Exploring the Fecal Microbial Composition and Metagenomic Functional Capacities Associated With Feed Efficiency in Commercial DLY Pigs

Abstract

Gut microbiota has indispensable roles in nutrient digestion and energy harvesting, especially in processing the indigestible components of dietary polysaccharides. Searching for the microbial taxa and functional capacity of the gut microbiome associated with feed efficiency (FE) can provide important knowledge to increase profitability and sustainability of the swine industry. In the current study, we performed a comparative analysis of the fecal microbiota in 50 commercial Duroc × (Landrace × Yorkshire) (DLY) pigs with polarizing FE using 16S rRNA gene sequencing and shotgun metagenomic sequencing. There was a different microbial community structure in the fecal microbiota of pigs with different FE. Random forest analysis identified 24 operational taxonomic units (OTUs) as potential biomarkers to improve swine FE. Multiple comparison analysis detected 8 OTUs with a significant difference or tendency toward a difference between high- and low-FE pigs (P < 0.01, q < 0.1). The high-FE pigs had a greater abundance of OTUs that were from the Lachnospiraceae and Prevotellaceae families and the Escherichia-Shigella and Streptococcus genera than low-FE pigs. A sub-species Streptococcus gallolyticus subsp. gallolyticus could be an important candidate for improving FE. The functional capacity analysis found 18 KEGG pathways and CAZy EC activities that were different between high- and low-FE pigs. The fecal microbiota in high FE pigs have greater functional capacity to degrade dietary cellulose, polysaccharides, and protein and may have a greater abundance of microbes that can promote intestinal health. These results provided insights for improving porcine FE through modulating the gut microbiome.

Keywords: 16S rRNA gene; DLY pigs; feed efficiency; gut microbiota; metagenome sequencing.

FIGURE 1

The feed conversion ratio value (FCR), pan OTUs, Good’s coverage and community composition in high- and low-feed-efficiency (FE) pigs. Groups are coded according to the feed efficiency status (High_FE, high feed efficiency; Low_FE, low feed efficiency). (A) FCR value in high- and low-FE pigs. (B) Pan OTU = sample size. The horizontal axis represents the number of samples. The vertical axis represents the number of OTUs contained in all samples. (C) Good’s coverage value in high- and low-FE pigs. (D) Community composition at the phylum level in high- and low-FE pigs. (E) Community composition at the genus level in high- and low-FE pigs.

FIGURE 2

The community diversity between fecal samples from high- and low-FE pigs at the OTU level. (A) The Chao1 index in high- and low-FE pigs. (B) The Shannon index in high- and low-FE pigs. (C) Principal component analysis (PCA) of the fecal microbiota based on OTUs.

FIGURE 3

Important biomarkers selected by random forest analysis and the different abundance of OTUs in high- and low-FE pigs. (A) Model evaluation by using top important variables. The horizontal axis represents the number of variables ranked by importance. The vertical axis denotes the average prediction error rate using 10-fold cross-validation when using the number of corresponding variables. (B) The ordination diagram of variables of importance. The horizontal axis is the measurement standard of variables of importance, and the value is equal to the measurement value of variables of importance/standard deviation. The vertical axis is the variable names sorted by importance. (C) ROC of the random forest classifier based on the 24 most important variables. The AUC value is the area under the corresponding curve. When the AUC > 0.5, the AUC value is closer to 1, the diagnostic effect is better. (D) The OTUs with a significantly different abundance between high- and low-FE pigs detected by STAMP software.

FIGURE 4

Heatmap of functional capacity profiles showing different enrichment in high- and low-FE pigs by metagenomic sequencing analysis. Samples are coded according to the feed efficiency status (HighFE, high feed efficiency; LowFE, low feed efficiency). For example, HighFE.1 represented the first sample that was collected from high-feed-efficiency pig. (A) Heatmap of KEGG pathways showing different enrichments in high- and low-FE pigs. (B) Heatmap of CAZy EC activities showing different enrichments in high- and low.