Effects of probiotic Enterococcus faecium NCIMB 11181 administration on swine fecal microbiota diversity and composition using barcoded pyrosequencing

Although our understanding of probiotics is increasing, basic information regarding their effect on the composition of the gut microbiome is scarce. The purpose of this study was to characterize the fecal microbiota of weaned piglets before and after probiotic intervention. The probiotic bacterium Enterococcus faecium NCIMB 11181 was administered to pigs for 2 weeks and fecal bacterial diversity using 16S rRNA gene pyrosequencing was analyzed. A more stable bacterial community, as indicated by increased bacterial diversity and richness, was observed after administration of the probiotic, compared with the control group. Regardless of the diet, Firmicutes and Bacteroidetes were found to be the dominant bacterial phyla in the pigs; however, inhibition of Proteobacteria was clearly evident in the probiotic group. In addition, the probiotic-fed group featured elevated levels of Lactobacillus, Enterococcus, Oscillibacter, Succinivibro, and Clostridium genera and decreased levels of Escherichia and Dialister genera, compared with the control group. This study demonstrated that the probiotic E. faecium NCIMB 11181 modulates the fecal microbiota of weaned piglets. This modulation is characterized by an increase in other bacterial species including L. johnsonii, L. fermentum, and L. kimchii and several Clostridium spp., which might be beneficial to the health of weaned piglets.