Abstract
Despite recent efforts to characterize longitudinal variation in the swine gut microbiome, the extent to which a host’s genome impacts the composition of its gut microbiome is not yet well understood in pigs. The objectives of this study were: i) to identify pig gut microbiome features associated with growth and fatness, ii) to estimate the heritability of those features, and, iii) to conduct a genome-wide association study exploring the relationship between those features and single nucleotide polymorphisms (SNP) in the pig genome. A total of 1,028 pigs were characterized. Animals were genotyped with the Illumina PorcineSNP60 Beadchip. Microbiome samples from fecal swabs were obtained at weaning (Wean), at mid-test during the growth trial (MidTest), and at the end of the growth trial (OffTest). Average daily gain was calculated from birth to week 14 of the growth trial, from weaning to week 14, from week 14 to week 22, and from week 14 to harvest. Backfat and loin depth were also measured at weeks 14 and 22. Heritability estimates (±SE) of Operational Taxonomic Units ranged from 0.025 (±0.0002) to 0.139 (±0.003), from 0.029 (±0.003) to 0.289 (±0.004), and from 0.025 (±0.003) to 0.545 (±0.034) at Wean, MidTest, and OffTest, respectively. Several SNP were significantly associated with taxa at the three time points. These SNP were located in genomic regions containing a total of 68 genes. This study provides new evidence linking gut microbiome composition with growth and carcass traits in swine, while also identifying putative host genetic markers associated with significant differences in the abundance of several prevalent microbiome features.
Highlights
In this study we identified fecal microbiome operational taxonomic units (OTUs) associated with 8 traits: 4 measures of weight gain, as well as two backfat thickness, and loin depth measures obtained at weeks 14 and 22 of the trial
In this study we found that gut microbiome diversity and specific constituents of the fecal microbiome were significantly associated with growth and fatness parameters in crossbred swine
Three-hundred-thirty-four OTUs were significantly associated with growth and fatness parameters, many of which were classified as Clostridium, Prevotella, Lactobacillus, and Eubacterium
Summary
The objectives of this study were: i) to identify pig gut microbiome features associated with growth and fatness, ii) to estimate the heritability of those features, and, iii) to conduct a genome-wide association study exploring the relationship between those features and single nucleotide polymorphisms (SNP) in the pig genome. Since the aim of this study was not to provide the ecological landscape of the population measured, in this study we reported the family level. The goal of this study was to estimate heritability of gut bacterial taxa that were important to the host’s growth and fatness, and to identify regions on the host genome that might influence the composition of the gut microbiome
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