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The adverse effects of antibiotics have attracted widespread attention, thus reducing the use of antibiotics in animal feed has become a very important issue in improving of the health of livestock. The effects of Enterococcus faecium ( E. faecium ) on growth performance and gut microbiota in weaned piglets were investigated in the present study. Piglets were randomly assigned to four treatments: a control group fed with a diet containing 75 mg/kg aureomycin (Diet 1 group) and three experimental groups fed with diets of 50 mg/kg aureomycin (Diet 2 group), 50 mg/kg aureomycin + 9 × 10 5 CFU/g E. faecium (Diet 3 group), or 50 mg/kg aureomycin + 1.2 × 10 6 CFU/g E. faecium (Diet 4 group). Their gut microbial communities were analyzed by sequencing the V3–V4 region of the 16SrRNA gene. The results showed that the final body weights and the average daily gain of the weaned piglets in the Diet 2 group were higher ( P = 0.05) than those in the Diet 1 or Diet 3 group. Decreasing trends ( P = 0.08) was observed in mortality rate in the Diet 3 and 4 group when compared with that in the Diet 1 group. Increases in the Sobs, Chao1, ACE, and Shannon indexes and a decrease in the Simpson index were observed at intervals from day 1 to 14 ( P < 0.05). The Sobs, Chao1, and ACE indexes in the Diet 3 group were the lowest on day 14 ( P < 0.05). The abundance of Bacteroidetes was increased and that of Proteobacteria was decreased from day 1 to 7, but both of them kept stable from day 7 to 14. Besides, the lowest abundance of Fusobacteria , Lentisphaerae , and Planctomycetes was observed on day 1 and the lowest abundance of Actinobacteria was observed on day 14 in the Diet 3 group ( P < 0.05). Overall, these results suggest that the antibiotics and E. faecium interventions result in different changes in the gut microbiota, and a reduced antibiotics diet supplemented with 1.2 × 10 6 CFU/g E. faecium does not affect the growth performance in weaned piglets. Electronic supplementary material The online version of this article (10.1186/s13568-019-0755-z) contains supplementary material, which is available to authorized users.