Nutrition et Ecosystèmes Digestifs

NED Research Activities

The NED (Nutrition and Digestive Ecosystems) team studies the gut microbiota in farm animals in the context of the transition towards more sustainable breeding systems. Our first objective is to limit antibiotic resistance in livestock by (i) preventing the use of antimicrobials through enhancement of animal defenses against pathogens and (ii) reducing the abundance of antimicrobial resistance genes in digestive ecosystems. Our second objective is to optimize the use of feed resources by improving the action of the gut microbiota on digestion, host metabolism and on the quality of productions (e.g. milk).

Latest News

Characterization of an organoid model to study the intestinal epithelium of piglets in vitro

Organoid of intestinal epithelium of piglets

Organoids are new models that reproduce in vitro the cellular complexity, tissue architecture and certain functions of the organs they represent. Organoids are now commonly used in many fields of biology such as nutrition, host-microorganism interactions or toxicology. Organoid models have recently been adapted to farm animals but their characterization remains incomplete (1). In particular, little is known about the ability of organoids to maintain the phenotype of the animals from which they are derived.

Early introduction of plant polysaccharides drives the establishment of rabbit gut bacterial ecosystems and the acquisition of microbial functions

sleepy rabbit in the nest

The timing of solid food introduction and plant polysaccharides ingestion are two different tools to modulate microbiota implantation and functionality. In mammals, the introduction of solid food is pivotal for the establishment of the gut microbiota. However, the effects of the first food consumed on long-term microbiota trajectory and host response are still largely unknown.

Better understanding of the links between ruminal microbiota and milk production in ewes

Ruminants are able to digest the dietary fibres present in their feed thanks to the micro-organisms - particularly bacteria - present in their fore-stomach (rumen). The relationship between the composition of this ruminal microbiota and various traits of interest, such as feed efficiency, milk composition and animal health, has been established in cattle. Researchers from the GesPR and NED teams of GenPhySE laboratory have studied these relationships in dairy sheep.

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.

FROGS: a software for easy analysis of metabarcoding data

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.


Corine Bayourthe
Martin Beaumont
Sylvie Combes
Christelle Knudsen
Djamila Lekhal
Annabelle Meynadier Webpage
Charlotte Paes
Géraldine Pascal
Olivier Zemb Webpage
Asma Zened
Laurent Cauquil
Marie-Luce Chemit
Yves Farizon
Corinne Lencina
Jean-Philippe Vergnes
PhD Students
Lisa Arnalot
Tania Malonga
Mathilde Rumeau
Florian Touitou
Gabryelle Agoutin
Julie Alberge
Vincent Darbot
Hélène Fougère
Elisabeth Jones
Former Members
Jennyfer Sauco
Amira Bousleh
Chloe Bredon
Francis Enjalbert
Lise Gallo
Lauren Jouaron
Maxime Long
Guillermo Martinez-Boggio
Eloïse Mussard
Lamia Zoudji