The intestinal microbiota is an ecosystem of several hundred microbial species (bacteria, yeasts, etc.) that gradually builds up after birth in animals and humans. While the composition of the intestinal microbiota is unique to each individual, recent studies in humans and animals have shown that the variety of microbiota observed within a population can be grouped into broad categories with similar characteristics in terms of the bacterial groups represented. The environment, in particular the maternal environment at birth, and diet are often considered to be the main factors influencing the composition of the microbiota in young people. On the other hand, the importance of host genetic factors on the microbiota is still debated, as it is poorly assessed. For the first time, an INRAE team has selected 2 lines of pigs whose sires were chosen according to 2 types of intestinal microbiota. The scientists thus studied the influence of genetic factors on the formation of the intestinal microbiota of 1,000 pigs over 3 generations.

Pig lines selected for their intestinal microbiotal

To assess whether it is possible to select pigs for the composition of their intestinal microbiota, the scientists first demonstrated that it is possible to divide 60-day-old piglets into 2 groups corresponding to 2 types of microbiota called enterotypes. Each enterotype is characterized by a relative overabundance of 2 bacterial genera: Prevotella and Mitsuokella for enterotype PM, and Ruminococcus and Treponema for enterotype RT. To set up the 2 selected lines, breeding animals were chosen on the basis of a faecal analysis, to select those with a PM or RT microbiota. Piglets from the 2 lines were then reared under exactly the same conditions (same location, same feed).

The results show that in the line selected for the PM enterotype, the frequency of this enterotype rose from 53% in the initial population before selection to 87% after 3 generations; in the other line, the frequency of the RT enterotype rose from 47% to 70%. Analyses of the growth rates of the 2 lines showed that pigs selected on the PM microbiota grew faster up to 70 days of age. Further analysis revealed that the 2 enterotypes contain bacteria with different metabolic activities. In particular, the PM enterotype is richer in bacterial genes capable of degrading starch, metabolizing sugars and synthesizing important amino acids. Using these 2 pig lines, work will continue on studying the stability of enterotypes throughout the life of the animals, and their influence on pig production, health and behavior.

These results show that the animal's genetics have a major influence on the formation of its gut microbiota, and that its composition does not depend solely on the environment. They confirm the importance of taking intestinal microbiota into account in selection schemes to improve sustainability and resilience in livestock breeding..

Scientific contacts GABI  :

• Jordi Estelle-Fabrellas
• Claire Rogel-Gaillard

Reference :

Larzul C., Estelle J., Borey M. et al. (2024). Driving enterotypes through host genetics. Microbiome 12, 116 DOI : https://doi.org/10.1186/s40168-024-01827-8