High-Quality Genome Sequence Assembly of R.A73 Enterococcus faecium Isolated from Freshwater fish mucus
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 2,884 genes in total including 2,834 coding sequences and 50 RNAs containing 3 rRNAs (one rRNA 16s, one rRNA 23s and one rRNA 5s) 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.
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This is a list of supplementary files associated with this preprint. Click to download.
Table S1 The DDH probabilities to distinguish between R.A73 strain and reference strains that belonged to the similar Enterococcus genus
Table S2 The Blastp output results between R.A73 protein sequences and BACTIBASE (a database dedicated to bacteriocins) protein sequences
Posted 18 Sep, 2020
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High-Quality Genome Sequence Assembly of R.A73 Enterococcus faecium Isolated from Freshwater fish mucus
Posted 18 Sep, 2020
On 23 Oct, 2020
On 17 Sep, 2020
On 17 Sep, 2020
On 08 Sep, 2020
On 03 Aug, 2020
On 02 Aug, 2020
On 02 Aug, 2020
On 03 Jul, 2020
Received 02 Jul, 2020
Received 01 Jul, 2020
Received 22 Jun, 2020
On 16 Jun, 2020
On 10 Jun, 2020
Invitations sent on 10 Jun, 2020
On 10 Jun, 2020
On 10 Jun, 2020
On 09 Jun, 2020
On 09 Jun, 2020
On 11 May, 2020
On 05 May, 2020
On 04 May, 2020
On 04 May, 2020
On 04 May, 2020
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 2,884 genes in total including 2,834 coding sequences and 50 RNAs containing 3 rRNAs (one rRNA 16s, one rRNA 23s and one rRNA 5s) 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.
Figure 1
Figure 2
Figure 3
Figure 4