The growing incidence of infections caused by antibiotic-resistant strains of pathogens is one of the key challenges of the 21^st century. The development of novel technological platforms based on single-cell analysis of antibacterial activity at the whole-microbiome level enables the transition to massive screening of antimicrobial agents with various mechanisms of action. The microbiome of wild animals remains largely underinvestigated. It can be considered a natural reservoir of biodiversity for antibiotic discovery. Here, the Staphylococcus pseudintermedius E18 strain was isolated from the oral microbiome of a raccoon dog (Nyctereutes procyonoides) using a microfluidic ultrahigh-throughput screening platform. S. pseudintermedius E18 efficiently inhibited the growth of pathogenic methicillin-resistant Staphylococcus aureus (MRSA). It was established that the main active substance of the S. pseudintermedius E18 strain was a bacteriocin with a molecular weight of 27 kDa. The identified bacteriocin had a high positive charge and an extremely narrow spectrum of activity. Bacteriocin S. pseudintermedius E18 was inactivated by elevated temperature, proteinase K, and EDTA. Further investigation on the structure of the bacteriocin produced by S. pseudintermedius E18 will provide a comprehensive understanding of its mechanism of action, which will open up prospects for developing novel DNA-encoded antimicrobials.