Characteristics of soil origin Pseudomonas batumici Koz11 isolated from a remote island in Japan
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Soil samples from a remote Japanese island (Kozushima) were processed and investigated for organisms exhibiting antimicrobial activity against pathogenic strains. A Pseudomonas strain demonstrating antimicrobial activity against Staphylococcus aureus ( S. aureus ) was identified, prompting further investigation. Whole-genome sequencing was employed to identify the species and conduct phylogenetic analysis, followed by in silico molecular analysis. Chemotaxonomic and biochemical analyses were conducted to further characterize the strain. Genomic analysis identified the strain of interest as Pseudomonas batumici ( P. batumici ), originally isolated from soil of the Black Sea coast of the Caucasus in 1980. P. batumici Koz11 is the second P. batumici strain to be isolated and identified outside its initial area of discovery. Similar to the type strain, P. batumici Koz11 showed antimicrobial activity against various S. aureus strains, including methicillin-resistant S. aureus (MRSA) and vancomycin-resistant S. aureus (VRSA). However, the previously reported ‘batumin gene cluster’, which synthesizes antimicrobial compounds, was absent from P. batumici Koz11. This study provides new insights into P. batumici . Since the type strain of P. batumici is exclusively deposited in the Ukrainian Collection of Microorganisms, the Koz11 strain may serve as a surrogate to facilitate continued study of P. batumici .
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All reviewer comments have been sufficiently addressed.
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The work presented in this manuscript is an interesting report, but merits some small revisions to clarify points and emphasize the importance of the study. Please be sure to address all reviewer comments.
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Comments to Author
The manuscript investigates a novel strain, Pseudomonas batumici Koz11, isolated from the soil of a remote Japanese island, Kozushima. The authors conduct comprehensive genomic, biochemical, and antimicrobial studies to characterize this strain. Their findings reveal significant antimicrobial activity against Staphylococcus aureus, including resistant strains like methicillin-resistant S. aureus (MRSA) and vancomycin-resistant S. aureus (VRSA). Despite the absence of the characteristic batumin gene cluster, responsible for antimicrobial compound synthesis, the strain demonstrates promising potential with a unique set of secondary metabolite regions, particularly encoding oviedomycin biosynthesis. The methods used in this study align with the research objectives, and the phylogenetic relationships were …
Comments to Author
The manuscript investigates a novel strain, Pseudomonas batumici Koz11, isolated from the soil of a remote Japanese island, Kozushima. The authors conduct comprehensive genomic, biochemical, and antimicrobial studies to characterize this strain. Their findings reveal significant antimicrobial activity against Staphylococcus aureus, including resistant strains like methicillin-resistant S. aureus (MRSA) and vancomycin-resistant S. aureus (VRSA). Despite the absence of the characteristic batumin gene cluster, responsible for antimicrobial compound synthesis, the strain demonstrates promising potential with a unique set of secondary metabolite regions, particularly encoding oviedomycin biosynthesis. The methods used in this study align with the research objectives, and the phylogenetic relationships were statistically validated through bootstrapping. I recommend accepting this paper after implementing several minor corrections: 1. Lines 68-71: o Current: "Although Bacillus spp. is another commonly isolated species from soil samples, some of these include highly pathogenic strains such as Bacillus anthracis. Our choice to focus on Pseudomonas spp. was based on the typically mild or non-pathogenic threat of Pseudomonas spp. to humans, which minimized the risk to investigators." o Suggested Revision: This statement appears overly simplistic. While B. anthracis is indeed a specific case, it is not commonly isolated from soil. Furthermore, pathogenic P. aeruginosa is abundant. Rather than contrasting different groups of beneficial microorganisms, it would be sufficient to highlight the abundance of bioactive secondary metabolite producers among soil Pseudomonas spp. Relevant citations include: https://doi.org/10.1007/s42398-018-0006-2 doi: 10.1016/j.tim.2016.12.002 doi: 10.1007/s13205-020-02585-8 doi: 10.1039/B817075B Use these references to replace reference [5], which is interesting but not relevant. 2. The second strain of P. batumici was isolated more than 50 years after the first, indicating a preference for rather specific environments, possibly coastal and halophilic. Providing detailed characterization of the soil sample, including properties, altitude, and distance from the sea, would enrich the study. 3. Table 2: o Replace the '+' signs with more informative values, such as the inhibition zone in millimeters.
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
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Comments to Author
This article provides insights into the chemotaxonomic and biochemical traits of P. batumici that have not been fully characterized to date. Given that the type strain of P. batumici is exclusively deposited in the Ukrainian Collection of Microorganisms, Koz11 may serve as surrogate to advance research on this organism and its potential benefits. The work described in the manuscript of sufficient novelty, quality, and potential significance to warrant publication, the provided methods sufficient for an interested reader to reproduce the results and the conclusions adequately supported by the data presented. So, the publication is recommended after revision: Comments 1. The manuscript should be improved in terms of the usage of English and writing style; please bear in mind that both are equally …
Comments to Author
This article provides insights into the chemotaxonomic and biochemical traits of P. batumici that have not been fully characterized to date. Given that the type strain of P. batumici is exclusively deposited in the Ukrainian Collection of Microorganisms, Koz11 may serve as surrogate to advance research on this organism and its potential benefits. The work described in the manuscript of sufficient novelty, quality, and potential significance to warrant publication, the provided methods sufficient for an interested reader to reproduce the results and the conclusions adequately supported by the data presented. So, the publication is recommended after revision: Comments 1. The manuscript should be improved in terms of the usage of English and writing style; please bear in mind that both are equally important. There are many grammatical and syntax errors as well as badly constructed sentences. Authors are strongly advised to get their manuscript edited by a native English speaker or by a Professional English Editing Service. Having done that, please provide the respective certificate along with the revision. 2. There are too many abbreviations in the manuscript; please avoid abbreviating terms used once or twice. A Table of Abbreviations/Nomenclatures/Symbols should also be included. 3. The introduction should be clarified in terms of uniqueness and advantage what is the 4. Figures/Tables should stand alone and therefore; their respective cations should effectively describe them. Please improve the captions in general. For insensate, abbreviations should be defined regardless of the fact that they have been defined in the text too. 5. Data Reproducibility: The study would benefit from providing more information on the reproducibility of the results, such as conducting replicate experiments or addressing potential variability in the experimental setup. This would enhance the reliability of the reported findings. 6. How many parallel experiments did you make? Are the results the only ones or means or what? 7. The experimental conditions for the removal process must be listed with the captions of Figures and Tables. 8. More profound discussions and comparisons with other published works are welcomed. 9. The Manuscript needs thorough revision to improve the text quality and readability of work.
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
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