title: Genomic Features and Niche-Adaptation of Enterococcus faecium Strains from Korean Soybean-Fermented Foods.
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.
authors.affiliation: Department of Animal Life Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, Kangwon-do, Republic of Korea.|Division of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, Kangwon-do, Republic of Korea.
authors.forename: Eun Bae
authors.initials: EB
authors.lastname: Kim
authors.affiliation: Department of Animal Life Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, Kangwon-do, Republic of Korea.
authors.forename: Gwi-Deuk
authors.initials: GD
authors.lastname: Jin
authors.affiliation: Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea.
authors.forename: Jun-Yeong
authors.initials: JY
authors.lastname: Lee
authors.affiliation: Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea.|Research Institute for Agriculture and Life Science, Seoul National University, Seoul, Republic of Korea.
authors.forename: Yun-Jaie
authors.initials: YJ
authors.lastname: Choi
mesh_terms: D000222:Adaptation, Physiological; D024881:Drug Resistance, Bacterial / Q000235:genetics; D016984:Enterococcus faecium / Q000235:genetics* / Q000472:pathogenicity / Q000502:physiology*; D019143:Evolution, Molecular; D005285:Fermentation; D005511:Food Handling; D005516:Food Microbiology; D005798:Genes, Bacterial; D006801:Humans; D010802:Phylogeny; D056910:Republic of Korea; D013025:Glycine max / Q000382:microbiology*; D014774:Virulence / Q000235:genetics