Genomic insights into Brevibacterium sediminis strain IMA_C3 isolated from an integrated mangrove aquaculture pond
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Brevibacterium sediminis strain IMA_C3, a Gram-positive bacterium, was isolated from an integrated mangrove aquaculture pond near the Sundarbans mangrove. The bacterium was isolated from mangrove leaf litter and grown on Luria-Bertani medium at a salinity of 20. Phylogenetic analysis based on 16S rRNA sequencing showed a 99.67% identity with Brevibacterium linens AE038-8 from the International Nucleotide Sequence Database Collaboration DNA databases (GenBank/DDBJ/ENA). Whole-genome sequencing was carried out using long-read sequencing on the Oxford Nanopore MinION platform, with genome annotation performed against the NCBI Reference Sequence Database and The Genome Taxonomy Database databases. The genome is ~4.1 Mb in size, with a G+C content of 64.59 mol%. Functional analysis of the genome revealed genes related to complex carbon utilization, nitrogen and phosphate metabolism and metal transport. Additionally, the genome encodes secondary metabolites, including ε-poly- l -lysine, ectoine, terpene and phenazine, which could have potential applications in controlling viral infections in indigenous shrimp populations within integrated mangrove aquaculture systems.
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I am pleased to tell you that your article has now been accepted for publication in Access Microbiology. Thank you for your revisions and responses (reduction in the strength of claims, inclusion of supporting metrics of rigor) to reviewers. Reviewer comments broadly have been addressed and those remaining revolve around novelty (which isn't a restricting issue with ACMI) adding additional metrics for analysis which, while beneficial, I would not agree are necessary for publication (i.e. core analysis is sufficient for a genome announcement/short communication).
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Comments to Author
The authors have resubmitted their manuscript after revision in response to reviewer comments. While some improvements are evident, several major concerns remain unresolved, and the changes made are not yet sufficient to support acceptance. Below is a point-wise critical evaluation of the rebuttal and revisions. 1. The authors have added ANI and dDDH values to support their claim of novelty. However, the reported values are still above the established thresholds used for defining new species. Since 16S rRNA identity with known Brevibacterium strains remains above 99%, novelty is not convincingly demonstrated. Without significantly lower ANI (
Please rate the manuscript for methodological rigour
Satisfactory
Please rate the quality of the presentation and structure of the …
Comments to Author
The authors have resubmitted their manuscript after revision in response to reviewer comments. While some improvements are evident, several major concerns remain unresolved, and the changes made are not yet sufficient to support acceptance. Below is a point-wise critical evaluation of the rebuttal and revisions. 1. The authors have added ANI and dDDH values to support their claim of novelty. However, the reported values are still above the established thresholds used for defining new species. Since 16S rRNA identity with known Brevibacterium strains remains above 99%, novelty is not convincingly demonstrated. Without significantly lower ANI (
Please rate the manuscript for methodological rigour
Satisfactory
Please rate the quality of the presentation and structure of the manuscript
Satisfactory
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
Authors have revised their manuscript in view of the comments raised by the reviewers. The revised manuscript may now be accepted for publication.
Please rate the manuscript for methodological rigour
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?
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 …
Comments to Author
Authors have revised their manuscript in view of the comments raised by the reviewers. The revised manuscript may now be accepted for publication.
Please rate the manuscript for methodological rigour
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?
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?
No: Not applicable
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Dear Dr Bhadury, Following reviews, reviewer 2 has highlighted more specific concerns building on their initial comments so i have once again selected major revisions. With the similarity to B. sediminis highlighted in table 2, it is important to clarify and specify justification as a new species or reframe the manuscript. I would discourage "potentially" here without further evidence and in general, consider including a distinct discussion section (rather than results) to offer claims for applications with limited data. Please address the reviewers comments. Best wishes, John.
