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Background  The development and utilization of probiotics had many environmental benefits for replacing antibiotics in animal production. Bacteria in the intestinal mucosa have better adhesion to the host intestinal epithelial cells compared to bacteria in the intestinal contents. In this study, lactic acid bacteria were isolated from the intestinal mucosa of broiler chickens and investigated as the substitution to antibiotic in broiler production.    Results  In addition to acid resistance, high temperature resistance, antimicrobial sensitivity tests, and intestinal epithelial cell adhesion,  Enterococcus faecium  PNC01 ( E. faecium  PNC01) was showed to be non-cytotoxic to epithelial cells. Draft genome sequence of  E. faecium  PNC01 predicted that it synthesized bacteriocin to perform probiotic functions and bacteriocin activity assay showed it inhibited  Salmonella  typhimurium from invading intestinal epithelial cells. Diet supplemented with  E. faecium  PNC01 increased the ileal villus height and crypt depth in broiler chickens, reduced the relative length of the cecum at day 21, and reduced the relative length of jejunum and ileum at day 42. Diet supplemented with  E. faecium  PNC01 increased the relative abundance of Firmicutes and  Lactobacillus , decreased the relative abundance of Bacteroides in the cecal microbiota.    Conclusion   E. faecium  PNC01 replaced antibiotics to reduce the feed conversion rate. Furthermore,  E. faecium  PNC01 improved intestinal morphology and altered the composition of microbiota in the cecum to reduce feed conversion rate. Thus, it can be used as an alternative for antibiotics in broiler production to avoid the adverse impact of antibiotics by altering the gut microbiota.    Graphic AbstractSupplementary Information  The online version contains supplementary material available at 10.1186/s12934-021-01609-z.

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Enterococcus faecium PNC01 isolated from the intestinal mucosa of chicken as an alternative for antibiotics to reduce feed conversion rate in broiler chickens