Draft genome sequence of an Acinetobacter albensis strain, isolated from untreated wastewater in Liverpool, UK.
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We report the isolation and draft genome sequence of an Acinetobacter albensis strain C1-4G isolated from untreated wastewater from the Liverpool School of Tropical Medicine in Liverpool, UK. The 3.0 Mb genome contained several genes encoding alkane and aromatic hydrocarbon degrading enzymes, a qacJ antimicrobial resistance gene, and several mobile genetic elements including a putative transposon containing arsenic resistance genes. In addition, analysis of the biosynthetic gene clusters suggested genes were present that would allow biosynthesis of baumannoferrin, a novel cyanobactin-type natural product and a novel beta-lactone natural product.
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Thank you for submitting your manuscript to Access Microbiology. It has now been reviewed by two experts in the filed, whose comments are attched below. They both agree that the manuscript is well written and is a good contribution to the literature, however they have provided a number of minor comments that need to be addressed in a revised manuscript. Please consider changing the subheading "Method" to "Isolation and Assembly Methods" to be more in line with the information presented.
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Comments to Author
In their manuscript, D'Arcy and colleagues present a Technical Resource document that details the isolation and sequencing of a strain of Acinetobacter albensis. Furthermore, the study includes a preliminary characterisation of the genome, highlighting the presence of genes potentially involved in the degradation of aromatic hydrocarbons, as well as genes associated with resistance. The resource presented is of significant value to the community, particularly to researchers who make extensive use of genomes deposited in public databases, and the manuscript is well written. Nevertheless, the following observations could be made to further enhance the quality and clarity of the work: 1. Introduction In this format, the introduction should be concise and focused on the value of the resources generated. In this regard, it …
Comments to Author
In their manuscript, D'Arcy and colleagues present a Technical Resource document that details the isolation and sequencing of a strain of Acinetobacter albensis. Furthermore, the study includes a preliminary characterisation of the genome, highlighting the presence of genes potentially involved in the degradation of aromatic hydrocarbons, as well as genes associated with resistance. The resource presented is of significant value to the community, particularly to researchers who make extensive use of genomes deposited in public databases, and the manuscript is well written. Nevertheless, the following observations could be made to further enhance the quality and clarity of the work: 1. Introduction In this format, the introduction should be concise and focused on the value of the resources generated. In this regard, it is recommended to: (i) briefly contextualize the relevance of A. albensis (if this species has been previously described), (ii) indicate the current availability of genomes for this species and any existing limitations (e.g., absence of high-quality reference genomes), and (iii) explicitly highlight the contribution of the genome presented in this study. 2. Taxonomic assignment The use of curated databases for 16S-based taxonomic assignments, such as SILVA or equivalent alternatives, is recommended, as they generally provide greater robustness and reduced background noise in taxonomic classification. 3. Assembly strategy In order to ensure the robustness of the presented genome, it is recommended that at least two assembly strategies are compared. Although SPAdes is a widely used and robust option, it may be useful to contrast the results with those obtained using tools such as Unicycler. Furthermore, it would be important to clarify whether additional assembly curation steps were applied, such as the removal of potential duplicated regions. 4. Coverage in genomic comparisons A comparatively low level of coverage is observed in the genome comparison. It is considered unusual for genomes belonging to the same species to exhibit values below 70%, and therefore it is recommended that potential technical causes be assessed, such as the quality or completeness of the assembly. An alternative hypothesis is that the observed strains could correspond to distinct subspecies that are currently indistinguishable due to the paucity of available data. 5. Interpretation of BGC regions Figure 2 presents a comparison of biosynthetic gene clusters (BGCs) identified using AntiSMASH. It is recommended that the use of the term "core" in this context be clarified, as it may lead to confusion with the concept of the core pangenome. In the event of the term referring to genes conserved within a specific BGC, it may be preferable to use alternative terminology or explicitly define it.
Please confirm that no generative AI tools or large language models have been used to generate this peer review report or to assist with any part of the peer review process.
I confirm no generative AI tools were used in preparation of this review.
Please rate the manuscript for methodological rigour
Satisfactory
Please rate the quality of the presentation and structure of the manuscript
Good
To what extent are the conclusions supported by the data?
