Microbiome composition differences among breeds impact feed efficiency in swine

Background Feed efficiency is a crucial parameter in swine production given both its economic and environmental impact. The gut microbiota plays an essential role in nutrient digestibility and is therefore likely to affect feed efficiency. This study aimed to characterize feed efficiency, production traits, and gut microbiome composition of three major breeds of domesticated swine, and to investigate a possible link between feed efficiency and gut microbiota composition. Results Average daily feed intake ( ADFI ), average daily gain ( ADG ), feed conversion ratio ( FCR ), residual feed intake ( RFI ), backfat, loin depth, and intramuscular fat of 615 pigs belonging to the Duroc ( DR ), Landrace ( LR ), and Large White ( LW ) breeds were measured. Gut microbiota composition was characterized by 16S rRNA gene sequencing. Orthogonal contrasts between paternal line (DR) and maternal lines (LR+LW) and between the two maternal lines (LR versus LW) were performed. Average daily feed intake and ADG were statistically different with DR having lower ADFI and ADG compared to LR and LW. Landrace and LW had a similar ADG and RFI, with higher ADFI and FCR for LW. Alpha diversity was higher in the fecal microbial communities of LR pigs than in those of DR and LW pigs for all time points considered. Duroc communities had significantly higher proportional representation of the Catenibacterium and Clostridium genera compared to LR and LW, while LR pigs had significantly higher proportions of Bacteroides than LW for all time points considered. We identified several amplicon sequencing variants members of certain genera including Anaerovibrio , Bacteroides , Blautia , Clostridium , Dorea , Eubacterium , Faecalibacterium , Lactobacillus, Oscillibacter , and Ruminococcus significantly associated with feed efficiency of pigs for all time points considered. Conclusions In this study we characterized differences in the composition of the fecal microbiota of three commercially relevant breeds of swine, both over time and between breeds. Correlations between different microbiome compositions and feed efficiency were established. This suggests that the microbial community may contribute in shaping host productive parameters. Moreover, our study provides important insights to understand how the intestinal microbial community might influence the host energy harvesting capacity. A deeper understanding of this process may allow us to modulate the gut microbiome for more efficient animals.