Functional Diversity within Gut Microbiomes: Implications for Conserving Biodiversity
Round 1
Reviewer 1 Report
The paper title "Functional Diversity in Wildlife Microbiomes: Implications for Conservation" by Cameron S. Dodd and Catherine E. Grueber submitted to conservation reviewed that how recent developments in functional microbiome research can be used to advance research into the microbiome of wild animals and how the results can help preserve microbial biodiversity and the important ecological functions of microbial communities. Overall, this is very important especially when more and more studies have focused on the functional traits of microbial communities in conservation. Authors did a very good job in the manuscript writing. However, I still have a few questions & suggestions here.
- I would suggest the author to add ‘gut’ in the title since it would be more clear to the reader.
- Abstract: Try to shorten the introduction words (Lines 7-15) and then extend the summary part of your review point (Lines 19-21).
- Lines 18-19: what do you mean ‘how best these can be accounted for’?
- It would be good to add ‘climate change’ as one of the keywords.
- Line 184: at least QIIME II should be mentioned here instead of QIIME.
See reference https://0-doi-org.brum.beds.ac.uk/10.1038/s41587-019-0209-9
- Lines 180-204: I would suggest the authors to shorten the indication of amplicon data analyses.
- Lines 225-274: Please mention the use of Bugbase (https://0-doi-org.brum.beds.ac.uk/10.1101/133462) for bacteria and FunGuild (https://0-doi-org.brum.beds.ac.uk/10.1016/j.funeco.2015.06.006) for fungi as functional predictions.
- Lines 437-494: for this part, I would suggest the author to include more details based on case studies. For example, there are more and more requests for microbiome study to collect samples from different time points.
Author Response
(author responses indicated in bold font)
The paper title "Functional Diversity in Wildlife Microbiomes: Implications for Conservation" by Cameron S. Dodd and Catherine E. Grueber submitted to conservation reviewed that how recent developments in functional microbiome research can be used to advance research into the microbiome of wild animals and how the results can help preserve microbial biodiversity and the important ecological functions of microbial communities. Overall, this is very important especially when more and more studies have focused on the functional traits of microbial communities in conservation. Authors did a very good job in the manuscript writing. However, I still have a few questions & suggestions here.
- I would suggest the author to add ‘gut’ in the title since it would be more clear to the reader.
RESPONSE: We have revised to title accordingly
- Abstract: Try to shorten the introduction words (Lines 7-15) and then extend the summary part of your review point (Lines 19-21).
RESPONSE: We have shortened the introduction part of the Abstract and extended the summary part. (Lines 11-31)
- Lines 18-19: what do you mean ‘how best these can be accounted for’?
RESPONSE: Reworded for clarity. (Lines 21-22)
- It would be good to add ‘climate change’ as one of the keywords.
RESPONSE: ‘Climate change’ is not a direct focus of our review, but we do touch on the more general effects of ‘environmental change’, so we have added that as a key word. (Line 32)
- Line 184: at least QIIME II should be mentioned here instead of QIIME. See reference https://0-doi-org.brum.beds.ac.uk/10.1038/s41587-019-0209-9
RESPONSE: Changed as suggested (Line 199)
- Lines 180-204: I would suggest the authors to shorten the indication of amplicon data analyses.
RESPONSE: We have made minor edits to make this section more succinct (Lines 170-172, 186-188, 202-204)
- Lines 225-274: Please mention the use of Bugbase (https://0-doi-org.brum.beds.ac.uk/10.1101/133462) for bacteria and FunGuild (https://0-doi-org.brum.beds.ac.uk/10.1016/j.funeco.2015.06.006) for fungi as functional predictions.
RESPONSE: These resources and their references have been added. (Line 248)
- Lines 437-494: for this part, I would suggest the author to include more details based on case studies. For example, there are more and more requests for microbiome study to collect samples from different time points.
RESPONSE: We have added more detail into how issues with sampling can be overcome, and edited for clarity. (Lines 513-530)
Reviewer 2 Report
Cameron S. Dodd and Catherine E. Grueber's review manuscript "Functional Diversity in Wildlife Microbiomes: Implications for Conservation" introduced a great perspective on wildlife conservation and study. The paper was well written. I only have a few comments on this paper shown below,
- Please define "wildlife". The entire article seemed about wild animals. Thus, do you mean wildlife equals wild animals?
- Line 57, please rephrase this sentence. I saw two "both" and was confused.
- No graphs and photos in the article? I would like to read a review with colourful photos and figures.
Author Response
(author responses indicated in bold font)
This review represents a valuable contribution. The MS shows us a good picture of microbiome studies beyond taxonomic diversity and how functional diversity is a reliable tool for biodiversity conservation at the micro and macro levels.
The organization of the MS is good, with sections on key topics covering sampling, study design, methodological approaches, and bioinformatics analysis starting from the baseline of taxonomic diversity to more complex strategies and nicely discuss their implications.
In my perspective, this review can be used as a practical guide for conservation biologists and microbiologists interested in creative approaches to conserve biodiversity.
I did not find issues for further review; therefore, I suggest its publication with only two minor corrections.
Minor corrections.
L283 'than taxonomic profiles', perhaps you mean 'functional profiles'?
RESPONSE: We do mean taxonomic profiles here as we are comparing the consistency of metagenome sequencing to amplicon methods, we have amended the text to make that methodological comparison clearer. (Lines 299-302)
L298 Add 'in' before 'conservation research.'
RESPONSE: Changed as suggested. (Line 317)
Reviewer 3 Report
Dear Editor,
This review represents a valuable contribution. The MS shows us a good picture of microbiome studies beyond taxonomic diversity and how functional diversity is a reliable tool for biodiversity conservation at the micro and macro levels.
The organization of the MS is good, with sections on key topics covering sampling, study design, methodological approaches, and bioinformatics analysis starting from the baseline of taxonomic diversity to more complex strategies and nicely discuss their implications.
In my perspective, this review can be used as a practical guide for conservation biologists and microbiologists interested in creative approaches to conserve biodiversity.
I did not find issues for further review; therefore, I suggest its publication with only two minor corrections.
Minor corrections.
L283 'than taxonomic profiles', perhaps you mean 'functional profiles'?
L298 Add 'in' before 'conservation research.'
Author Response
(author responses indicated in bold font)
This review represents a valuable contribution. The MS shows us a good picture of microbiome studies beyond taxonomic diversity and how functional diversity is a reliable tool for biodiversity conservation at the micro and macro levels.
The organization of the MS is good, with sections on key topics covering sampling, study design, methodological approaches, and bioinformatics analysis starting from the baseline of taxonomic diversity to more complex strategies and nicely discuss their implications.
In my perspective, this review can be used as a practical guide for conservation biologists and microbiologists interested in creative approaches to conserve biodiversity.
I did not find issues for further review; therefore, I suggest its publication with only two minor corrections.
Minor corrections.
L283 'than taxonomic profiles', perhaps you mean 'functional profiles'?
RESPONSE: We do mean taxonomic profiles here as we are comparing the consistency of metagenome sequencing to amplicon methods, we have amended the text to make that methodological comparison clearer. (Lines 299-302)
L298 Add 'in' before 'conservation research.'
RESPONSE: Changed as suggested. (Line 317)
