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

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

doi:10.1186/s12866-020-01980-8

Abstract

BackgroundWhole-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.ResultsThe 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.ConclusionData 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.

Highlights

Whole-genome sequencing using high throughput technologies has revolutionized and speeded up the scientific investigation of bacterial genetics, biochemistry, and molecular biology
The Genomic annotations illustrated a total number of 2884 genes, corresponding to 2834 coding sequences (CDSs) and 50 RNAs with single predicted copies of the 16S, 23S, and 5S rRNA genes and 47 predicted tRNAs (Fig. 1)
Genes associated with carbohydrate transport and metabolism (294 Open Reading Frames (ORFs)), translation (206 ORFs), and transcription (205 ORFs) were ranked among the most abundant Clusters of Orthologous Groups (COGs) functional categories

Summary

Introduction

Whole-genome sequencing using high throughput technologies has revolutionized and speeded up the scientific investigation of bacterial genetics, biochemistry, and molecular biology. This study investigated the whole genome sequences of the Enterococcus faecium strain (HG937697), isolated from the mucus of freshwater fish in Tunisian dams. Probiotic LABs are widely used, as an alternative to antibiotics uses, to prevent animal and human bacterial infections [3]. Enterococcus is a LABs large genus, ubiquitous, having the capacity to adapt challenging environments. Such species are isolated from different habitats including water (i.e. waste, freshwater, and seawater), soil, plants, and the digestive tract of warm-blooded animals and/or humans [4]. Several studies have demonstrated Enterococcus faecium beneficial effects as probiotic in humans, animals, and aquatic culture [5,6,7,8,9,10]

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Conclusion