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Nutrition et Ecosystèmes Digestifs

NED Research Activities

The NED team (Nutrition and Digestive Ecosystems) is focused on symbiotic microbiota that colonizes the digestive tract, which enables host to use energy from plant fibers. The co-evolution of microbiota with the host results in important interactions between the microbial community and digestive physiology of the host. Thus, beside nutrition function, digestive microbiota plays a trophic role on the digestive tract, is involved in innate host immunity (barrier role), and stimulates the innate and adaptive immune response. Furthermore, the use of antibiotics for therapeutic or prophylactic purposes in animal farming has led to the emergence of bacterial antibiotic resistance genes and the gastrointestinal microbiota is a reservoir of these genes.

The goal of NED team is twofold: firstly optimize ecosystem services related to the production of nutrients and the development and stimulation of the immune system, and also restore the ecosystem by decreasing occurrence of antibiotic resistance genes. For this the NED team will use a multidisciplinary and integrated ecological engineering approach. Applied to digestive microbial ecosystems, it aims to shape and stabilize the specific and functional diversity and interactions with the host in order to optimize ecosystem services. Leverage to achieve ecological engineering of digestive ecosystem concerned mainly dietary composition: fiber quality, nature and quality of fat and yeast additive. Ecological principles used are related to colonisation, biotope modification, introduction of microbial species or complex microbial community. Finally, metagenomics offers a new framework for microbial ecosystem investigation in both their composition and their function components but lead to huge data production. Development of bioinformatics pipeline to analyze this data mass while adapting to current IT architectures and infrastructures is also a crucial issue.

The NED team has expertise in animal husbandry, nutrition, digestive physiology, molecular microbiology, microbial ecology, in vitro cultures of digestive content and bioinformatics. Target animal models of NED team are both monogastric (pig and rabbit) and two polygastric species (sheep and cow).

Latest News

FROGS: Find Rapidly OTU with Galaxy Solution

Microbial communities play a major role in various environmental processes, including carbon recycling and health. The engineering of these ecosystems is largely based on the control of their diversity. FROGS is a user-friendly pipeline dedicated to biologists that gives access to specific diversity of microbial communities from high-throughput sequencing of amplicons. FROGS has been developed to be very fast even on large amounts of data in using cutting-edge tools and an optimized design.

Gut microbiota derived metabolites contribute to intestinal barrier maturation at the suckling-to-weaning transition

pig intestine organoid (©Martin Beaumont)

The metabolites produced by the microbiota at the onset of solid food ingestion contribute to the maturation of the gut barrier at the suckling-to-weaning transition. Targeting the gut microbiota metabolic activity during this key developmental window might therefore be a promising strategy to promote intestinal homeostasis.


Caroline Achard Webpage
Corine Bayourthe
Martin Beaumont
Sylvie Combes
Francis Enjalbert
Christelle Knudsen
Djamila Lekhal
Annabelle Meynadier Webpage
Géraldine Pascal
Olivier Zemb Webpage
Asma Zened
Céline Barilly
Laurent Cauquil
Marie-Luce Chemit
Yves Farizon
Corinne Lencina
Jean-Philippe Vergnes
PhD Students
Eloïse Mussard
Florian Touitou
Joanna Fourquet
Maryse Poli
Former Members
Malo Le Boulch
Mathilde Le Sciellour
Charlotte Paes