Genomic and phenotypic characterization of a honey-derived Enterococcus faecium isolate from the Brazilian semiarid region
4 affiliations
- 1Department of Genetics, Federal University of Pernambuco, Recife, Brazil
- 2Institute of Biological Sciences, University of Pernambuco, Recife, Brazil
- 3Department of Microbiology, Institute Aggeu Magalhães, FIOCRUZ, Recife, Brazil
- 4Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Av. Prof. Moraes Rego, 1235, Cidade Universitária, Recife, 50670-901 Pernambuco Brazil
Abstract
Background: Enterococcus faecium has attracted considerable scientific interest. While some strains are recognized as opportunistic nosocomial pathogens, several non-pathogenic isolates have demonstrated beneficial properties associated with food fermentation and probiotic potential. Therefore, this study aimed to perform a functional genomic characterization of the native E. faecium strain EFBI58, isolated from honey in the Brazilian semiarid region.
Materials and methods: Enterococcus faecium strain EFBI58 was sequenced using Illumina MiSeq. Bioinformatic tools were employed for comparative genomics, phylogeny, and detection of resistance, virulence, prophage, CAZyme, and bacteriocin genes. Additionally, in vitro tests assessed antimicrobial susceptibility and survival under simulated gastrointestinal conditions.
Results: The EFBI58 genome presented 2,457,210 base pairs, containing 2,330 coding sequences. Phylogenomic analyses demonstrated that honey-derived isolates formed a genetically distinct group. The ANI showing belonging to clade A2 of animal-associated species. Antimicrobial resistance assessment revealed the absence of acquired genes related to clinical resistance, which was confirmed by the phenotypic susceptibility profile to the evaluated antibiotics. In addition, genes associated with important virulence factors were not identified. A prophage was 21 kb also identified in the genome. The strain EFBI58 showed survival capacity under simulated gastrointestinal conditions and the presence of stress-response proteins, demonstrating mechanisms of adaptation to adverse environments. The profile of carbohydrate-active enzymes and growth in prebiotics sugars revealed a conserved metabolic repertoire associated with the utilization of different substrates.
Conclusions: Honey- and bee-associated E. faecium isolates possess genomic characteristics that provide a basis for future investigations involving natural antimicrobial compounds, microbial interactions, and biotechnological applications.
Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1007/s11033-026-13025-w.
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BibTeX
@article{santos2026genomic,
title = {{Genomic and phenotypic characterization of a honey-derived Enterococcus faecium isolate from the Brazilian semiarid region}},
author = {Dayane da Silva Santos and Allyson Andrade Mendonça and Maria Cecília de Lima e Silva and Marcia Maria Camargo De Morais and Danilo Elias Xavier and José Carlos da Rocha Neto and Rafael Barros De Souza and Marcos Antônio De Morais Junior},
journal = {Molecular Biology Reports},
year = {2026},
month = nov,
doi = {10.1007/s11033-026-13025-w},
url = {https://doi.org/10.1007/s11033-026-13025-w},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Genomic and phenotypic characterization of a honey-derived Enterococcus faecium isolate from the Brazilian semiarid region
AU - Dayane da Silva Santos
AU - Allyson Andrade Mendonça
AU - Maria Cecília de Lima e Silva
AU - Marcia Maria Camargo De Morais
AU - Danilo Elias Xavier
AU - José Carlos da Rocha Neto
AU - Rafael Barros De Souza
AU - Marcos Antônio De Morais Junior
PY - 2026
DA - 2026/11/01
JO - Molecular Biology Reports
DO - 10.1007/s11033-026-13025-w
UR - https://doi.org/10.1007/s11033-026-13025-w
AB - Background: Enterococcus faecium has attracted considerable scientific interest. While some strains are recognized as opportunistic nosocomial pathogens, several non-pathogenic isolates have demonstrated beneficial properties associated with food fermentation and probiotic potential. Therefore, this study aimed to perform a functional genomic characterization of the native E. faecium strain EFBI58, isolated from honey in the Brazilian semiarid region. Materials and methods: Enterococcus faecium strain EFBI58 was sequenced using Illumina MiSeq. Bioinformatic tools were employed for comparative genomics, phylogeny, and detection of resistance, virulence, prophage, CAZyme, and bacteriocin genes. Additionally, in vitro tests assessed antimicrobial susceptibility and survival under simulated gastrointestinal conditions. Results: The EFBI58 genome presented 2,457,210 base pairs, containing 2,330 coding sequences. Phylogenomic analyses demonstrated that honey-derived isolates formed a genetically distinct group. The ANI showing belonging to clade A2 of animal-associated species. Antimicrobial resistance assessment revealed the absence of acquired genes related to clinical resistance, which was confirmed by the phenotypic susceptibility profile to the evaluated antibiotics. In addition, genes associated with important virulence factors were not identified. A prophage was 21 kb also identified in the genome. The strain EFBI58 showed survival capacity under simulated gastrointestinal conditions and the presence of stress-response proteins, demonstrating mechanisms of adaptation to adverse environments. The profile of carbohydrate-active enzymes and growth in prebiotics sugars revealed a conserved metabolic repertoire associated with the utilization of different substrates. Conclusions: Honey- and bee-associated E. faecium isolates possess genomic characteristics that provide a basis for future investigations involving natural antimicrobial compounds, microbial interactions, and biotechnological applications. Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1007/s11033-026-13025-w.
SN - 0301-4851
SN - 1573-4978
ER -