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. 2023 May 24;9(6):e16253.
doi: 10.1016/j.heliyon.2023.e16253. eCollection 2023 Jun.

Genome sequencing of Enterococcus faecium NT04, an oral microbiota revealed the production of enterocin A/B active against oral pathogens

Nashwa Tarek  1   2 , Ahmed F Azmy  3 , Ahmed S Khairalla  3   4 , Medhat Abdel-Fattah  1 , Ohoud A Jefri  5 , Mohamed Shaban  6   7 , Abdelaziz A A El-Sayed  8   9 , Ahmed O El-Gendy  3
Affiliations

Genome sequencing of Enterococcus faecium NT04, an oral microbiota revealed the production of enterocin A/B active against oral pathogens

Nashwa Tarek et al. Heliyon. .

Abstract

Objective: This study aimed to isolate and investigate a bacterium from an Egyptian adult's healthy oral cavity, focusing on its probiotic properties, especially its antagonistic activity against oral pathogens.

Methods: The isolated bacterium NT04 using 16S rRNA gene sequencing, was identified as Enterococcus faecium. In this study, the whole genome of Enterococcus faecium NT04 was sequenced and annotated by bioinformatics analysis tools.

Results: Numerous genes encoding the production of diverse metabolic and probiotic properties, such as bacteriocin-like inhibitory substances (Enterocin A and B), cofactors, antioxidants, and vitamins, were confirmed by genomic analysis. There were no pathogenicity islands or plasmid insertions found. This strain is virulent for host colonization rather than invasion.

Conclusion: Genomic characteristics of strain NT04 support its potentiality as an anti-oral pathogen probiotic candidate.

Keywords: Enterococcus faecium; Oral cavity; Probiotics; WGS.

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Conflict of interest statement

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Figures

Fig. 1
Fig. 1
Graphical abstract showing the overall aim and steps followed in this study.
Fig. 2
Fig. 2
Results for the experiments conducted for the characterization of physicochemical properties of E. faecium NT04. This study showed the stability of bacteriocin NT21 against different conditions of hydrolytic enzymes (RNAase enzyme, proteinase enzyme, α-chymotrypsin enzyme, and amylase enzyme), PH (acidic media 3 and alkaline media 9), temperature (heating to 55 °C, 80 °C, 100 °C, and 121 °C) and DTT. Staphylococcus aureus ATCC 25923 (MRSA) was used as a control. The percentage of activity was calculated (% activity = inhibition zone of the treated sample/inhibition zone of the control sample × 100).
Fig. 3
Fig. 3
Summary of annotation for E. faecium NT04 based on RAST subsystem.
Fig. 4
Fig. 4
Phylogenetic tree developed based on investigation of single-nucleotide polymorphisms (SNPs) of the center gene of the examined strain, with intently associated taxa primarily based on 16S rRNA gene sequences. The phylogenetic trees have constructed the usage of the neighbor-joining approach.
Fig. 5
Fig. 5
Genome atlas of strain NT04. The atlas shows a circular view of the complete DNA genome sequence of Enterococcus faecium NT04. This circle was constructed by using a server CG viewer. The innermost circle 1 and circle 6 show CDS’s (dark blue). Circle 2 shows GC content (black), circle 3 shows GC skew+ (green) and GC skew−(violet), and circle 4 represents contigs.
Fig. 6
Fig. 6
a) Bacteriocin Gene clusters of enterocin A and alignment of the DNA sequences containing the genetic determinants for enterocin A; b) Bacteriocin Gene cluster of enterocin B and alignment of the DNA sequences comprising the enterocin B genetic determinants.
See this image and copyright information in PMC

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