Genomic insights into probiotic functionality of Enterococcus hirae 3K isolated from Egyptian coastal sediments with special reference to exopolysaccharide production and antimicrobial activity potential

Abstract

Marine lactic acid bacteria (LAB) are beneficial microbes that play a vital role in maintaining aquatic ecosystems and have significant potential for developing innovative products. Notably, marine LAB represent promising probiotic candidates due to their high efficacy and adaptability. In this study, strain 3K was isolated from coastal sediments in Egypt. Phenotypically, isolate 3K strain was susceptible to most antibiotics assessed, exhibited tolerance to low pH and high bile salts conditions, and revealed the absence of hemolytic activity. Furthermore, whole genome sequencing (WGS) was conducted using the Illumina NovaSeq 6000 platform with 60X coverage to assess the genomic probiotic attributes of marine strain 3K. In addition, the genome size of the Enterococcus hirae 3K strain was 2.91 Mb, with a G + C content of 36.65%. Genomic analysis confirmed the absence of critical virulence-factor determinants in the sequenced genome. Nevertheless, vancomycin resistance determinants were not identified in the genome sequence. Genome mining identified genes encoding enterolysin A and lanthipeptide bacteriocins, signifying a broad antimicrobial potential that correlates with the observed inhibitory activity against the target microbial pathogens. Additionally, exopolysaccharide (EPS) biosynthetic clusters were also predicted in silico, indicating the capacity for EPS production. Furthermore, the comparative genomic analysis revealed 2,216 shared orthologous clusters, confirming species-level conservation. The findings of WGS and phenotypic analyses confirmed the safety, metabolic versatility, and probiotic potential of the marine E. hirae 3K. Notably, its isolation from marine sediment highlights an underexplored ecological niche, reinforcing its potential as a health-promoting probiotic candidate with distinct biotechnological relevance for sustainable aquaculture applications.