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.
Highlights
Feed costs account for 60–70% of the total costs involved in pig production
We identified four bacterial species from the Clostridiales including Ethanoligenens harbinense, Syntrophobotulus glycolicus, Clostridium clariflavum, and Clostridium cellulosi, and two species from the Bacteroidales including Rikenellaceae bacterium M3, and Bacteroidales bacterium CF showing the enrichments in pigs with high feed efficiency
We investigated the fecal microbial composition of commercial Duroc pigs, and systematically evaluated the association of gut microbiome with pig feed efficiency from both enterotype and microbial taxa with 16S rRNA gene sequencing and shotgun metagenomic sequencing data
Summary
Improving feed efficiency has been an important task of commercial pig breeding. Porcine Feed Efficiency-Associated Bacteria suggested that gut microbiota should have a profound effect on porcine feed efficiency (Lamendella et al, 2011; Vigors et al, 2016). Animal gastrointestinal microbiota is a heterogeneous ecosystem and dominated by bacteria. Several previous studies reported the structure and functional capacity of porcine gut microbiome. McCormack et al identified several gut microbes potentially associated with porcine feed efficiency (McCormack et al, 2017). Ramayo-Caldas et al (2016) defined the interaction network of gut microbiota in pigs, and found that the enterotype-like clustering was significantly associated with porcine growth traits Bacterial communities in piglets could be separated into two different enterotype-like clusters, primarily distinguished by unclassified Ruminococcaceae and Prevotella levels (Mach et al, 2015). Ramayo-Caldas et al (2016) defined the interaction network of gut microbiota in pigs, and found that the enterotype-like clustering was significantly associated with porcine growth traits
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