High-quality genome sequence assembly of R.A73 Enterococcus faecium isolated from freshwater fish mucus
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RESEARCH ARTICLE
Open Access
High-quality genome sequence assembly of R.A73 Enterococcus faecium isolated from freshwater fish mucus Rim El Jeni1,2†, Kais Ghedira3†, Monia El Bour1, Sonia Abdelhak4, Alia Benkahla3 and Balkiss Bouhaouala-Zahar2,5*
Abstract 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. Keywords: Enterococcus faecium, Bacteriocin, Freshwater fish, Lactic acid bacteria, Whole-genome sequencing
* Correspondence: [email protected]; [email protected] † Rim El Jeni and Kais Ghedira contributed equally to this work. 2 Laboratory of Venoms and Therapeutic Molecules, Pasteur Institute of Tunis, Tunis, Tunisia 5 Medical School of Tunis, University of Tunis El Manar, 1007 Tunis, Tunisia Full list of author information is available at the end of the article © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included
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