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High-quality genome sequence assembly of R.A73 Enterococcus faecium isolated from freshwater fish mucus
BMC Microbiology ( IF 4.2 ) Pub Date : 2020-10-23 , DOI: 10.1186/s12866-020-01980-8
Rim El Jeni 1, 2 , Kais Ghedira 3 , Monia El Bour 1 , Sonia Abdelhak 4 , Alia Benkahla 3 , Balkiss Bouhaouala-Zahar 2, 5
Affiliation  

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. 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. 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.

中文翻译:

从淡水鱼粘液中分离出的 R.A73 屎肠球菌的高质量基因组序列组装

使用高通量技术的全基因组测序彻底改变并加速了细菌遗传学、生物化学和分子生物学的科学研究。乳酸菌 (LAB) 已广泛用于发酵,最近还被用作促进健康的食品中的益生菌。LABs 品种的基因组测序和功能基因组学研究提供了有关其多样性和进化的快速而重要的信息,揭示了重要的分子基础。本研究调查了从突尼斯水坝淡水鱼的粘液中分离出来的屎肠球菌菌株 (HG937697) 的全基因组序列。使用 Quick-GDNA 试剂盒提取基因组 DNA,并使用 Illumina HiSeq2500 系统进行测序。使用 FastQC 软件进行序列质量评估。使用子系统技术 (RAST) 网络服务器和 NCBI PGAAP 使用快速注释进行完整的基因组注释。屎肠球菌 R.A73 组装成 28 个重叠群,由 2,935,283 bps 组成。基因组注释共显示2884个基因,包括2834个编码序列和50个RNA,其中包含3个rRNA(1个rRNA 16 s、1个rRNA 23 s和1个rRNA 5 s)和47个tRNA。在屎肠球菌 R.A73 菌株中鉴定出 22 个与细菌素产生有关的基因。获得的数据为进一步研究在工业制造过程中测试这种屎肠球菌 R.A73 菌株的有效策略提供了见解。用生物信息学工具研究它们的代谢代表了未来的挑战和对提高食品中多用途细菌利用的贡献。
更新日期:2020-10-26
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