الفهرس 
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Abstract
The human microbiota has a vital function within the human body; more efforts should be made to cultivate, investigate, and analyze the genomes of bacteria with potential health benefits.
Enterococcus spp. are a long-standing and non-pathogenic commensal bacterium, representing an important part of the normal. They provide a beneficial effect on humans, such as the bio preservation of food, especially by means of bacteriocin production (anti-microbial agents).
Whole-genome sequencing has been a revolutionary force that has transformed the life sciences and public health microbiology. Microgenomics represents a novel boundary in microbiology related to public health, requiring a significant amount of development and confirmatory studies. Bacterial genome-based research is gaining attention for public health issues, but optimal approaches to bioinformatics and data analysis are still under development. This study illustrates the benefits of introducing microbial genomics into public health microbiology.
This study aimed to isolate and investigate two Enterococcus spp. from an Egyptian adult’s healthy oral cavity. This study evaluated the security of our strains by using whole-genome sequencing (WGS), physicochemical features, beneficial probiotic properties, and antimicrobial activity.
The first isolated bacterium NT04 using 16S rRNA gene sequencing, was identified as Enterococcus faecium NT04 and the second strain NT21 as Enterococcus durans NT21.
Enterococcus faecium represents a commensal microbiota in the gastrointestinal tract and oral cavity of humans and animals. In this study, the whole genome of E. faecium NT04 was sequenced and annotated by bioinformatics tools to identify the bacteriocin genes, virulence genes, antibiotic resistance genes, Crisper-Cas and pathogenicity islands. Whole genomic sequencing (WGS) confirmed the existence of genes encoding for the production of bacteriocin such (enterocin A and B) and a putative bacteriocin immunity gene (entl). No pathogenicity islands and only one CRISPR area was recognized. Enterococcus faecium NT04 lacks plasmids and has a smaller genome than other virulent or non-virulent species. This strain contains two virulence factors associated with collagen binding adhesion (acm) and endocarditis antigen protein (efaAfm gene). The strain NT04 showed antibiotic resistance to tetracycline, aminoglycosides, and streptogramin B, but no genetic evidence for resistance to quinolones or vancomycin. Genomics investigation of strain E. faecium NT04 revealed the presence of diverse genes encoding for cofactors, antioxidants (Glutathione), vitamins (folate biosynthesis).
Enterococcus durans is a rarely isolated species from animals and humans, and it was a tiny constituent of human oral cavity and animal intestinal flora, as well as animal-derived foods, particularly dairy products. The complete genomic of our strain Enterococcus durans NT21was sequenced and analyzed by using several bioinformatics tools to identify bacteriocin genes, virulence genes, antibiotic resistance genes, Crispr-Cas and pathogenicity islands. The results showed that our strain NT21 lacks the presence of virulence genes, pathogenicity islands, plasmids and has only two antibiotic resistance genes. On the other hand, it produces three bacteriocin-like inhibitory substances (Enterolysin A, P and L50a). It has six gene-encoded Crisper-Cas and one cluster Crispr-Cas gene. According to our findings, E. durans NT21 is a possible probiotic strain that is safe for both human and animal use. The strain has the ability to produce sereval metabolities that play a vital and useful role as biosynthesis of proteins (Histidine, tyrosine, phenylalanine, and tryptophan metabolism), antioxidant (selenocompound metabolism) and source of energy (fatty acid degradation).