Reviewer ’s report  
 
Title: Impact of nutrition and rotavirus infection on the infant gut microbiota in a humanized pig 
model  
 
Version: 1 Date: 02 Mar 2018  
 
Reviewer: Benoit Chassaing  
 
Reviewer's report:  
 
Few important points remained.  
- Regarding my comment on PCoA approach, the authors answered "it is hard to appreciate the 
results generated by the PCoA". That can be true, but PCOA of the Unifrac distance is the 
gold standard approach to see global microbial community structure in an u nbiased approach. 
This need to be performed and reported, since as written and as reported, it is impossible to 
appreciate the impact of nutrition and RV infection on the intestinal microbiota.  
 
- "Caesarean -derived GF piglets were housed individually in st erile isolators (to ensure no 
environmental contamination) throughout the experiment.". More details need to be given 
here. Which isolators, which methods were used to ensure protection against environmental 
contamination, etc...  
 
- Figure 3C: the authors m ay have misinterpreted my request. I was talking about the LogCFU 
x days post HRV challenge figure, which show clear effects for some groups 
(deficient+HIFM+HRV and Deficient+GF+HRV). Hence, having an estimation of global 
HRV shedding during the entire inf ection, using area under the curve, will for sure lead to 
statistically significant differences that will be easy to appreciate for the readers.  
Are the methods appropriate and well described?  
If not, please specify what is required in your comments to the authors.  
 
No 
 
Does the work include the necessary contro ls? 
If not, please specify which controls are required in your comments to the authors.  
 
Yes 
 
Are the conclusions drawn adequately supported by the data shown?  
If not, please explain in your comments to the authors.  
 
Yes 
Are you able to assess any statistics in the manuscript or would you recommend an  
additional statistical review?  
If an additional statistical review is recommended, please specify what aspects require further  
assessment in your comments to the editors.  
 
I am able to assess the statistics  
 
Quality of written English  
Please indicate the quality of language in the manuscript:  
 
Acceptable  
 
Declaration of competing interests  
Please complete a declaration of competing interests, considering the following questions:  
 
1. Have you in the past five year s received reimbursements, fees, funding, or salary from an  
organisation that may in any way gain or lose financially from the publication of this  
manuscript, either now or in the future?  
 
2. Do you hold any stocks or shares in an organisation that may in a ny way gain or lose  
financially from the publication of this manuscript, either now or in the future?  
 
3. Do you hold or are you currently applying for any patents relating to the content of the  
manuscript?  
 
4. Have you received reimbursements, fees, funding , or salary from an organization that 
holds  or has applied for patents relating to the content of the manuscript?  
 
5. Do you have any other financial competing interests?  
 
6. Do you have any non -financial competing interests in relation to this paper?  
 
If you  can answer no to all of the above, write 'I declare that I have no competing interests' 
below.  If your reply is yes to any, please give details below.  
 
I declare that I have no competing interests.  
 
I agree to the open peer review policy of the journal. I u nderstand that my name will be included  
on my report to the authors and, if the manuscript is accepted for publication, my named report  
including any attachments I upload will be posted on the website along with the authors'  
responses.  I agree for my repor t to be made available under an Open Access Creative Commons 
CC-BY license ( http://creativecommons.org/licenses/by/4.0/ ). I understand that any comments 
which I do  not wish to be included in my named report can be included as confidential comments 
to the  editors, which will not be published.  
 
I agree to the open peer review policy of the journal  
Reviewer ’s report  
 
Title: Impact of nutrition and rotavirus infection on the infant gut microbiota in a humanized pig 
model  
 
Version: 1 Date: 02 Mar 2018  
 
Reviewer: Benoit Chassaing  
 
Reviewer's report:  
 
Few important points remained.  
- Regarding my comment on PCoA approach, the authors answered "it is hard to appreciate the 
results generated by the PCoA". That can be true, but PCOA of the Unifrac distance is the 
gold standard approach to see global microbial community structure in an u nbiased approach. 
This need to be performed and reported, since as written and as reported, it is impossible to 
appreciate the impact of nutrition and RV infection on the intestinal microbiota.  
 
- "Caesarean -derived GF piglets were housed individually in st erile isolators (to ensure no 
environmental contamination) throughout the experiment.". More details need to be given 
here. Which isolators, which methods were used to ensure protection against environmental 
contamination, etc...  
 
- Figure 3C: the authors m ay have misinterpreted my request. I was talking about the LogCFU 
x days post HRV challenge figure, which show clear effects for some groups 
(deficient+HIFM+HRV and Deficient+GF+HRV). Hence, having an estimation of global 
HRV shedding during the entire inf ection, using area under the curve, will for sure lead to 
statistically significant differences that will be easy to appreciate for the readers.  
Are the methods appropriate and well described?  
If not, please specify what is required in your comments to the authors.  
 
No 
 
Does the work include the necessary contro ls? 
If not, please specify which controls are required in your comments to the authors.  
 
Yes 
 
Are the conclusions drawn adequately supported by the data shown?  
If not, please explain in your comments to the authors.  
 