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Comments to Author
The manuscript describes the genome of Brevibacterium sp. IMA_C3 isolated from mangrove litter. While sequencing and annotation are competently done, the work lacks robust taxonomic novelty, experimental validation of predicted functions, and clear presentation. Substantial revisions are needed before it can be considered for publication. 1. The major disappointing aspect is the unproven Novelty and Taxonomic Validation. 16S rRNA similarity (>99%) to known B. linens and close relatives, and incomplete reporting of ANI/AAI/dDDH metrics, do not support designation as a novel species. Authors must present clear ANI (≤95%), AAI, and digital DNA-DNA hybridization (70% and full strain names. They should enhance Table 1 with additional metrics (e.g., N's, coverage depth). 6. There are also issue with …
Comments to Author
The manuscript describes the genome of Brevibacterium sp. IMA_C3 isolated from mangrove litter. While sequencing and annotation are competently done, the work lacks robust taxonomic novelty, experimental validation of predicted functions, and clear presentation. Substantial revisions are needed before it can be considered for publication. 1. The major disappointing aspect is the unproven Novelty and Taxonomic Validation. 16S rRNA similarity (>99%) to known B. linens and close relatives, and incomplete reporting of ANI/AAI/dDDH metrics, do not support designation as a novel species. Authors must present clear ANI (≤95%), AAI, and digital DNA-DNA hybridization (70% and full strain names. They should enhance Table 1 with additional metrics (e.g., N's, coverage depth). 6. There are also issue with manuscript Organization, Style, and Language. The text is verbose, repetitive, and contains grammatical errors. Abstract and Discussion contain unsubstantiated claims. References are inconsistently formatted. Authors should thoroughly edit for clarity and brevity—use active voice, remove redundancy, and ensure each paragraph has a clear focus. In Abstract, please limit claims to data-supported findings. Standardize references with journal guidelines and include DOIs. 7. Typos (e.g., "Avicennia offcinalis" → officinalis). 8. Inconsistent citations (e.g., "James et al. 2023" without full reference). 9. Use of "high-quality genome" without explicit criteria (refer to MISAG/MIMAG standards). 10. Mislabeling RGI "loose hits" as confirmed resistance genes—clarify their predictive status. 11. Data-availability statement should include BioProject, BioSample, and SRA accession numbers.
Please rate the manuscript for methodological rigour
Satisfactory
Please rate the quality of the presentation and structure of the manuscript
Poor
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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Dear Dr Bhadury, Thank you for your submission. Following reviews i have selected major revision. Taking specific note of Reviewer 2's comments, while some are subjective suggestions for improvements there are comments with merit as methodological rigor. Please address their concerns where possible. While novelty is not an essential criteria fro ACMI, i would note that in cases where there has potentially been an over reach in the conclusions drawn (or at least from the in text content), stating clearly limitations of the analysis/data is an acceptable compromise. Also, in regards to species identification, reviewer 2's comments in either using a larger number of Brevibacterium species or rationalising why these were used specifically would be valuable. Please do not hesitate to be in contact with any questions. Best wishes, John
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Comments to Author
The manuscript describes the genome of a Brevibacterium sp. strain IMA_C3 isolated from a mangrove aquaculture pond and presents extensive genomic analyses including assembly, annotation, phylogeny, and predictions on functional gene clusters. While the study has potential and contains a wealth of technical data, there remain significant concerns regarding clarity, experimental rationale, and contextual interpretation that require major revisions before the work could be considered for publication. * The overall novelty of the study is not convincingly demonstrated. Although the 16S rRNA analysis shows high identity (around 99%) with known Brevibacterium strains, the manuscript does not clearly justify the claim of "potentially novel species." The criteria for species delineation need to be more …
Comments to Author
