ProbiHôte

Commensal and Probiotic Microorganisms-Host Interactions

Our four major objectives are:

  1. To study intestinal and pulmonary microbial ecosystems in order to identify potential beneficial effects on the host as well as their mechanisms of action
  2. To explore the immune and physiological responses of the host to bacteria and fungi, commensal and probiotic bacteria in different nutritional contexts
  3. To study the host-microbiota crosstalk through diet and supplementation with prebiotics
  4. To integrate our work into health issues of physiology (ageing) and physio-pathology (inflammation, colorectal cancer, asthma, metabolic syndrome and obesity) to move towards translational and to propose both complementary prevention and therapy strategies.

Jean-Marc Chatel

Commensal and Probiotic Microorganisms-Host Interactions / ProbiHôte

Our team is organized in 4 groups & 2 technical workshops

Even all the groups are studying crosstalk bacteria-host, we can consider that the groups I and II are mainly composed of microbiologists expert of the bacterial side whereas the groups III and IV are mainly composed of physiologists and immunologists in charge of the host side. The 4 groups are sharing common important tools as our commensal and probiotic bacterial collection as well as our panel of conventional and gnotobiotic mice models and cellular models.

We have also two platforms: the first dedicated to the engineering of commensal and probiotic bacteria and the second devoted to the isolation and characterization of commensal and probiotic bacteria.

Research groups

Probiotics and Therapies based on Microbiota - ProbiHôte The main goal of our Protect research group is to investigate the complex interactions between probiotic and commensal bacteria (with potential beneficial properties) and their host organisms. Our major interest is to unravel the molecular mechanisms underlying these beneficial effects on human and animal health. Through our research, we aim to pave the way for innovative preventive and curative strategies focused on modulating the gut microbiota, aimed at improving host well-being. In particular, we focus on addressing various intestinal pathologies, such as inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), colorectal cancer (CRC) and intestinal parasitosis. In addition, we explore the concept of primocolonization and how modern western practices (such as C-section delivery) could impact our microbiota and consequently influence short- and long-term effects on the host. Applying a holistic approach (that integrates mechanistic and global methodologies) with cellular models, in vivo studies and human and animal clinical trials, our overall goal is to explore the potential beneficial effects of probiotic and commensal bacteria while deciphering the intricate molecular mechanisms underlying their effects. In addition, we are among the leaders in the use of recombinant lactic acid (LAB) as vectors for the delivery of health-promoting molecules such as antioxidants, anti-inflammatories, vaccines and others (see axis 5 of our team). We are also working on the identification and characterization of next-generation probiotic strains, from new ecological niches (see axis 6 of our team)., in order to develop novel probiotic strategies.

  • Leader: L. Bermudez
  • Permanent members: P. Langella, R. Martin-Rosique, E. Huillet, F. Chain, A. Aucouturier, S. Chadi and AJ Waligora

Mechanisms of action of commensal microorganisms of health interest - ProbiHôte The ProbiHôte team has demonstrated for many years that the intestinal microbiota, mainly composed of bacteria and yeasts, is a new source of microorganisms of interest called next-generation probiotics. The aim of our group is to study the mechanisms of action of these commensal bacteria and yeasts of health interest. We want to obtain a better understanding of these new nutritional intervention strategies, namely next-generation probiotics, and to optimise them in the context of inflammatory pathologies. We are mainly studying the bacterial species Faecalibacterium, which is abundant in healthy human intestinal microbiota and whose anti-inflammatory properties have demonstrated in numerous preclinical models. Our main projects involve understanding its mechanisms of action via the production of MAM (Microbial Anti-inflammatory Molecule) proteins and extracellular vesicles, as well as its mechanisms of resistance to oxidative stress. Recently, we have also developed strategies using nex-generation probiotics in the intestine-brain axis, particularly in the prevention of Alzheimer’s disease. We are also interested in the different interactions that can develop between the fungi and bacteria of the intestinal microbiota and their effects on intestinal homeostasis in healthy or inflammatory contexts. These issues are addressed using various approaches, both in vitro (co-culture with epithelial cells) and in vivo (colitis model in mice), and are also based on bioinformatics studies of bacterial (16S marker) and fungal (ITS marker) diversity.