Yes 
Are you able to assess any statistics in the manuscript or would you recommend an  
additional statistical review?  
If an additional statistical review is recommended, please specify what aspects require further  
assessment in your comments to the editors.  
 
I am able to assess the statistics  
 
Quality of written English  
Please indicate the quality of language in the manuscript:  
 
Acceptable  
 
Declaration of competing interests  
Please complete a declaration of competing interests, considering the following questions:  
 
1. Have you in the past five year s received reimbursements, fees, funding, or salary from an  
organisation that may in any way gain or lose financially from the publication of this  
manuscript, either now or in the future?  
 
2. Do you hold any stocks or shares in an organisation that may in a ny way gain or lose  
financially from the publication of this manuscript, either now or in the future?  
 
3. Do you hold or are you currently applying for any patents relating to the content of the  
manuscript?  
 
4. Have you received reimbursements, fees, funding , or salary from an organization that 
holds  or has applied for patents relating to the content of the manuscript?  
 
5. Do you have any other financial competing interests?  
 
6. Do you have any non -financial competing interests in relation to this paper?  
 
If you  can answer no to all of the above, write 'I declare that I have no competing interests' 
below.  If your reply is yes to any, please give details below.  
 
I declare that I have no competing interests.  
 
I agree to the open peer review policy of the journal. I u nderstand that my name will be included  
on my report to the authors and, if the manuscript is accepted for publication, my named report  
including any attachments I upload will be posted on the website along with the authors'  
responses.  I agree for my repor t to be made available under an Open Access Creative Commons 
CC-BY license ( http://creativecommons.org/licenses/by/4.0/ ). I understand that any comments 
which I do  not wish to be included in my named report can be included as confidential comments 
to the  editors, which will not be published.  
 
I agree to the open peer review policy of the journal  
Please review this paper.
user
Reviewer ’s report  
 
Title: Impact of nutrition and rotavirus infection on the infant gut microbiota in a humanized pig 
model  
 
Version: 1 Date: 02 Mar 2018  
 
Reviewer: Benoit Chassaing  
 
Reviewer's report:  
 
Few important points remained.  
- Regarding my comment on PCoA approach, the authors answered "it is hard to appreciate the 
results generated by the PCoA". That can be true, but PCOA of the Unifrac distance is the 
gold standard approach to see global microbial community structure in an u nbiased approach. 
This need to be performed and reported, since as written and as reported, it is impossible to 
appreciate the impact of nutrition and RV infection on the intestinal microbiota.  
 
- "Caesarean -derived GF piglets were housed individually in st erile isolators (to ensure no 
environmental contamination) throughout the experiment.". More details need to be given 
here. Which isolators, which methods were used to ensure protection against environmental 
contamination, etc...  
 
- Figure 3C: the authors m ay have misinterpreted my request. I was talking about the LogCFU 
x days post HRV challenge figure, which show clear effects for some groups 
(deficient+HIFM+HRV and Deficient+GF+HRV). Hence, having an estimation of global 
HRV shedding during the entire inf ection, using area under the curve, will for sure lead to 
statistically significant differences that will be easy to appreciate for the readers.  
Are the methods appropriate and well described?  
If not, please specify what is required in your comments to the authors.  
 
No 
 
Does the work include the necessary contro ls? 
If not, please specify which controls are required in your comments to the authors.  
 
Yes 
 
Are the conclusions drawn adequately supported by the data shown?  
If not, please explain in your comments to the authors.  
 
Yes 
Are you able to assess any statistics in the manuscript or would you recommend an  
additional statistical review?  
If an additional statistical review is recommended, please specify what aspects require further  
assessment in your comments to the editors.  
 
I am able to assess the statistics  
 
Quality of written English  
Please indicate the quality of language in the manuscript:  
 
Acceptable  
 
Declaration of competing interests  
Please complete a declaration of competing interests, considering the following questions:  
 
1. Have you in the past five year s received reimbursements, fees, funding, or salary from an  
organisation that may in any way gain or lose financially from the publication of this  
manuscript, either now or in the future?  
 
2. Do you hold any stocks or shares in an organisation that may in a ny way gain or lose  
financially from the publication of this manuscript, either now or in the future?  
 
3. Do you hold or are you currently applying for any patents relating to the content of the  
manuscript?  
 
4. Have you received reimbursements, fees, funding , or salary from an organization that 
holds  or has applied for patents relating to the content of the manuscript?  
 
5. Do you have any other financial competing interests?  
 
6. Do you have any non -financial competing interests in relation to this paper?  
 
If you  can answer no to all of the above, write 'I declare that I have no competing interests' 
below.  If your reply is yes to any, please give details below.  
 
I declare that I have no competing interests.  
 
I agree to the open peer review policy of the journal. I u nderstand that my name will be included  
on my report to the authors and, if the manuscript is accepted for publication, my named report  
including any attachments I upload will be posted on the website along with the authors'  
responses.  I agree for my repor t to be made available under an Open Access Creative Commons 
CC-BY license ( http://creativecommons.org/licenses/by/4.0/ ). I understand that any comments 
which I do  not wish to be included in my named report can be included as confidential comments 
to the  editors, which will not be published.  
 
I agree to the open peer review policy of the journal  
assistant