Genome Analysis and Characterization of Enterococcus sp. SB12 Isolated from Carpathian Artisanal Cheese

The use of probiotics is becoming increasingly popular in animal husbandry and medicine and is offered as an alternative to antibiotics. Due to the ability to produce bacteriocins with antimicrobial effects and survival in the gastrointestinal tract, certain strains of Enterococcus faecium are used in probiotics to prevent diseases of the digestive system. Here, we present the genomic analysis and characterization of Enterococcus sp. SB12 isolated from Carpathian cheese. Whole-genome sequencing and analysis revealed that the genome of strain SB12 is represented by one circular chromosome and two circular plasmids, with a total size of 2.69 Mb. Phylogenetic analysis positioned Enterococcus sp. SB12 within a clade of Enterococcus strains with recognized probiotic potential. The genome analysis identified several antibiotic resistance genes (AAC(6')-Ii, vanY in vanB cluster, efrA, eatAv). Several virulence factors were also identified in the genome; however, none of them were major virulence factors typically found in clinical E. faecium strains. In addition, we identified clusters of genes for the synthesis of bacteriocins: enterocin A, enterocin SE-K4, enterocin P, enterolysin A, and enterocin L50. The Enterococcus sp. SB12 strain showed a limited capacity for tyrosine decarboxylation. Notably, this strain also showed resistance to high temperatures, salinity, lysozyme and low pH.