The manuscript describes the genome of a Brevibacterium sp. strain IMA_C3 isolated from a mangrove aquaculture pond and presents extensive genomic analyses including assembly, annotation, phylogeny, and predictions on functional gene clusters. While the study has potential and contains a wealth of technical data, there remain significant concerns regarding clarity, experimental rationale, and contextual interpretation that require major revisions before the work could be considered for publication. * The overall novelty of the study is not convincingly demonstrated. Although the 16S rRNA analysis shows high identity (around 99%) with known Brevibacterium strains, the manuscript does not clearly justify the claim of "potentially novel species." The criteria for species delineation need to be more rigorously discussed using genomic metrics (e.g. ANI thresholds, digital DDH) and compared against a broader dataset. * The rationale behind isolating the bacterium from an integrated mangrove aquaculture pond and linking its genomic features to potential applications (e.g. control of white spot syndrome virus) is speculative. There is insufficient experimental evidence or validation to support the claim that the biosynthetic potential (e.g. ε-Poly-L-lysine, ectoine, terpene, phenazine clusters) translates into bio-control activity. * The methods section, although detailed in many aspects, suffers from lack of clarity in several points. For instance, the description "grown on Luria-Bertani medium of salinity 20" is ambiguous—details of the salinity conditions (e.g. units, rationale for use) need to be explicitly provided. Similarly, the isolation protocol would benefit from clearer justification of each step and discussion of controls or replicates. * In the phylogenetic analysis, while the authors have used standard tools, the dataset seems limited. The manuscript would be strengthened by incorporating a more comprehensive phylogenetic comparison with a larger number of closely related Brevibacterium species. Moreover, the interpretation of the evolutionary relationships and the robustness of the tree topology are not fully discussed. * The analysis of secondary metabolite biosynthetic gene clusters is only superficially addressed. There is a need for a deeper discussion on the predicted products, their novelty, and how they might function in the ecological niche. Experimental or in silico validation of these predictions (e.g. comparison with known clusters) would enhance the impact of the study. * There are several language issues and inconsistencies in the manuscript. Numerous grammatical errors, awkward phrasing (e.g. in the abstract and methods sections), and occasional typographical mistakes reduce the clarity of the presentation. The authors should seek thorough language editing to improve readability. * The manuscript's structure could be improved. For instance, while the methods are exhaustive, there is no dedicated conclusion section to succinctly summarize the findings, implications, and future directions. Additionally, the reference formatting shows inconsistencies that need to be standardized according to the journal's guidelines. * The figures and tables are informative but lack adequate description in the text. The legends and in-text references should be expanded to explain the significance of the data presented, and higher resolution images may be required for clear visualization. * Minor technical details, such as the reporting of genome statistics and assembly metrics, while acceptable, would benefit from a brief discussion on quality control benchmarks (e.g. comparison with standards from Bowers et al.) to contextualize the completeness and quality of the assembly.
Please rate the manuscript for methodological rigour
Satisfactory
Please rate the quality of the presentation and structure of the manuscript
Poor
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?
No: Not applicable
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Comments to Author
The study conducted by Yash et al. entitled Genome description of a potentially novel species of Brevibacterium sp. strain IMA_C3 isolated from an integrated mangrove aquaculture pond describes isolation and sequencing of a new species of Brevibacterium genus. I have few queries regarding manuscript therefore, I suggest following revision: Specific points: 1. Grammatical correction is required in line no 63-65. 2. The hypothesis for conducting the isolation and sequencing study is missing and should be added at the end of introduction section. 3. As mentioned in line no 79 the washed leaf extract was used as inoculum and in LB plates numerous colonies could be observed but on which basis this particular isolate/strain has been selected for going in depth sequencing study and the others were …
Comments to Author
The study conducted by Yash et al. entitled Genome description of a potentially novel species of Brevibacterium sp. strain IMA_C3 isolated from an integrated mangrove aquaculture pond describes isolation and sequencing of a new species of Brevibacterium genus. I have few queries regarding manuscript therefore, I suggest following revision: Specific points: 1. Grammatical correction is required in line no 63-65. 2. The hypothesis for conducting the isolation and sequencing study is missing and should be added at the end of introduction section. 3. As mentioned in line no 79 the washed leaf extract was used as inoculum and in LB plates numerous colonies could be observed but on which basis this particular isolate/strain has been selected for going in depth sequencing study and the others were overlooked is not mentioned in the manuscript. Justification for using this isolate should be incorporated. 4. How this isolate could be useful against white spot syndrome virus (WSSV) shrimps should be addressed more precisely.
Please rate the manuscript for methodological rigour
Satisfactory
Please rate the quality of the presentation and structure of the manuscript
Satisfactory
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
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