Interplay between host genetics and the dynamics of the gut microbiota in pigs

Pig gut microbiota displays high inter-individual variability and it remains an open question to determine to what extent its taxonomic composition relies on host genetic determinism and not only on environmental conditions. We will illustrate links between host genetics and gut microbiota composition by reporting results from different experiments carried out on Large White pig cohorts. Under similar controlled feeding and environmental conditions, we have shown that the gut microbiota after weaning can be consistently classified into two enterotypes by sequencing the V3-V4 variable region of the 16S rRNA gene from fecal DNA. The two enterotypes are characterized by either an overabundance of the genera Prevotella and Mitsuokella or Ruminococcus and Treponema. We explored the contribution of host genetics to the gut microbiota composition by estimating genetic parameters and by launching a directional selection based on the enterotype assignment of 60-day-old pigs. Calculated heritabilities of the relative abundance of fecal microbiota bacteria genera and the response to selection confirmed a significant contribution of host genetics to microbiota variability. The results on this ongoing selection experiment should help to investigate coevolution of the gut microbiota with its host.