Unraveling the Fecal Microbiota and Metagenomic Functional Capacity Associated with Feed Efficiency in Pigs

Abstract

Gut microbiota plays fundamental roles in energy harvest, nutrient digestion, and intestinal health, especially in processing indigestible components of polysaccharides in diet. Unraveling the microbial taxa and functional capacity of gut microbiome associated with feed efficiency can provide important knowledge to improve pig feed efficiency in swine industry. In the current research, we studied the association of fecal microbiota with feed efficiency in 280 commercial Duroc pigs. All experimental pigs could be clustered into two enterotype-like groups. Different enterotypes showed the tendency of association with the feed efficiency (P = 0.07). We further identified 31 operational taxonomic units (OTUs) showing the potential associations with porcine feed efficiency. These OTUs were mainly annotated to the bacteria related to the metabolisms of dietary polysaccharides. Although we did not identify the RFI-associated bacterial species at FDR < 0.05 level, metagenomic sequencing analysis did find the distinct function capacities of gut microbiome between the high and low RFI pigs (FDR < 0.05). The KEGG orthologies related to nitrogen metabolism, amino acid metabolism, and transport system, and eight KEGG pathways including glycine, serine, and threonine metabolism were positively associated with porcine feed efficiency. We inferred that gut microbiota might improve porcine feed efficiency through promoting intestinal health by the SCFAs produced by fermenting dietary polysaccharides and improving the utilization of dietary protein. The present results provided important basic knowledge for improving porcine feed efficiency through modulating gut microbiome.

Keywords: 16S rRNA gene; feed efficiency; gut microbiota; metagenome; swine.

Figure 1

Environmental and host factors affecting porcine fecal microbial community structure. (A) Canonical Correspondence Analysis (CCA) found significant effects of pen, sex and kinship on fecal microbial community structure. (B) Comparison of Unweighted UniFrac distance among full-siblings, half-siblings, and unrelated individuals. (C) Pen shows significant effect on fecal microbial community. The pigs housed in the same pen showed a higher similarity of microbial composition than pigs in different pens. (D) Significant difference of alpha-diversity of fecal microbial community between boars and gilts (^***P < 0.001 for Student's t-test; mean ± SEM).

Figure 2

Enterotype-like clustering in a cohort of 280 experimental pigs and association with porcine feed efficiency. (A) Enterotype-like clustering of 280 pigs. (B) Relative abundances of the main contributors of each enterotype. Orange color represents the enterotype cluster 1 and blue color indicates the enterotype cluster 2. (C) Association of enterotype-like clusters with porcine feed efficiency (Cluster 1: n = 90 and cluster 2: n = 190).

Figure 3

Heatmap of bacterial species showing different enrichment between high and low RFI pigs in the metagenomic sequencing analysis. The X-axis shows the sample IDs, e.g., RFI.HM9 representing the sample 9, a male with high RFI-value; RFI.HF8: the sample 8, a female with high RFI-value; RFI.LF9: the sample 9, a female with low RFI-value, and so on. The Y axis represents the microbial species.

Figure 4

The KEGG function terms showing different enrichment between high and low RFI pigs. (A) Heatmap of KEGG orthologs showing different enrichments between high and low RFI pigs. The X-axis shows the sample IDs, e.g., RFI.HM9 representing the sample 9, a male with high RFI-value; RFI.HF8: the sample 8, a female with high RFI-value; RFI.LF9: the sample 9, a female with low RFI-value, and so on. The Y-axis represents the KEGG orthologies. (B) Differential KEGG pathways between high and low RFI pigs detected by STAMP software.