Metabonomic Analysis of Macrobrachium rosenbergii with Iron Prawn Syndrome (IPS)

Round 1

Reviewer 1 Report (New Reviewer)

Authors have used advanced techniques and tools to elucidate the Iron Prawn Syndrome manifestation. Having such huge data but authors have not clearly presented the data by correlating the KEGG metabolic pathways with LC-MS/MS data. For example, carbohydrate and amino acid metabolism decreased in female iron prawns- What are the corresponding metabolites measured by LC-MS/MS are reflected? The main objective of these types of omics-based studies is to find the solutions/treatments to enhance the productivity of aquaculture where in conventional approaches fail to find the solutions. Correlation of phenotypic observations (LC-MS/MS) with KEGG metabolic pathways is required and have to be interpreted to understand the IPS.  

Author Response

Thank you for the suggestions. We are sorry that we didn't explain it clearly in the manuscript. The results for the combined analysis of metabonomic and transcriptomic data revealed in Fig. 6, and the relationship references between the metabolites including MEDN200 (L-Malic Acid), 201 (Succinic Acid), 335 (Methylmalonic Acid), 478 (Aminomalonic Acid), MEDP174 (Purine), 250 (Riboflavin), 550 (18-Hydroxycorticosterone); MEDN242 (L-Ascorbate), 588 (Glycerol 3-phosphate), MEDP251 (Trigonelline), and the pathway have been searched. According to the reviewer's good instruction, we have written the sentences. Please see lines 361-364, page 19; lines 503-523, pages 23-24.

Reviewer 2 Report (New Reviewer)

The authors describe the characterization of the metabolome and transcriptome of males and females iron prawn and normal prawns, respectively.  While the idea of using combined omics datasets is novel and a great approach, the authors fail to adequately describe what they did.  I believe there may be some language issues that are likely leading to this, but given this, I cannot judge the validity of the approach or the findings.  further, the introduction does not adequately describe the condition being studied.  Specific comments are below:

Sentence starting line 47: I am not sure I understand the sentence.  “…underlying pathways through which animals are exposed to toxic substances..” sounds like the author is referring to an exposure pathway, however, the example given in the second part of the sentence sounds like a response pathway.  Consider clarifying

Paragraph beginning line 51:  the authors state that transcriptomics and metabolic responses could be responsible for growth effects but not molt cycle effects (citation 17) and then in the next sentence say that there have never been transcriptomic or metabolic studies done on the iron prawn.  It is hard to see how those two things can connect.  If there is a previous study that has suggests transcriptomic or metabolic effects in a different organism, then the authors should state that and also why that isn’t sufficient to extrapolate to the iron prawn.

Materials and Methods: this is likely my own ignorance, but it would be helpful if you could contrast the iron prawn from a normal prawn.  Is an iron prawn a separate species than normal prawn.  Along these lines, you never really explain what IPS is or its origins.  It might be helpful to do so.

Line 74. Ultrasonically detected? Is that the correct word?

Lines 120 – 124: consider putting the search parameters into a table.

Section 2.3: so there is a very detailed description of the metabolomics analysis but no description at all of how the samples were handled for the transcriptional analysis.  There is a reference but it doesn’t seem to have anything obviously to do with the current study. It is not even clear from the M&M section how you generated the transcriptomic data (RNA-seq? microarrays?).  What analysis package did you use, did you do an FDR correction, there is literally no information given.

In this same section (line 167), it sounds like maybe these are not transcriptomic data but are maybe metabolomic data?

Section 2.4: line 186: p value of 0.05 is that a corrected p value?

Sentence starting line 195: what database are you referring to here?

Results section:

Line 210: Significantly increased/decreased - The contrasts are not stated anywhere in the M&M section.  There appear to be four groups male and female of normal and iron prawns.  Were males compared to males and females to females or were all groups analyzed together

Author Response

Thanks very much for your kind letter and for the reviewers’ comments on our manuscript previously entitled “Metabonomic Analysis of Macrobrachium rosenbergii with Iron Prawn Syndrome (IPS)” (Manuscript ID: fishes-2262660). Those comments are all valuable and very helpful for revising and improving our paper. We have studied comments carefully and have made corrections which we hope meet with approval. The changes have been marked in red in the revised manuscript in doc. format.

Author Response File: Author Response.pdf

This manuscript is a resubmission of an earlier submission. The following is a list of the peer review reports and author responses from that submission.

Round 1

Reviewer 1 Report

The manuscript described provided metabolic and RNA-seq information of shrimp showing IPS. I do not see much difference between this study and the study done by Na Ying et al., 2021 (https://doi.org/10.1016/j.jip.2022.107752). Thus, I would not recommend publishing this manuscript 

Reviewer 2 Report

Metabolomic and transcriptome studies of animals are a very relevant and promising topic, because such studies help to solve practical problems of animal husbandry, agro and aquaculture and are a source of a huge amount of fundamental knowledge about biochemical reactions in the tissues of various organisms. The use of a multi-omics approach is also an indisputable advantage of this work. The resulting datasets themselves are valuable for publication in open access. However, the work has a number of obvious disadvantages. The main problem with this manuscript is poorly prepared graphics. Their actual form both with the main text of the article and in additional materials does not allow assessing the scientific potential of the work. Figure 1 consists of important and informative graphs, however they are presented in a completely unreadable format. This figure must be divided into several with the following changes: graph C requires labels for at least extremely different features, labels for graphs A, B and E must be increased. Figure 2 also needs correction. The authors used a raster image, so even when enlarged, the signatures remain unreadable. Use vector images, enlarge captions. Figure 2S does not contain the element "a", which is described in the figure caption. The authors repeatedly use the term quantitative metabolomic analysis, but the described methods allow obtaining only semi-quantitative data. The description of all analytical methods in paragraphs 2.3-2.5 does not contain appropriate references to the results of this analysis in the article. line 194: Applying the Smirnov-Kolmogorov test to samples of size n = 6 is completely speculative. line 203-206: The conclusion does not match the data presented. The authors did a great job and obtained valuable and interesting data, but the analysis and presentation of the results are not sufficient for publication.