Porcine RFI-associated intestinal microbiota

Our aim was therefore to characterize the intestinal microbiota of pigs ranked as low, medium and high residual feed intake (RFI; a metric for FE), where genetic, nutritional and management effects were minimized, in order to explore a possible link between the intestinal microbiota and FE. A total of 81 pigs were ranked on RFI between weaning and day 126 post-weaning, and 32 were selected as the extremes in RFI (12 low, 10 medium, 10 high). Intestinal microbiota diversity, composition and predicted functionality were assessed by sequencing the V3-V4 region of the 16S rRNA gene from faeces and intestinal digesta. No differences in microbial diversity were found between the three RFI ranks. However, some RFI-associated compositional differences were found, mainly among members of Firmicutes and predominantly in faeces collected at the end of the finishing period. In particular, microbes previously associated with a leaner and healthier host (e.g. Christensenellaceae, Oscillibacter, Cellulosilyticum) were enriched in highly feed efficient pigs. Differences were also observed in the ileum of low RFI (more feed efficient) pigs, the most notable being that Nocardicaceae (Rhodococcus) were considerably less abundant. Predictive functional analysis suggests improved metabolic capabilities in these animals, especially in the ileal microbiota, which were corroborated by higher ileal isobutyric acid concentrations. Taken together, these data indicate differences, albeit relatively subtle, within the intestinal microbiota of low RFI pigs compared to their high RFI counterparts, demonstrating a potential link between the intestinal microbiota and FE in pigs.