Journal Article

High-quality genome sequence assembly of R.A73 Enterococcus faecium isolated from freshwater fish mucus

Ghedira, Kais, El Bour, Monia, Bouhaouala-Zahar, Balkiss, El Jeni, Rim, Abdelhak, Sonia, Benkahla, Alia

2020

Overview

Background Whole-genome sequencing using high throughput technologies has revolutionized and speeded up the scientific investigation of bacterial genetics, biochemistry, and molecular biology. Lactic acid bacteria (LABs) have been extensively used in fermentation and more recently as probiotics in food products that promote health. Genome sequencing and functional genomics investigations of LABs varieties provide rapid and important information about their diversity and their evolution, revealing a significant molecular basis. This study investigated the whole genome sequences of the Enterococcus faecium strain (HG937697), isolated from the mucus of freshwater fish in Tunisian dams. Genomic DNA was extracted using the Quick-GDNA kit and sequenced using the Illumina HiSeq2500 system. Sequences quality assessment was performed using FastQC software. The complete genome annotation was carried out with the Rapid Annotation using Subsystem Technology (RAST) web server then NCBI PGAAP. Results The Enterococcus faecium R.A73 assembled in 28 contigs consisting of 2,935,283 bps. The genome annotation revealed 2884 genes in total including 2834 coding sequences and 50 RNAs containing 3 rRNAs (one rRNA 16 s, one rRNA 23 s and one rRNA 5 s) and 47 tRNAs. Twenty-two genes implicated in bacteriocin production are identified within the Enterococcus faecium R.A73 strain. Conclusion Data obtained provide insights to further investigate the effective strategy for testing this Enterococcus faecium R.A73 strain in the industrial manufacturing process. Studying their metabolism with bioinformatics tools represents the future challenge and contribution to improving the utilization of the multi-purpose bacteria in food.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Amino acids / Animals / Annotations / Antibiotics / Antimicrobial agents / Bacteria / Bacterial Infections - veterinary / Bacteriocin / Bacteriocins / Bacteriocins - genetics / Bioinformatics / Biological Microscopy / Biomedical and Life Sciences / Carbohydrates / Comparative analysis / Deoxyribonucleic acid / DNA / DNA sequencing / Drug resistance / Enterococcus faecium / Enterococcus faecium - genetics / Fermentation / Fish / Fishes / Fishes - microbiology / Food / Fresh Water / Freshwater fish / Gene sequencing / Genes / Genetics / Genome, Bacterial / Genomes / Genomics / genomics and proteomics / Health promotion / High-Throughput Nucleotide Sequencing / Lactic acid / Lactic acid bacteria / Lactobacillales - genetics / Life Sciences / Manufacturing industry / Metabolism / Microbial genetics / Microbiology / Molecular biology / Mucus / Mycology / Nucleotide sequence / Parasitology / Peptides / Phylogeny / Probiotics / Proteins / Quality assessment / Quality control / Research Article / RNA / rRNA / Subsystems / Virology / Virulence / Whole Genome Sequencing