Probiotic potential of Enterococcus faecium ED22: evidence from genomic analysis and in vitro characterization
Abstract
Enterococcus species are ubiquitous members of the human microbiota, but their potential to act as opportunistic pathogens requires careful, strain-specific safety assessment. This study characterized Enterococcus faecium ED22 using a polyphasic approach combining whole-genome sequencing (WGS) with in vitro phenotypic assays. The strain was initially identified by MALDI-TOF/MS and subsequently confirmed by WGS. Genomic analyses included genome assembly and annotation, antimicrobial resistance (AMR) and virulence-associated gene screening, plasmid characterization. Functional characterization included antibacterial and antifungal activity, DPPH radical-scavenging activity, gastrointestinal tolerance, and aggregation assays, while hemolytic and gelatinase activities were evaluated as safety-related traits. ED22 exhibited detectable antibacterial activity against Staphylococcus aureus , Escherichia coli , and Pseudomonas aeruginosa , with proteinase K-sensitive activity suggesting a contribution of proteinaceous antimicrobial compounds. Antifungal activity was observed against Trichophyton rubrum , but not Candida albicans . Fermented milk containing ED22 showed DPPH radical-scavenging activity of 66.23 ± 0.38%, together with measurable phenolic and flavonoid contents. ED22 remained viable under simulated gastrointestinal conditions and exhibited auto-aggregation and co-aggregation properties. The strain was non-hemolytic and gelatinase-negative. Genomic screening detected no major acquired vancomycin resistance determinants, key virulence genes, or plasmid-borne AMR genes. A RiPP biosynthetic cluster displayed 66% similarity to enterocin A. These findings support ED22 as a preliminary candidate for probiotic development, though further MIC profiling, genomic validation, plasmid transferability assessment, and in vivo efficacy trials remain essential.
Related
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BibTeX
@article{khalid2026probiotic,
title = {{Probiotic potential of Enterococcus faecium ED22: evidence from genomic analysis and in vitro characterization}},
author = {Ibtissame Khalid and Fatima Zahra Lafdil and Asmae Sellam and Said Ezrari and Moussa Elayachi and Khaoula Bachiri and Hassane Mekhfi and Ammar Mohammed AL-Farga and Habib Bouazzi and Mustapha Meziane and Bouchra Elguerrouj},
journal = {Scientific Reports},
year = {2026},
month = oct,
doi = {10.1038/s41598-026-73022-8},
url = {https://www.nature.com/articles/s41598-026-73022-8},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Probiotic potential of Enterococcus faecium ED22: evidence from genomic analysis and in vitro characterization
AU - Ibtissame Khalid
AU - Fatima Zahra Lafdil
AU - Asmae Sellam
AU - Said Ezrari
AU - Moussa Elayachi
AU - Khaoula Bachiri
AU - Hassane Mekhfi
AU - Ammar Mohammed AL-Farga
AU - Habib Bouazzi
AU - Mustapha Meziane
AU - Bouchra Elguerrouj
PY - 2026
DA - 2026/10/05
JO - Scientific Reports
DO - 10.1038/s41598-026-73022-8
UR - https://www.nature.com/articles/s41598-026-73022-8
AB - Enterococcus species are ubiquitous members of the human microbiota, but their potential to act as opportunistic pathogens requires careful, strain-specific safety assessment. This study characterized Enterococcus faecium ED22 using a polyphasic approach combining whole-genome sequencing (WGS) with in vitro phenotypic assays. The strain was initially identified by MALDI-TOF/MS and subsequently confirmed by WGS. Genomic analyses included genome assembly and annotation, antimicrobial resistance (AMR) and virulence-associated gene screening, plasmid characterization. Functional characterization included antibacterial and antifungal activity, DPPH radical-scavenging activity, gastrointestinal tolerance, and aggregation assays, while hemolytic and gelatinase activities were evaluated as safety-related traits. ED22 exhibited detectable antibacterial activity against Staphylococcus aureus , Escherichia coli , and Pseudomonas aeruginosa , with proteinase K-sensitive activity suggesting a contribution of proteinaceous antimicrobial compounds. Antifungal activity was observed against Trichophyton rubrum , but not Candida albicans . Fermented milk containing ED22 showed DPPH radical-scavenging activity of 66.23 ± 0.38%, together with measurable phenolic and flavonoid contents. ED22 remained viable under simulated gastrointestinal conditions and exhibited auto-aggregation and co-aggregation properties. The strain was non-hemolytic and gelatinase-negative. Genomic screening detected no major acquired vancomycin resistance determinants, key virulence genes, or plasmid-borne AMR genes. A RiPP biosynthetic cluster displayed 66% similarity to enterocin A. These findings support ED22 as a preliminary candidate for probiotic development, though further MIC profiling, genomic validation, plasmid transferability assessment, and in vivo efficacy trials remain essential.
SN - 2045-2322
ER -