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).
We explore host-microbiota interactions in monogastric (rabbit, pig and chicken) and ruminant (sheep and cattle) species by using a combination of multi-omics technologies (metagenomics, metabolomics, transcriptomics and culturomics). Our experimental approaches range from in vivo experiments designed to modulate the gut microbiota (e.g. breeding and feeding practices, prebiotics, probiotics, microbiota transplantation, genetic selection) to in vitro experiments to explore molecular and cellular mechanisms (e.g. batch-fermentations, cell lines and intestinal organoids culture).
Our main research goals are:
- Identify early life factors driving the colonization of the gut by the microbiota (e.g. milk composition, quantity and quality of solid feed at the onset of ingestion, maternal transmission of microbes)
- Understand the role of the gut microbiota and its metabolites in the postnatal maturation of the intestinal barrier and immune system
- Understand the link between microbiota and its metabolites on feed efficiency and infectious disease resistance
- Explore the impact of digestive microbiota transplantation on animal phenotypes
- Identify the “active fraction” of the gut microbiota and characterize them through bacterial strain isolation and inoculation
- Understand the construction of the holobiont using genetically divergent breeding lines selected for feed efficiency or disease resistance
Our methodological tools are related to :
- Development of bioinformatics solutions to analyse metabarcoding and metagenomics (i.e. frogs.toulouse.inra.fr - macadam.toulouse.inra.fr - https://forgemia.inra.fr/genotoul-bioinfo/metagwgs) data from current and innovative sequencing technologies
- Culture of rabbit and pig intestinal organoids link
- High-throughput culture of anaerobic gut bacteria (in progress)
- Metabolomics (1H-NMR), 16S rDNA gene sequencing, metagenomics sequencing, RNAseq and targeted transcriptomics