Gut Microbiota in Swine: Composition, Genetic Parameters, and Links with Immunity and Production Traits

A cohort of 60 day-old Large White piglets and a subset of 31 piglets 14, 36, 48, 60 and 70 days old were assessed for fecal microbiota composition by pyrosequencing the 16S rRNA gene. All animals were weaned at 28 days and measured for immunity and production traits. Bacteroidetes, Firmicutes, and Proteaobacteria phyla were predominant at all ages. Microbiota of suckling piglets mainly included Bacteroides, Oscillibacter, Escherichia/Shigella, Lactobacillus and unclassified Ruminococcaceae genera with a switch towards a predominance of Acetivibrio, Dialister, Oribacterium, Succinivibrio and Prevotella genera after weaning. The temporal trajectory of bacterial communities revealed a stratification of the 31 piglets in two main groups after weaning that were primarily distinguished by the levels of unclassified Ruminococcaceae and Prevotella, respectively. Dominance of Prevotella was positively correlated to increased concentrations of luminal secretory IgA, average daily gain and body weight. Genetic parameters of the gut microbiota composition were estimated from a set of 299 60 day-old animals. Among a set of 63 genera, 7 had low (0.1<h2<0.2), 15 medium (0.2<h2<0.4) and 8 high (h2>0.4) heritabilities for abundance variations. At the genetic level, the relative abundances of Prevotella, Oribacterium, Selenomonas, Dialister and Megasphaera were found positively correlated with each other. Regularized canonical correlations and sparse Partial Least Squares analyses highlighted both positive and negative correlations between immunity traits (e.g. monocytes, eosinophils, platelets) and genera such as Prevotella, Roseburia and Dialister. Thus, the gut microbiota composition in swine is influenced by the host’s genetics and is linked to immune and production traits.