Host contributes to longitudinal diversity of fecal microbiota in swine selected for lean growth

Background: In pigs, gut bacteria have been shown to play important roles in nutritional, physiological, and immunological processes in the host. However, the contribution of their metagenomes or part of them, which are normally reflected by fragments of 16S rRNA-encoding genes, has yet to be fully investigated. Results: Fecal samples, collected from a population of crossbred pigs at three time points, including weaning, week 15 post weaning (hereafter week 15), and end-of-feeding test (hereafter off-test), were used to evaluate changes in the composition of the fecal microbiome of each animal over time. This study used 1205, 1295, and 1283 samples collected at weaning, week 15, and off-test, respectively. There were 1039 animals that had samples collected at all three time points and also had phenotypic records on back fat thickness (BF) and average daily body weight gain (ADG). Firmicutes and Bacteroidetes were the most abundant phyla at all three time points. The most abundant genera at all three time points included Clostridium, Escherichia, Bacteroides, Prevotella, Ruminococcus, Fusobacterium, Campylobacter, Eubacterium, and Lactobacillus. Two enterotypes were identified at each time point. However, only enterotypes at week 15 and off-test were significantly associated with BF. We report herein two novel findings: (i) alpha diversity and operational taxonomic unit (OTU) richness were moderately heritable at week 15, h(2) of 0.15 +/- 0.06 to 0.16 +/- 0.07 and 0.23 +/- 0.09 to 0.26 +/- 0.08, respectively, as well as at off-test, h2 of 0.20 +/- 0.09 to 0.33 +/- 0.10 and 0.17 +/- 0.08 to 0.24 +/- 0.08, respectively, whereas very low heritability estimates for both measures were detected at weaning; and (ii) alpha diversity at week 15 had strong and negative genetic correlations with BF, -0.53 +/- 0.23 to -0.45 +/- 0.25, as well as with ADG, -0.53 +/- 0.32 to -0.53 +/- 0.29. Conclusions: These results are important for efforts to genetically improve the domesticated pig because they suggest fecal microbiota diversity can be used as an indicator trait to improve traits that are expensive to measure.