assistant Engineer

IMG_0706.2 - Copie

Vinciane Saint-Criq

Senior Scientist - Lung physiologist


Paul Biscarrat

PhD student (2020-2023)

Mélanie B

Mélanie Briard

PhD student (2020-2023)


Elsa Fissier

Engineer (contract)


Anaïs Lemoine

PhD student (2021-2024)


Gerlando Natalello

PhD student (2021-2024)

Photo Fred.2

Frédéric Pepke

Research Technician (contract)

Marine Polinacci

Engineering internship

Anciens membres (tous) / 5 last years:

Gladys Ferrere (post-doc 2021-2022)
Cassandre Bedu-ferrari (Doctorante 2018-2022)
Sophie Verstraeten (Ingénieure CDD)
Stagiaires 2022 : Sawiya Charif (M2), Charlotte Moisset (BTS), Aya Jeaidi (stage de fin d’études), Juliette Ménard (M1), Léa Largange
Marie-Thérèse Barba Goudiaby (Ingénieure CDD)
Stagiaires 2021 : Sarah Stutzmann (BTS) Julien Lopez (M2), Marie Masson (2ème année cycle ingénieur), Oscar Kubiec (3ème année cycle ingénieur)
Alexandre David-hachette (Ingénieur CDD)
Jennifer Palomo (Post-Doctorante)
Camille Mayeur (Ingénieur d’Etude INRAE)
Elliot Mathieu (Doctorant 2017-2020)
Yohannes Seyoum (Doctorant 2016-2019)

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

Muriel Thomas : Microbiota and digestive and respiratory health

We are studying the bi-directional cross-talk between microbiota and gut epithelium.
Read more
Muriel Thomas, Research Director, INRA - PI of the group

Muriel Thomas : "Epithelium and microbiota"

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