Partially 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
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Comments to Author
Running Title: Draft Acinetobacter albensis genome sequence Suggested: Draft genome sequence of Acinetobacter albensis from untreated wastewater Abstract: The sentence is unclear: In addition, analysis of the biosynthetic gene clusters suggested genes were present that would allow biosynthesis of baumannoferrin, a novel cyanobactin-type natural product and a novel beta-lactone natural product. Recommendation: In addition, analysis of the biosynthetic gene clusters suggested the presence of genes that could enable the biosynthesis of baumannoferrin, a novel cyanobactin-type natural product, as well as a novel beta-lactone natural product. Intro Lns 33: replace remediation for bioremediation Lns 34-36. But it has been A. albensis reported as a human pathogen? Maybe check in …
Comments to Author
Running Title: Draft Acinetobacter albensis genome sequence Suggested: Draft genome sequence of Acinetobacter albensis from untreated wastewater Abstract: The sentence is unclear: In addition, analysis of the biosynthetic gene clusters suggested genes were present that would allow biosynthesis of baumannoferrin, a novel cyanobactin-type natural product and a novel beta-lactone natural product. Recommendation: In addition, analysis of the biosynthetic gene clusters suggested the presence of genes that could enable the biosynthesis of baumannoferrin, a novel cyanobactin-type natural product, as well as a novel beta-lactone natural product. Intro Lns 33: replace remediation for bioremediation Lns 34-36. But it has been A. albensis reported as a human pathogen? Maybe check in https://www.microbiologyresearch.org/content/journal/micro/10.1099/mic.0.001269 Suggestion: Consider adding a final sentence clearly stating the aim and relevance of the work. Although it is evident that this is a genome announcement, explicitly stating the objective in the final sentence of the introduction would improve clarity. Methods Line 49: What is Azenta? Please clarify whether this refers to a sequencing service/company. The manuscript mentions the use of additional annotation tools (e.g., CARD, antiSMASH, etc.). These should be explicitly described in the Methods section, including the versions and parameters used. Line 97: Please define the abbreviation MGE at first mention (e.g., mobile genetic elements). Genome announcement: Consider adding a final concluding sentence highlighting the main relevance of the genome sequence and its potential implications. This would strengthen the closing of the manuscript and emphasize the importance of the findings.
Please confirm that no generative AI tools or large language models have been used to generate this peer review report or to assist with any part of the peer review process.
I confirm no generative AI tools were used in preparation of this review.
Please rate the manuscript for methodological rigour
Satisfactory
Please rate the quality of the presentation and structure of the manuscript
Good
To what extent are the conclusions supported by the data?
Partially 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
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Thank you very much for submitting your manuscript to Access Microbiology. Before sending manuscript to review, I have gone through it to assess it. It is an interesting work describing an Acinetobacter albensis genome. However, I would like to suggest a major revision before starting the review process, shifting the scope of the manuscript. Most Acinetobacter species grow pretty well on hydrocabons and aromatic compounds, and hence encode the cognate enzymatic machinery to use them as carbon and energy sources, so the fact that this strain encodes these enzymes does not really make this strain stand out from other Acinetobacter strains. Also the siderophores detected by AntiSMASH (baumannoferrin-like) are Acinetobacter-specific and wide-spread in this genus, thus not being a very distinctive feature of this stran compared to others. I …
Thank you very much for submitting your manuscript to Access Microbiology. Before sending manuscript to review, I have gone through it to assess it. It is an interesting work describing an Acinetobacter albensis genome. However, I would like to suggest a major revision before starting the review process, shifting the scope of the manuscript. Most Acinetobacter species grow pretty well on hydrocabons and aromatic compounds, and hence encode the cognate enzymatic machinery to use them as carbon and energy sources, so the fact that this strain encodes these enzymes does not really make this strain stand out from other Acinetobacter strains. Also the siderophores detected by AntiSMASH (baumannoferrin-like) are Acinetobacter-specific and wide-spread in this genus, thus not being a very distinctive feature of this stran compared to others. I would like to suggest that the manuscript is reworked as a more general genome announcement, with a deeper description of the genome features (summarised in a table if possible). The abovementioned features can of course be mentioned, but contextualised as usual features of the Acinetobacter genus. This change in scope would also entail potential changes in the title. Please provide a revised manuscript including the proposed changes within 60 days.
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