Abstract
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.
Highlights
Enterococcus faecium is a Gram-positive bacterium found in the gastro-intestinal tracts (GIT) of animals [1], fermented foods [2,3], and a variety of other environments [4]
8,850 single nucleotide polymorphisms (SNPs) from 990 core genes, which are commonly found in 113 strains, were identified among the 10 soybean strains
E. faecium strains are frequently found in soybeans [27,28] and soybean-fermented foods [3,6], to our knowledge, the genomes of soybean-originated E. faecium have never been investigated
Summary
Enterococcus faecium is a Gram-positive bacterium found in the gastro-intestinal tracts (GIT) of animals [1], fermented foods [2,3], and a variety of other environments [4]. E. faecium is a lactic acid bacterium, which produces lactic acid as a final product of carbohydrate fermentation [5], and it may have hypothetical roles in the early stages of soybean fermentation [3,6]. Some strains of E. faecium have beneficial roles in GIT health as commensal or probiotic bacteria [7]; others are associated with nosocomial infections such as bacteremia and endocarditis in humans [1]. Certain E. faecium strains have emerged as critical hospital pathogens due to their resistance to vancomycin treatments [1]. The pathogenicity of E. faecium has not been yet fully defined, many antibiotic resistance (AR) genes and virulence factors (VF) have been identified [1].
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