Prediction of Influence Transmission by Water Temperature of Fish Intramuscular Metabolites and Intestinal Microbiota Factor Cascade Using Bayesian Networks
Round 1
Reviewer 1 Report
After reading the title and abstract, I do not know what fish species will be studied, which seems to be pretty important when the metabolic approach is presented.
You write about aquaculture and then sample unknown species in some localities without clear experimental factor.
I would like to know:
Experimental factor,
Aim of the study
Clearly stated hypothesis
What does the study brings to worlds science?
Author Response
After reading the title and abstract, I do not know what fish species will be studied, which seems to be pretty important when the metabolic approach is presented.
You write about aquaculture and then sample unknown species in some localities without clear experimental factor
. [response]
Thank you for your comment. This study speculates on the effects of environmental factors on fish muscular metabolites, regardless of the type of fish. On the other hand, as you said, if there is a bias in the fish species, the metabolic profiles will have a characteristic composition.
I would like to know:
Experimental factor,
[response]
In this study, we measured metabolite in many types of fish collected from the nature sea around Japan, clustered them into groups that were better separated by machine learning with their muscular metabolites, and estimate the effects of environmental factors using bioinformatics from the distribution of the data. There is no clear experimental condition, but what can be called experimental conditions were the sea water temperature as an experimental factor.
Aim of the study
[response]
The environment surrounding organisms contains various energies, and we evaluate the effect of environmental factors on organisms using temperature as an index and developing estimation scheme of those impact. This is the aim of study, using fish and water temperature.
Clearly stated hypothesis
[response]
Living organisms are affected by environmental factors, and we are proceeding with the analysis under the hypothesis that this can be estimated from some index by making full use of various computational techniques such as artificial neural networks.
What does the study brings to worlds science?
[response]
This research scheme can estimate impact of environmental factor to organisms. In aquaculture, the scheme can help clarify the factors that are important in providing a suitable environment for fish.
Author Response File: 
Author Response.docx
Reviewer 2 Report
In this study, the authors collected the published data, and adopted a machine learning and network analysis approach to investigate the relationship between metabolites in fish muscle, water temperature, and intestinal microbiota by using the NMR-based bioinformatics methodology. The results showed that the analysis approach worked well. It is an interesting paper, although a bit outside of my field of study. It is recommended for publish after some revisions.
Comments:
1. Abstract：
The text seems not organized well. It is suggested to revise the abstract and give some significant conclusions.
2. The authors analyzed the relationship between metabolites in fish muscle, water temperature, and intestinal microbiota. The results also showed that water temperature had direct link with fish metabolites and intestinal microbiota. Should the background information on the effect of water temperature on fish metabolism and gut microbes be added to the Introduction?
Author Response
In this study, the authors collected the published data, and adopted a machine learning and network analysis approach to investigate the relationship between metabolites in fish muscle, water temperature, and intestinal microbiota by using the NMR-based bioinformatics methodology. The results showed that the analysis approach worked well. It is an interesting paper, although a bit outside of my field of study. It is recommended for publish after some revisions.
[response]
We are glad that you are interested in our analysis approach. Thank you again for your useful suggestions.
Comments:
- Abstract：
The text seems not organized well. It is suggested to revise the abstract and give some significant conclusions.
[response]
According to your comment, we rewrote abstract including our conclusion. Line 11~ 25
- The authors analyzed the relationship between metabolites in fish muscle, water temperature, and intestinal microbiota. The results also showed that water temperature had direct link with fish metabolites and intestinal microbiota. Should the background information on the effect of water temperature on fish metabolism and gut microbes be added to the Introduction?
[response]
Thank you for your nice suggestion. We made some revisions to the introduction and decided to introduce reports on the relationship between water temperature and fish muscular metabolites and gut microbiota. Line 55~ 65
Author Response File: Author Response.docx
Reviewer 3 Report
Applied Sciences (ISSN 2076-3417)
Manuscript Number: applsci-2198395
Title: Prediction of influence transmission by water temperature of fish intramuscular metabolites and intestinal microbiota factor cascade using Bayesian networks
Article Type: Review Article
The subject of research includes in this journal. Research work is very interesting. In the paper titled “Prediction of influence transmission by water temperature of fish intramuscular metabolites and intestinal microbiota factor cascade using Bayesian networks” The use of artificial intelligence methods is widely known.
In my recommendation is major revision.
The paper needs major revision and need to take care of following:
1. The quality of the language is insufficient. Have a native speaker or similar assist you.
2. The Introductionis quite random with broad and varying statements and not very well focused. The authors in the introduction did not analyze the literature in the area of application of artificial intelligence methods.
3. Please clarify what the size of the learning set was. What characteristics this set included. The authors very generally scharacterized the learning set.
4. Authors should improve the readability of drawings such as 2.
5. The authors describe the research method quite generally. The article does not include the structure of the research paper. It is very difficult to identify how the neural modeling process was carried out.
