Abstract
Greater feed efficiency (FE) is critical in increasing profitability while reducing the environmental impact of pig production. Previous studies that identified swine FE-associated bacterial taxa were limited in either sampling sites or sequencing methods. This study characterized the microbiomes within the intestine of FE contrasting Duroc × (Landrace × Yorkshire) (DLY) pigs with a comprehensive representation of diverse sampling sites (ileum, cecum, and colon) and a metagenomic sequencing approach. A total of 226 pigs were ranked according to their FE between weaning to 140 day old, and six with extreme phenotypes were selected, three for each of the high and low groups. The results revealed that the cecum and colon had similar microbial taxonomic composition and function, and had higher capacity in polysaccharide metabolism than the ileum. We found in cecum that the high FE pigs had slightly higher richness and evenness in their micriobiota than the low FE pigs. We identified 12 phyla, 17 genera, and 39 species (e.g., Treponema porcinum, Treponema bryantii, and Firmicutes bacterium CAG:110) that were potentially associated with swine FE variation in cecum microbiota through LEfSe analysis. Species enriched in the cecum of the high FE pigs had a greater ability to utilize dietary polysaccharides and dietary protein according to the KEGG annotation. Analysis of antibiotic resistance based on the CARD database annotation indicated that the macB resistant gene might play an important role in shaping the microbial community in the cecum of pigs with contrasting FE. The bacteria from the genus Prevotella was highly enriched in the cecum of low FE pigs, which may impair the establishment of a more effective nutrient harvesting microbiota because of the interaction between Prevotella and other benefical microbes. These findings improved our understanding of the microbial compositions in the different gut locations of DLY pigs and identified many biomarkers associated with FE variation wich may be used to develop strategies to improve FE in pigs.
Highlights
MATERIALS AND METHODSThe pig is an important food animal, which provides ∼36% of all meat utilization by the world population in 2018 (FAO, 2019)
We found that the functional characteristics of the non-ileum sites were dominated by signaling and cellular processing and carbohydrate metabolism, which was consistent with the carbohydrate-active enzymes (CAZy) annotation, and that the ileum was specialized in genetic information processing and nucleotide metabolism
We found that species in the Prevotella genus were the biggest contributors of macB gene in the cecum low feed efficiency (FE) group, while species in the Treponema and Clostridium genera were among the top contributors in the cecum high FE group (Supplementary Figure S14)
Summary
The pig is an important food animal, which provides ∼36% of all meat utilization by the world population in 2018 (FAO, 2019). The feed accounts for ∼70% of the total cost (Teagasc, 2018). Greater feed efficiency (FE) would increase profitability while reducing the environmental impact of pig production. This is especially important given that pig is one of the major sources of meat in human diet. Feed efficiency is a complex phenotype influenced by genetic and environmental factors, including nutrition, management, and the physiological and health status of the animals (Armstrong et al, 2000; Martinez et al, 2009; Oliveira et al, 2009; Ding et al, 2018). Strategies to improve FE may target one or more of these factors
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