Understanding the importance of gut microbiota for the improvement of swine efficiency and robustness – MICROFEED

MICROFEED will study a generally ignored partner of livestock, the gut microbiota, to refund the improvement of production efficiency and robustness in pig breeding. The gut microbiota is an essential contributor to the availability of nutrients in the animal gut, contributing to its growth, health and immunity.
MICROFEED will explore the gut microbiota component and its link with the genetic and genomic of feed efficiency and robustness of the host in two unique designs developed to study the pig feed efficiency. The first design relies on 10 generations of divergent selection for feed efficiency in two pig lines fed a conventional diet, to identify and quantify the impact of the gut microbiota potentially co-selected in response to genetic improvement for feed efficiency. The second design is based on a commercial population currently selected for production by the French pig breeders, from which the divergent lines were selected. It will be divided into two sub-designs of related pigs fed either a conventional diet or a high dietary fibers diet more difficult to digest. This second design is the result of collaboration between INRA and the pig breeders grouped in FGPorc in the frame of the H2020 Feed-a-Gene project to study the pig feed efficiency in response to lowered feed quality. In a first step, MICROFEED will produce new data (phenotypes, genotypes) in the two designs (908 pigs in Design 1 and 1700 in Design 2), together with feces samples for partial sequencing (16S) of the gut microbiota (600 + 1600 samples) to evaluate quantitatively the contribution of the gut microbiota to the variability of pig feed efficiency, and to test the effect of diet changes on this contribution. Prediction equations from the gut microbiota and host genomic data will be established. In a second step, whole-metagenome sequencing of 96 samples representing key microbiota profiles for extreme feed efficiency phenotypes, and whole-genome sequencing of 40 pigs best representing the two designs diversity will be obtained. These will be combined to identify the host and gut microbiota genes and functions involved in the feed efficiency of the pig and its robustness to diet changes, and to dissect the underlying biological mechanisms. Finally, external feces samples, genotypes and phenotypes available among the consortium from other projects, including different breeds, feeds, breeding conditions, will be used for validating the prediction equations established in the first step, to test their robustness to these factors and to then propose new selection and management strategies for pig breeding. By identifying which microbes contribute to feed efficiency and which are robustness to feed changes, MICROFEED will propose new genomic tools to jointly pilot the gut microbiota composition and the host genetic in terms of genetic selection for pig breeders, but also in terms of nutrition and feeding for the feeding industry.
MICROFEED is structured in eight tasks, including one for the project management (Task 0) and one for the dissemination and transfer (Task 7). The two first tasks will concern data acquisition, the three following tasks will concentrate on acquisition of new knowledge on the relationships between host, gut microbiota and feed. Task 6 will validate these results and propose new strategies for selection and feeding.
The consortium is composed of seven INRA groups specialized in pig genetics and genomics, feed efficiency and gut microbiota, plus two private partners from the French pig breeding industry representing more than 75% of the French pig genetic market. The total cost of MICROFEED is 1.4 million euros (not including INRA salaries), comprising a contribution of 258 k€ from the private companies and a demand to the ANR of 719 k€, for a labor of 227 person.months during 4 years.