Draft genome sequence of Flavobacterium aquidurense strain, isolated from untreated wastewater

  1. Alexander D. H. Kingdon
  2. Kara D’Arcy
  3. Anya Breen
  4. Claudia McKeown
  5. Ellie Allman
  6. Priyanka Sharma
  7. Amy McLeman
  8. Adam P. Roberts

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Abstract

Here, we report the draft 5.8 Mb genome sequence of a Flavobacterium aquidurense isolate from untreated wastewater in Liverpool, UK. The reported isolate has the potential to produce both flexirubin and β-carotene, and contains an additional biosynthetic gene cluster for a putative novel beta-lactone. The genome also contains a gene for a putative beta-lactamase blaJOHN-1 analogue and putative novel insertion sequences of the IS3 family.

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  1. Access Microbiology

    Comments to Author

    Title: Draft genome sequence of Flavobacterium aquidurense strain, isolated from untreated wastewater The authors have presented draft genome sequence of Flavobacterium aquidurense strain, isolated from untreated wastewater, which is a valuable genomic resource for the scientific community. The genome announcement is clearly presented, and data is accessible. I have some specific comments with the line numbers listed below. Comments: * Line No. 34-35: What was the culture volume used? The OD600 value of 9.0 seems quite high and may not present mid-log phase. Also rephrase the sentence 'OD600 equivalent to 9.0 was pelleted' * Line No. 38: how many microliters of proteinase K and SDS were used? * I suggest authors to report the quality of the sequenced genome and genome assembly completeness. * Mention genome accession numbers of Flavobacterium frigidimaris DSM15937 and Flavobacterium aquidurense DSM18293 used for ANI analysis. * Although the authors referenced the ANI paper, I would suggest specifying the version of ANI calculator used? If a web server was used instead of the standalone version, please include the URL of the website. * Line No. 60-61: Is the spread of the genes across the genome not due to contig breaks? Were the genes identified located in the middle of the contig sequences rather than at the ends? * I suggest that the authors add one or two sentences in the abstract or at the end of the manuscript to highlight the significance of the genome announcement. In addition to reporting the presence of biosynthetic gene clusters, novel beta-lactone and insertion sequence, it would be helpful to briefly mention the implication of these findings. * While not required, dividing the manuscript into sections such as Introduction, Methods, and Genome Description would make it more organized and easier for readers to follow. Additionally, for line No. 56-60: consider presenting this information in a table format, listing reported genes from the literature along with their locus tags and observed similarities. Minor comments: * Line No. 22: "genome sequence of a Flavobacterium spp." Rephrase it to "an isolate belonging to Flavobacterium spp." or "genome sequence of a Flavobacterium spp. Isolate" * Line No. 46: correct 'Prokaryotic Annotation Pipeline' to 'Prokaryotic Genome Annotation Pipeline' * Line No. 47 correct sp to spp. * Line No. 49: correct 436,906 to 436,906 bp ? * Line No. 54: Mention URL and version used. * Line No. 58: 'β-carotene production may also occur' rephrase the sentence.

    Please rate the manuscript for methodological rigour

    Good

    Please rate the quality of the presentation and structure of the manuscript

    Good

    To what extent are the conclusions supported by the data?

    Strongly support

    Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?

    No

    Is there a potential financial or other conflict of interest between yourself and the author(s)?

    No

    If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?

    Yes

  2. Access Microbiology

    Thank you for submitting your paper to Access Microbiology. It has now been reviewed and I would like you to revise the paper in line with the reviewers' reports and any Editorial Office requirements below.

  3. Access Microbiology

    Comments to Author

    Kingdon and colleagues report a draft genome sequence of a Flavobacterium aquidurense strain, isolated from untreated wastewater. A have a few short comments to improve the value of this resource announcement. -Line 29-31: how as the taxonomic identification made? (e.g., BLASTn? Which database?) -I would recommend including a figure showing the pathways for pigment production and the genes identified in the genome that are involved in these pathways. -Line 61: why would this suggest lower levels of transcription? -Lines 61-63: I am a bit confused by this statement. How can a metabolite be "encoded"? What is meant by "no known matches". How were you able to identify this compound from the genome sequence alone?

    Please rate the manuscript for methodological rigour

    Very good

    Please rate the quality of the presentation and structure of the manuscript

    Very good

    To what extent are the conclusions supported by the data?

    Strongly support

    Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?

    No

    Is there a potential financial or other conflict of interest between yourself and the author(s)?

    No

    If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?

    Yes

  4. Version published to 10.1099/acmi.0.000976.v1 on Access Microbiology