Abstract
BackgroundEnterococcus faecium though commensal in the human gut, few strains provide a beneficial effect to humans as probiotics while few are responsible for the nosocomial infection. Comparative genomics of E. faecium can decipher the genomic differences responsible for probiotic, pathogenic and non-pathogenic properties. In this study, we compared E. faecium strain 17OM39 with a marketed probiotic, non-pathogenic non-probiotic (NPNP) and pathogenic strains.ResultsE. faecium 17OM39 was found to be closely related with marketed probiotic strain T110 based on core genome analysis. Strain 17OM39 was devoid of known vancomycin, tetracycline resistance and functional virulence genes. Moreover, E. faecium 17OM39 genome was found to be more stable due to the absence of frequently found transposable elements. Genes imparting beneficial functional properties were observed to be present in marketed probiotic T110 and 17OM39 strains. Genes associated with colonization and survival within gastrointestinal tract was also detected across all the strains.ConclusionsBeyond shared genetic features; this study particularly identified genes that are responsible for imparting probiotic, non-pathogenic and pathogenic features to the strains of E. faecium. Higher genomic stability, absence of known virulence factors and antibiotic resistance genes and close genomic relatedness with marketed probiotics makes E. faecium 17OM39 a potential probiotic candidate. The work presented here demonstrates that comparative genome analyses can be applied to large numbers of genomes, to find potential probiotic candidates.
Highlights
Enterococcus faecium though commensal in the human gut, few strains provide a beneficial effect to humans as probiotics while few are responsible for the nosocomial infection
Strain selection Whole genome sequences were downloaded from NCBI genome database, and the strains were grouped into probiotic, non-pathogenic non-probiotic (NPNP) and pathogenic based on the literature survey (Table 1)
The study was carried out on 10 strains, and these strains were grouped into probiotic, non-pathogenic non-probiotic (NPNP) and pathogenic based on the literature survey (Table 1)
Summary
Enterococcus faecium though commensal in the human gut, few strains provide a beneficial effect to humans as probiotics while few are responsible for the nosocomial infection. Comparative genomics of E. faecium can decipher the genomic differences responsible for probiotic, pathogenic and non-pathogenic properties. Along with conferring health benefits the organism should have or lack series of properties. In the Mediterranean region, Enterococcus spp. have been used in the preparation of various meat and fermented milk products for centuries [5]. They exhibit the beneficial property of bacteriocin production [5, 7] presenting activity against potential pathogens viz. They exhibit the beneficial property of bacteriocin production [5, 7] presenting activity against potential pathogens viz. group D streptococci and Listeria in various foods and GIT [7]
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