Genetic selection for residual feed intake impacts the functional redundancy of the gut microbiota in pigs during the growing-finishing period

BackgroundImproving feed efficiency is an unvarying goal in livestock production. The role of gut microbial communities in feed efficiency was investigated in two divergent pig lines selected for their residual feed intake (RFI), which is the difference between the observed feed consumption of an animal and that predicted for its maintenance and production requirements. Hence, RFI is a measure of net feed efficiency. ResultsBy sequencing the 16S rRNA genes from fecal samples, we found that the microbiota of low RFI pigs (LRFI; n=12) was significantly depleted in four operational taxonomic units (OTUs) belonging to Prevotella, Feacalibacterium and Lactobacillus genera by comparison to high RFI pigs (HRFI; n=11). Inferring KEGG orthologs from the 16S rRNA gene sequencing data showed that LRFI pigs have 20% more functional redundancy than HRFI pigs. The inferred orthologs held more discriminative power than the OTU approach, which might be inherently flawed if functionally equivalent OTUs compete for the same niche. ConclusionsGut microbiota of LRFI pigs had different microbial operational taxonomic units and a higher functional redundancy, which were more shared suggesting a role of the gut microbiota in the global feed efficiency according to Tax4Fun but this inference based on 16S data has to be verified in future work.