  • Leader: J.-M. Chatel and S. Auger
  • Permanent members : M. Richard and V. Robert

Immunity and Intestinal Microbiota - ProbiHôte The gastro-intestinal tract is a complex milieu in which coexist host epithelial and immune cells, a wide array of microorganisms and food antigens. The intestinal microbiota is notably composed of trillions of bacteria, which are strikingly well tolerated by the host, whereas pathogenic microorganisms are recognized and eradicated by the immune system. The mechanisms involved in the distinction between harmful and symbiotic microorganisms remain unclear. In some circumstances, the tolerance toward the intestinal microbiota is broken, leading to inappropriate immune response and intestinal or extra-intestinal inflammation. This is the case in inflammatory bowel diseases (IBD) such as Crohn’s disease (CD) and ulcerative colitis, characterized by chronic and relapsing inflammation of the gastrointestinal tract.

The aim of the lab is to decipher the mechanisms involved in the complex cross-talk between the gut microbiota and the host immune system, and its alterations leading to human diseases such as IBD. For this, our goal is to identify the microorganisms and microbiota-derived metabolites impacting immune cells functional properties and energy metabolism at homeostasis and in IBD. We also study the influence of diet on the microbiota/immunity interaction.

  • Co-Leaders: H. Sokol and ML Michel
  • Permanent member:  G. Da Costa

Microbiota and Gut and Lung Health - ProbiHôte Our group is interested in the interactions between the microbiota and the host, specifically in the digestive and respiratory tracts. Our projects revolve around

  1. Bacteria cross-feeding
  2. Bacteria-Food interaction
  3. Bacteria-Epithelia interactions
  4. The gut-lung axis. We have optimized several in vitro and in vivo models that provide physiologically relevant systems to study host-microbes interactions.

These range from ‘simple’ (in vitro aerobic and anaerobic bacterial cultures), to more complex settings (differentiated epithelial models derived from primary human and murine tissues such as organoids and polarized gut or bronchial epithelia) to in vivo studies using conventional, germ-free and gnotobiotic animals.

  • Leader : C. Cherbuy and V. Saint Criq
  • Permanent members : A. Bruneau, ML Noordine, C Le Poupon, F. Pepke and M. Thomas

Technical workshops

Commensal and Probiotic Bacteria Engineering Platform - ProbiHôte Commensal and Probiotic Bacteria Engineering Platform - ProbiHôte

Initially, the aim of our Commensal and Probiotic Bacteria Engineering Platform (acronym CLONING) was to genetically modify classical Lactic Acid Bacteria (LAB, such as Lactococcus lactis) in order to deliver proteins of interest for human and animal health. However, over the last 5 years, we have developed tools for the genetic manipulation of probiotic strains more difficult to manipulate than lactococci, such as lactobacilli and bifidobacteria, and finally we have developed a whole platform for the expression and purification of recombinant proteins. More recently, we have also started to apply our LAB genetic tools to commensal bacteria isolated from the intestinal microbiota to develop next-generation probiotics (NGPs) for the needs of the various projects being developed there. The aim of the Atelier new research axis is to develop genetic tools for commensal microorganisms that are extremely sensitive to oxygen (EOS, and therefore very difficult to manipulate) in order to better understand their mechanisms of action, enhance their beneficial effects and to test their use in different physiopathological situations. In addition to their applied aspects, these genetically modified bacteria are excellent tools for studying the probiotic/host crosstalk. Today, we are in a capacity to provide support to the numerous national and international sollicitations received from academic and industrial partners in the framework of research collaborations.

We propose to:

  1. construct and characterize recombinant strains to deliver molecules of therapeutic interest to humans and animals
  2. purify the proteins produced by the constructed recombinant strains.

