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High-Quality Genome Sequence Assembly of R.A73 Enterococcus faecium Isolated from Freshwater fish mucus
Balkiss Bouhaouala-Zahar
Institut Pasteur de Tunis
Corresponding Author
ORCiD: https://orcid.org/0000-0003-3147-245X
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at BMC Microbiology.
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.
Keywords
Enterococcus faecium, Bacteriocin, Freshwater fish, Lactic acid bacteria, Whole-genome sequencing.
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This is a list of supplementary files associated with this preprint. Click to download.
- TableS1.xlsx
Table S1 The DDH probabilities to distinguish between R.A73 strain and reference strains that belonged to the similar Enterococcus genus
- TableS2.xlsx
Table S2 The Blastp output results between R.A73 protein sequences and BACTIBASE (a database dedicated to bacteriocins) protein sequences
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Received 02 Jul, 2020
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On 16 Jun, 2020
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This preprint is under consideration at BMC Microbiology. A preprint is a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
High-Quality Genome Sequence Assembly of R.A73 Enterococcus faecium Isolated from Freshwater fish mucus
Balkiss Bouhaouala-Zahar
Institut Pasteur de Tunis
Corresponding Author
ORCiD: https://orcid.org/0000-0003-3147-245X
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Published
Version 4
Posted 18 Sep, 2020
Published
On 23 Oct, 2020
No community comments so far
Submission checks complete
On 17 Sep, 2020
Editorial decision: Accept
On 17 Sep, 2020
No comments provided
Editorial decision: Minor revision
On 08 Sep, 2020
Editor assigned
On 03 Aug, 2020
Submission checks complete
On 02 Aug, 2020
Editor invited
On 02 Aug, 2020
No comments provided
Editorial decision: Major revision
On 03 Jul, 2020
Review #3 received
Received 02 Jul, 2020
Review #2 received
Received 01 Jul, 2020
Review #1 received
Received 22 Jun, 2020
Reviewer #3 agreed
On 16 Jun, 2020
Editor assigned
On 10 Jun, 2020
Reviewers invited
Invitations sent on 10 Jun, 2020
Reviewer #1 agreed
On 10 Jun, 2020
Reviewer #2 agreed
On 10 Jun, 2020
Submission checks complete
On 09 Jun, 2020
Editor invited
On 09 Jun, 2020
No comments provided
Editorial decision: Revise before sending to peer reviewers
On 11 May, 2020
Editor assigned
On 05 May, 2020
First submitted
On 04 May, 2020
Submission checks complete
On 04 May, 2020
Editor invited
On 04 May, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at BMC Microbiology.
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