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<p><i>Enterococcus</i> species are widely distributed in traditional fermented foods and have shown probiotic potential. However, their food-grade application has been limited because the European Food Safety Authority excluded the genus from the qualified presumption of safety (QPS) list. Therefore, strain-specific safety assessment is essential. In this study, we characterized <i>Enterococcus</i> isolates from Korean Doenjang and Meju using an integrated phenotypic and whole-genome sequencing approach. Sixteen strains were isolated and identified/determined by 16S rRNA gene sequencing. We evaluated phenotypic safety and probiotic traits, and five candidates were further tested in HT-29 wound-healing scratch assays and a 115-gene host expression array. The two best wound-healing strains were then analyzed by whole-genome sequencing using a multi-database approach (VirulenceFinder, VFDB, ResFinder, CARD/RGI, PlasmidFinder, CRISPRCasFinder, and antiSMASH). The 16 isolates belonged to the five species, among which <i>E. durans</i> Edu-1 showed the highest wound closure ability (18.75 ± 1.24% at 72&#xa0;h), followed by <i>E. raffinosus</i> Era-1 (16.71 ± 0.49%). Whole-genome sequence analysis showed that Edu-1 had no acquired transmissible antibiotic resistance and virulence factors genes and in addition, contains a plasmid-borne Bacteriocin_II family biosynthetic gene cluster, which can explain/support its broad-spectrum antimicrobial activity. In contrast, Era-1 carried <i>tet</i>(M) gene on the chromosome and <i>ermB</i> gene on an insertion-sequence-rich mobile element, although it also has a functional Type I-B CRISPR-Cas system and three glutamate decarboxylase (<i>gadB</i>) genes for γ-aminobutyric acid biosynthesis. These findings identify/suggest <i>E. durans</i> Edu-1 as a food-grade probiotic candidate with epithelial wound-healing activity, while <i>E. raffinosus</i> Era-1 represents a strain of biological interest for mechanistic wound-healing research rather than food application.</p>

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Phenotypic and Whole-Genome Characterization of Enterococcus Isolates from Korean Doenjang and Meju: E. durans Edu-1 as a Food-Grade Probiotic Candidate with Epithelial Wound-Healing Activity

  • 期刊论文

  • 发表日期：

    2026年7月28日

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  • Jihee Kang,
  • Hee-Hyeon Kim,
  • Hye Min Yoon,
  • Yunseo Choi,
  • Jungkyung Heo,
  • Yeonju Woo,
  • Seonmi Yu,
  • Kyung-Hye Lee,
  • Yunho Lee

摘要

Enterococcus species are widely distributed in traditional fermented foods and have shown probiotic potential. However, their food-grade application has been limited because the European Food Safety Authority excluded the genus from the qualified presumption of safety (QPS) list. Therefore, strain-specific safety assessment is essential. In this study, we characterized Enterococcus isolates from Korean Doenjang and Meju using an integrated phenotypic and whole-genome sequencing approach. Sixteen strains were isolated and identified/determined by 16S rRNA gene sequencing. We evaluated phenotypic safety and probiotic traits, and five candidates were further tested in HT-29 wound-healing scratch assays and a 115-gene host expression array. The two best wound-healing strains were then analyzed by whole-genome sequencing using a multi-database approach (VirulenceFinder, VFDB, ResFinder, CARD/RGI, PlasmidFinder, CRISPRCasFinder, and antiSMASH). The 16 isolates belonged to the five species, among which E. durans Edu-1 showed the highest wound closure ability (18.75 ± 1.24% at 72 h), followed by E. raffinosus Era-1 (16.71 ± 0.49%). Whole-genome sequence analysis showed that Edu-1 had no acquired transmissible antibiotic resistance and virulence factors genes and in addition, contains a plasmid-borne Bacteriocin_II family biosynthetic gene cluster, which can explain/support its broad-spectrum antimicrobial activity. In contrast, Era-1 carried tet(M) gene on the chromosome and ermB gene on an insertion-sequence-rich mobile element, although it also has a functional Type I-B CRISPR-Cas system and three glutamate decarboxylase (gadB) genes for γ-aminobutyric acid biosynthesis. These findings identify/suggest E. durans Edu-1 as a food-grade probiotic candidate with epithelial wound-healing activity, while E. raffinosus Era-1 represents a strain of biological interest for mechanistic wound-healing research rather than food application.