Genetic determinism of pig fecal enterotype. Enterotypig

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 carried out a study to demonstrate coevolution of the host and its gut microbiota established 1 mo postweaning, by directional selection over 2 generations. The gut microbiota was characterized by sequencing the V3-V4 variable region of the 16S rRNA gene from fecal samples collected on 60-d-old Large White piglets. Amplicon sequence variants were inferred from amplicon data and the microbial community was further studied at the genus level. Based on the stratification of the initial population (generation G0) according to the 2 major pig enterotypes, characterized by relative overabundance of either Prevotella and Mitsuokella or Ruminococcus and Treponema, we used the relative abundance of these 4 genera as selection criteria. From the G0 population of 317 piglets, we selected 6 males and 30 females per line and produced 2 successive generations (G1 and G2) of approximately 130 pigs per line. We consistently confirmed a moderate heritability for each of the selected genera (h2 = 0.3 to 0.4). We also estimated the heritability values of the relative abundances for 64 additional bacterial genera, which ranged from 0.1 to 0.5. We showed significant differences between the 2 lines in the relative abundance of the 4 bacterial genera at G1 (P < 0.001, from 0.6 genetic standard deviation for Treponema to 1.3 for Prevotella). In the following generation G2, response to selection was maintained for Prevotella and was even increased for the 3 other genera. The observed contrasts were in the expected direction for the genera under direct selection, and we extended the analysis to the 64 other bacterial genera with estimated heritabilities higher than 0.1. All these results confirm a significant influence of host genetics on the composition of gut microbiota at 60 d of age in pigs, and a capacity of directional selection over generations that will be further explored together with early and late host traits.