6. The paper needs a very large revision in terms of substantive and methodological aspects to be accepted for publication.
7. In my opinion, the final conclusions should also be drawn up as they are not as specific as the scope of work.
Author Response
The subject of research includes in this journal. Research work is very interesting. In the paper titled “Prediction of influence transmission by water temperature of fish intramuscular metabolites and intestinal microbiota factor cascade using Bayesian networks” The use of artificial intelligence methods is widely known.
In my recommendation is major revision.
The paper needs major revision and need to take care of following:
[response]
Thank you for understanding of our research concept and we apologize that there was a part that you could not understand due to our lack of explanation. We rewrote for detailed explanation in section of introduction, material and method and redrew a figure.
- The quality of the language is insufficient. Have a native speaker or similar assist you.
[response]
I apologize for my poor English writing skills. The manuscript was rewritten where the reviewers pointed it out, and a professional English proofreading was requested.
- The Introductionis quite random with broad and varying statements and not very well focused.The authors in the introduction did not analyze the literature in the area of application of artificial intelligence methods.
[response]
According to your comment, we rewrote an introduction section and added background of A.I. for analysis in biology. Line 55 ~
- Please clarify what the size of the learning set was. What characteristics this set included. The authors very generally scharacterized the learning set.
[response]
Thank you for your kind comment, we had provided detailed information about the samples in Materials and Methods and added sample statistics. Line 105 ~ and table
- Authors should improve the readability of drawings such as 2.
[response]
Sorry for the hard to see figure. We enlarged the figure 2 to make the plot easier to see and changed the plots color and shape coding. Line 163
- The authors describe the research method quite generally. The article does not include the structure of the research paper. It is very difficult to identify how the neural modeling process was carried out.
[response]
Thank you for your comment, we revised Materials and Methods according to your comment. More details had been given especially regarding Bayesian network. Line 139 ~ 153
- The paper needs a very large revision in terms of substantive and methodological aspects to be accepted for publication.
[response]
Thank you for your revision suggestion. We believe that we were able to revise the manuscript for publication in response to the comments of the reviewers. If you need any corrections, please leave a comment.
- In my opinion, the final conclusions should also be drawn up as they are not as specific as the scope of work.
[response]
Thank you for your suggestion, we reviewed the data analysis results again and rewrote the conclusions. Line 269 ~ 274
Author Response File: Author Response.docx
Reviewer 4 Report
The study conducted by the authors revealed interesting information regarding the evaluation of the effects of water temperature on the metabolic profiling of fish muscle and the relationship between temperature changes and the intestinal microbiota in fish. The authors used artificial neural network analysis and machine learning methods to analyse comprehensive information. The results could have a good impact in the development of knowledges in the field of ichthyology. Therefore, the analytical scheme proposed in the study can be used to infer the impact of some of the factors that change water temperature on metabolic variation as the sum of environmental factors. The study provides valid data. After minor revision, according with the specific comments I mentioned bellow, the paper might be published.
Some specific comments:
Line 34: the words "fish species" would be preferable instead of "types of fish"
Line 90: the species of fish used for sampling should be specified. Also, the size/age of the fish would also be a useful information
Line 132: the figure is not clear and does not fit well on the page
Line 148: the legend should give information about groups 1 and 2. What they are …
Author Response
Comment1
The study conducted by the authors revealed interesting information regarding the evaluation of the effects of water temperature on the metabolic profiling of fish muscle and the relationship between temperature changes and the intestinal microbiota in fish. The authors used artificial neural network analysis and machine learning methods to analyse comprehensive information. The results could have a good impact in the development of knowledges in the field of ichthyology. Therefore, the analytical scheme proposed in the study can be used to infer the impact of some of the factors that change water temperature on metabolic variation as the sum of environmental factors. The study provides valid data. After minor revision, according with the specific comments I mentioned bellow, the paper might be published.
[Response]
Thanks for your understanding and appropriate comments on our suggestion of the study.
We rewrote the text according to your comment.
Comment2
Line 34: the words "fish species" would be preferable instead of "types of fish"
[Response]
We replaced “fish species” to “ types pf fish”.
Comment3
Line 90: the species of fish used for sampling should be specified. Also, the size/age of the fish would also be a useful information
[Response]
Thank you for your comment, we prepared the sample characteristic table and added information in the section materials and methods. Line 100 ~ 111
Comment4
Line 132: the figure is not clear and does not fit well on the page
[Response]
We enlarged the figure 2 to make the plot easier to see and changed the plots color and shape coding. Line 163
Comment5
Line 148: the legend should give information about groups 1 and 2. What they are …
[Response]
Sorry for the lack of explanation. We added description of the figure. Line 177
Author Response File: Author Response.docx
Round 2
Reviewer 3 Report
I don't have any comments.
Author Response
Thank you for your previous comments.
