Pangenome-Scale Mathematical Modelling of ANAMMOX Bacteria Metabolism

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

The present manuscript, entitled Pangenome-Scale Mathematical Modelling of ANAMMOX Bacteria Metabolism is a research report by the authors. This is interesting research that describes a hot topic. In this manuscript, a good effort has been made by the authors to explore the possibility of mathematical modeling in the Annamox metabolism of the bacterial community to reduce the energy requirement and simultaneous treatment of wastewater. In general, the topic is in line with the journal's scope. The authors try to explain how different carbon and energy sources in the growth medium affect the nitrogen removal rates and the growth rates of ANAMMOX bacteria by constructing a pangenome-scale constraint-based metabolic model of ANAMMOX, iRB399. Thus, the manuscript is critically evaluated to detect errors in the writing of English, novelty, and scientific merit including English grammar. The manuscript has scientific merit and is well fits the scope of this journal. In addition, some points related to the organization of the text, grammar, and language can be revised to improve the article. Therefore, I recommend that a major revision is warranted. A more detailed review can be found in the specific comments below.

 

1.What conclusion was drawn from this study? Concluding remark should be inserted in the abstract.

 

2.  Arrange the keywords in alphabetical order.

 

3. Why do authors propose the pangenome-Scale Mathematical Modelling of ANAMMOX Bacteria Metabolism instead of Core Genome?

 

4. Introduction; The researchers should revise the introduction section to include fundamental and insight information of Pangenome and present their relationship with ANAMMOX process, its importance, and research direction.

 

5. What are the differences between this study and others in the literature?

 

6. The originality/novelty of the paper should be clearly stated in the manuscript.

 

7. Provide one nice and technically sound paragraph at the end of introduction section about what is covered in the manuscript.

 

8.Additionally, the introduction should cover the recent literature related to this subject. Introduction is completely lacking with the citation from the years 2022; 2023.

 

9. The main concern I have about the paper is with respect to the selection of studies and documents, i.e., the methodological part of the review. It is important to understand how the relevant literature was selected. Did you use any criteria to help mitigate biases?

10. The displayed data is devoid of any quantitative values or any statistical presentation which makes the understanding of it theoretical only without confirmation, can this point be treated?

11.The difference of this paper with already published works is unclear.

 

12. Discussion is better described, but the authors should state each citation to its specific discovery.

13. How do the authors define the practical implications of this study? An additional discussion about this critical aspect should be included in the revised manuscript.

 

14. Manuscript should be checked once for any grammatical as well as typological errors like somewhere spaces and commas (,), if not given, this should be corrected.

15. All the cited references must be critically checked where the volume number, issue number, and page numbers are missing, should be mentioned.

Comments on the Quality of English Language

The technical language of the manuscript is good, however, few grammatical, English, and punctuation errors should be corrected before publication.

Author Response

Authors' response to reviewer's comments are described in the attached work document.

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

1. Regarding the genetic diversity of ANAMMOX bacteria, what genes are included in the unique, dispensable, and core genomes, and what functional differences exist among them?

2. In fig 6, How do the fluxes through reactions in the central carbon metabolism of ANAMMOX bacteria vary, and what factors influence the magnitude and direction of these fluxes.

3. How does the efficiency of the electron transport chain (ETC) in ANAMMOX bacteria impact their growth rate, and what is the relationship between the efficiency of the ETC, the availability of ammonium in the growth medium, and the observed growth rate

Author Response

Authors' response to reviewer's comments are described in the attached word document.

Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

The authors have made the necessary corrections. I believe that the article is ready for publication in terms of its subject and content. Accept.

Reviewer 2 Report

Comments and Suggestions for Authors

There were no special comments.