Gut microbiome composition differences among breeds impact feed efficiency in swine

Abstract

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, fatness traits, and gut microbiome composition in three major breeds of domesticated swine and 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. Amplicon sequence variants from multiple genera (including Anaerovibrio, Bacteroides, Blautia, Clostridium, Dorea, Eubacterium, Faecalibacterium, Lactobacillus, Oscillibacter, and Ruminococcus) were found to be significantly associated with feed efficiency, regardless of the time point 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 to shaping host productive parameters. Moreover, our study provides important insights into how the intestinal microbial community might influence host energy harvesting capacity. A deeper understanding of this process may allow us to modulate the gut microbiome in order to raise more efficient animals. Video Abstract.

Keywords: Feed efficiency; Genetics; Microbiome; Performance; Swine.

Fig. 1

Average daily gain and feed efficiency (least squares mean ± confidence interval) of Duroc (DR), Landrace (LR), and Large White (LW) at three time points 73 days (T1), 123 days (T2), and 158 days (T3) in the growth trial

Fig. 2

Linear discriminant analysis (LDA) of feed efficiency and fatness trait data from three breeds of pig. Scores [a] and loadings [b] are reported

Fig. 3

Relative abundance of microbiome taxa at family level of Duroc (DR), Landrace (LR), and Large White (LW) in three time points 73 days (T1), 123 days (T2), and 158 days (T3) of the feeding trial

Fig. 4

Measurements of fecal microbiome alpha diversity at ASV level using the Shannon, Simpson, and Inverse Simpson indices (least squares means ± confidence interval) in the Duroc (DR), Landrace (LR), and Large White (LW) breeds for three time points 73 days (T1), 123 days (T2), and 158 days (T3) in the growth trial.

Fig. 5

Clustering and LDA analyses of gut microbiome data collected from Duroc [a], Landrace [b], and Large White [c] pigs at three time points 73 days (T1), 123 days (T2), and 158 days (T3) of the feeding trial. (Above) Genera that differentiate enterotypes at each time point. Bar length represents a log₁₀-transformed linear discriminant score. Color corresponds to the enterotype in which a genus was found to be most abundant. (Below) Enterotype clusters identified using Calinski–Harabasz (CH) index maximization

Fig. 6

ASV with significantly higher or lower relative abundance when comparing the Duroc (DR) sire line vs the average of the Landrace and Large White maternal lines (DR vs (LR+LW)/2) (left panel) or the two maternal lines (LR vs LW) (right panel) at three time points (73 days (T1) [a], 123 days (T2) [b], and 158 days (T3) [c]). Each volcano plot simultaneously indicates the log₂ fold change (x-axis) and the –log₁₀(p value) (y-axis) for each ASV plotted. Dashed lines indicate arbitrary thresholds of logFC and p value. Each point represents an ASV, annotation highlight the genus of the ASV, while color represents the phylum.

Fig. 7

Heat maps showing Spearman correlations and level of significance between genera, feed efficiency, and fatness traits of Duroc, Landrace, and Large White in three time points of the growth trial (73 days (T1) [a], 123 days (T2) [b], and 158 days (T3) [c]). Correlations were analyzed between ASV at the genus level. The color represents the correlation while the saturation represents the level of significance