Permanent members: L. Bermudez & A. Aucouturier

Isolation and characterization of commensal and probiotic anaerobic bacteria atelier - ProbiHôte The Atelier of commensal and probiotic bacteria is dedicated to the isolation and characterization of new strains from biological samples (mainly human and animal origin) from healthy individuals or patients of diseased related to microbiota alteration. The Atelier also deals with the management of anaerobic bacterial strains from international collections as well as strains specific to (or isolated by) the ProbiHôte team.

We are responsible for the fonctionality of three flexible anaerobic chambers (H2 5%, CO2 5%, N2 90%) with incubator at 37ºC available to Micalis teams according to a booking calendar. Each new user must obligatorily follow a training and sign the Operating Charter. We also provide training in anaerobic microbiology to private companies.

For further information please contact us

Permanent members: R.Martin Rosique, V. Robert, C. Chadi, G. Da costa

Team members

anonymous user

Anaïs LEMOINE

  • Scientist

Sead CHADI

  • Engineer

Bruna MAITAN SANTOS

  • Scientist

Harry SOKOL

  • Scientist

Marisol LOPEZ HIDALGO

  • Scientist

Frédéric PEPKE

  • Technician
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Marina FUENTES

  • Student

Muriel THOMAS

  • Scientist

Monique FERRARY AMERICO

  • PhD student
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Manon JACOUTOT

  • PhD student

Luis BERMUDEZ HUMARAN

  • Scientist

Claire CHERBUY

  • Engineer

Jean-Marc CHATEL

  • Scientist

Alicia BREST

  • Student

Lise SANCHEZ

  • PhD student

Ronan SOUDY

  • PhD student

Loïc CHOLLET

  • Engineer

Vinciane SAINT CRIQ

  • Scientist

Anne AUCOUTURIER

  • Engineer

Livia DA ROCHA NATALINO MONTEIRO

  • Scientist

Aude DUMENIL

  • Engineer

Guillaume DIOP

  • Engineer
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Aurélia BRUNEAU

  • Engineer
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Augustin GUICHARD

  • PhD student

Giovanna ORIANNE

  • Engineer

Gregory DA COSTA

  • Technician

Emilie GRIMAUD

  • Student

Hugo MATHE

  • Student

Claire LE POUPON

  • Engineer

Florian CHAIN

  • Engineer

Eugénie HUILLET

  • Scientist

Philippe LANGELLA

  • Scientist
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Damien OLIVEIRA

  • PhD student

Julina HELLE

  • PhD student

Rebeca MARTIN-ROSIQUE

  • Scientist
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Célyne BRIVES

  • Engineer

Mathias RICHARD

  • Scientist

Jade LOISEAU

  • Engineer

Sandrine AUGER

  • Scientist
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Anne-Judith WALIGORA

  • Scientist

Oriane DE CHANTERAC

  • PhD student
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Evan LAISNEY

  • Student
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Danielle AYRES DE OLIVEIRA

  • Scientist
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Thomas BAZIN

  • Scientist

Yassine BELHANDA

  • Student

Liliia PANIUSHKINA

  • Scientist

Marie-Laure MICHEL

  • Scientist
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Véronique ROBERT

  • Engineer
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Key points

News

  • Conference

Des microbiotes de l’environnement au microbiote intestinal

Des microbiotes de l'environnement au microbiote intestinal
  • Conference

Human Microbiome: From Models and Mechanism to Medicine

Human Microbiome: From Models and Mechanism to Medicine
  • Research article

Identification of Gut Biomarkers of FPIES (Food protein induced enterocolitis syndrome) in a Longitudinal Comparative Pediatric Study

Anais Lemoine, a paediatrician at APHP’s Trousseau hospital, did her PhD at Micalis, in the Probihôte team. This study is the result of collaboration with clinicians from the APHP at Trousseau and Pitié-Salpétrière hospitals and two INRAE laboratories at UPSaclay (Micalis and MTS/LIAA). Food protein-induced enterocolitis syndrome (FPIES) is a non-IgE-mediated allergy without known biomarkers. […]
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