Genomic and phenotypic characterization of a honey-derived Enterococcus faecium isolate from the Brazilian semiarid region

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.

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.

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.

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.