Abstract: Using the 16S rRNA gene high through-put sequencing technique, the microbial composition of the gut microbiota in post-weaning piglets was characterized. The compositional alterations induced by two strains of Enterococcus faecium were studied. The resulting dominant species in the guts were found to be of Firmicutes and Bacteroidetes phyla with contribution rates of 50.5% and 42.2%, respectively. The richness and diversity of the bacterial community increased after the E. faecium administration. The populations of 6 phyla (i.e., Firmicutes, Proteobacteria, Tenericutes, Actidobacteria, Gemmatimonadetes, and Actinobacteria) were increased, while that of Bacteroidetes significantly declined. A low abundance of Enterococcus spp. was detected in the piglet guts. However, the increase was merely 0.07% over control and 0.12 over the treatment group, SF1, and 0.14% over group SF2 after the feeding. Consequently, the primary effects induced by the probiotics, E. faecium strains, were contributed mainly to the changes on the richness and diversity, or the composition, of the gut microbes. It appeared that the positive results observed on the growth performances of the post-weaning piglets in the field experiment due to the introduction of the probiotics warned further attention.