Links between gut microbiome functions and feed efficiency in two divergently selected pig lines
Résumé
The gut microbiota plays a major role in the digestive, absorptive and metabolic processes in pigs. The study of the combined impact of host genetics and the gut microbiota composition and its functions is fundamental to develop new strategies in order to improve feed efficiency traits in livestock. Based on 16S sequencing data, previous results on 588 faecal samples from two Large White pig lines divergently selected for residual feed intake (RFI), showed that the gut microbiota composition has relevant genetic relationships with feed efficiency traits. In this study, we predicted KEGG Orthologs (KO) functions using PICRUSt2 software on these datasets, in order to gain insights on the microbiota functions potentially relevant for feed efficiency. A non-metric multidimensional scaling on KO abundances showed a large difference between the two lines, and differential abundance analysis revealed over 3000 differentially abundant (DA) KO functions, confirming the major microbiota differences already found in 16S analyses. Using RFI values, differential analysis revealed over 25 DA KO within the RFI-plus line associated with feed efficiency. In contrast, no KO was significant in RFI-minus line, suggesting that different mechanisms could explain the variability of RFI within each line. Finally, KO enrichment analysis highlighted functions and pathways consistently associated with feed efficiency. Currently, we are validating these results with whole meta-genome sequencing performed on a subset of samples. Overall, this study will provide new insights to better understand the relationships between gut microbiome functions and feed efficiency in pigs.