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Muriel Thomas : "Epithelium and microbiota"

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

Our increasing knowledge on the essential role of microbiota in health has led us to reconsider our view of digestive physiology and pathologies; the maintenance of homeostasis between microbes with each other and between microbes and host dictates the balance between health and disease. Although the demonstration of the main impact of gut microbiota for the structure and maturation of gut immune system has been done; the role of microbiota in maturation of epithelium is less known.Thus, we investigated the role of intestinal microbiota in main functions of the digestive tract, like absorption, protection, storage and renewal. Conversely, we also investigated the impact of gut environment on microbiota function and composition

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Main results and activities:

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1/ Fundamental research. We showed that microbiota is a key player in essential digestive functions by modifying the life cycle, the structure and absorptive and protective functions of intestinal epithelium (Cherbuy et al,  Am J Physiol Gastrointest Liver Physiol, 2010) and highlighted the prominent role of primocolonizing bacteria on these processes (Tomas et al, Faseb J, 2013). In particular, we showed that a pioneer strain of Escherichia coli elicits a sequential, coordinated colonic epithelial responses that can drive a novel state of homeostasis (Tomas et al, ISME J, 2014). We have also shown for the first time that the metabolic crosstalk between the two dominant commensal bacteria Bacteroides thetaiotaomicron and F. prausnitzii can impact on the proliferation of goblet cells and on the homeostasis of intestinal epithelium (Wrzosek et al, BMC Biol, 2013). Recently, we have shown that the colonisation of gut with the microbiota shifts the iron sensing and storage in eptihelium cells (Deschemin et al, Faseb J, 2016).

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2/ Applied research with industrial network.  By using gnotobiotic rodents, we have shown effects of food-grade lactic acid bacteria (LAB) on the structure and absorptive and protective functions of intestine (Turpin et al, Plos One, 2013; Rul et al, J. Biol. Chem, 2011). We have then detected that yoghurt bacteria are metabolically active in intestinal lumen and can send signals to host (Rul et al, J. Biol. Chem., 2011 ;  Thomas, et al, PLoS One, 2011). Bacteria from African fermented product were analyzed for their adhesion properties (Turpin et al, Plos One, 2012) and adaptative response in gnotobiotic rodents (Turpin et al, Plos One, 2013). We have contributed to better understand the mechanisms involved in the beneficial effects of Faecalibaterium prausnitzii (Miquel et al, Mbio 2015; Miquel et al, Scientific reports, 2016).

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3/ Translational Research. We have very tight connections with the Nutrition department of the Beaujon Hospital (F. Joly) allowing our Lab to get high quality human samples from patients with short bowel syndrome. In these patients, both microbiota (Joly et al, Biochimie, 2010) and host (Joly et al, Am.J. Physiol. Gastro.liver, 2009) are modified after the gut resection. We have also proposed that faecal D/L lactate may be informative for identifying patients at risk fro D-encephalopathy (Mayeur et al, Plos One, 2013 ; Mayeur et al, microorganism, 2016 ). We have initiated a new collaboration with clinicians from (IGR, Créteil) to better understand the two barriers (intestinal layer and microbiota) in patients with cancer.

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4/ Teaching and expertise. Evaluation of scientific projects, PhD thesis and HDR, contributions to thesis advisory committees ;  reviewing ; member of scientific board of SFNEP (Société française de Nutrition Entérale et Parentérale). We have published an opinion paper on the EFSA helath policy in the domain of novel food and porbiotics (Miquel et al, MICF, 2015).

They are currently working with us :

Claire Cherbuy. Research Ingeneer /

Claire Cherbuy (Engeneer, INRA)


Unai Escribano-Vasquez (M2, student)


Neike Fernandez (Engeneer, non-permanent)

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Laura Gillard (PhD student, INSERM, APHP)

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Camille Mayeur (Engeneer, INRA)

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Marie-Louise Noordine (Technician, INRA)

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Aude Remot (Post-doc, INRA- AgreenSkill)

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Véronique Robert (Assistant Engeneer, INRA)

See also

They were working with us :


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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Pauline talbot (M2 student ; 2014)

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Julie Tomas - PhD student (2010-2013)

Sylvie M

Sylvie Miquel - Post-doc (2011-2013)


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