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Certain strains of  Enterococcus faecium  contribute beneficially to human health and food fermentation. However, other  E .  faecium  strains are opportunistic pathogens due to the acquisition of virulence factors and antibiotic resistance determinants. To characterize  E .  faecium  from soybean fermentation, we sequenced the genomes of 10  E .  faecium  strains from Korean soybean-fermented foods and analyzed their genomes by comparing them with 51 clinical and 52 non-clinical strains of different origins. Hierarchical clustering based on 13,820 orthologous genes from all  E .  faecium  genomes showed that the 10 strains are distinguished from most of the clinical strains. Like non-clinical strains, their genomes are significantly smaller than clinical strains due to fewer accessory genes associated with antibiotic resistance, virulence, and mobile genetic elements. Moreover, we identified niche-associated gene gain and loss from the soybean strains. Thus, we conclude that soybean  E .  faecium  strains might have evolved to have distinctive genomic features that may contribute to its ability to thrive during soybean fermentation.

Genomic Features and Niche-Adaptation of Enterococcus faecium Strains from Korean Soybean-Fermented Foods