Reviewer ’s report  
 
Title: Impact of nutrition and rotavirus infection on the infant gut microbiota in a humanized pig 
model  
 
Version: 0 Date: 12 Oct 2017  
 
Reviewer: Benoit Chassaing  
 
Reviewer's report:  
 
In this manuscript by Anand Kumar and collaborators, the authors aimed to investigate the 
impact of malnutrition on rotavirus -induced disease severity, with a focus on microbiota 
composition. For this endeavor, they used a model of humanized pig model, in which pig born 
by C -section were colonized with human microbiota. Subsequently, dietary intervention was 
applied and animals were infected with rotavirus.  
Whil e highly descriptive in nature, this study nonetheless provide important evidence of the 
detrimental role played by malnutrition during rotavirus infection. I provide the following 
comments to the authors:  
- Figure 1 : the use of taxa summarization, for e xample at the phylum level, will be very useful 
here. Such representation can be generated through QIIME, and will help in comparing 
global microbiota composition between recipient and donor.  
 
- Figure 2: with the innovative approach used by the authors, I entirely agree that this figure is 
useful. However, I recommend to put it as figure 1.  
 
- It is not clear, in the method section, how the pig were housed following inoculation with 
human microbiota. Were they protected from environmental contamination?  
 
- Figure 3C: generating area under the curve representation will be useful here.  
 
- The authors should consider using principal coordinate analysis of the Unifrac distance in 
order to compare microbiota composition between individual (beta diversity). For examp le, 
as represented figure 6, it is impossible to appreciate inter -individual variations.  
Are the methods  appropriate and well described?  
If not, please specify what is required in your comments to the authors.  
 
Yes 
  
Does the work include the necessary controls?  
If not, please specify which controls are required in your comments to the authors.  
 
Yes 
 
Are the conc lusions 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 addit ional 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:  
 
Accept able 
 
Declaration of competing interests  
Please complete a declaration of competing interests, considering the following questions:  
 
1. Have you in the past five years 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 any way gain or lose  
financially from the publication of this manuscript, either now or in th e 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 conte nt 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 understand 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 report to be made available under an Open Access Creative Commons 
CC-BY license ( http://creativeco mmons.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: 0 Date: 12 Oct 2017  
 
Reviewer: Benoit Chassaing  
 
Reviewer's report:  
 
In this manuscript by Anand Kumar and collaborators, the authors aimed to investigate the 
impact of malnutrition on rotavirus -induced disease severity, with a focus on microbiota 
composition. For this endeavor, they used a model of humanized pig model, in which pig born 
by C -section were colonized with human microbiota. Subsequently, dietary intervention was 
applied and animals were infected with rotavirus.  
Whil e highly descriptive in nature, this study nonetheless provide important evidence of the 
detrimental role played by malnutrition during rotavirus infection. I provide the following 
comments to the authors:  
- Figure 1 : the use of taxa summarization, for e xample at the phylum level, will be very useful 
here. Such representation can be generated through QIIME, and will help in comparing 
global microbiota composition between recipient and donor.  
 
- Figure 2: with the innovative approach used by the authors, I entirely agree that this figure is 
useful. However, I recommend to put it as figure 1.  
 
- It is not clear, in the method section, how the pig were housed following inoculation with 
human microbiota. Were they protected from environmental contamination?  
 
- Figure 3C: generating area under the curve representation will be useful here.  
 
- The authors should consider using principal coordinate analysis of the Unifrac distance in 
order to compare microbiota composition between individual (beta diversity). For examp le, 
as represented figure 6, it is impossible to appreciate inter -individual variations.  
Are the methods  appropriate and well described?  
If not, please specify what is required in your comments to the authors.  
 
Yes 
  
Does the work include the necessary controls?  
If not, please specify which controls are required in your comments to the authors.  
 
Yes 
 
Are the conc lusions 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 addit ional 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:  
 
Accept able 
 
Declaration of competing interests  
Please complete a declaration of competing interests, considering the following questions:  
 
1. Have you in the past five years 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 any way gain or lose  
financially from the publication of this manuscript, either now or in th e 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 conte nt 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 understand 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 report to be made available under an Open Access Creative Commons 
CC-BY license ( http://creativeco mmons.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: 0 Date: 12 Oct 2017  
 
Reviewer: Benoit Chassaing  
 
Reviewer's report:  
 
In this manuscript by Anand Kumar and collaborators, the authors aimed to investigate the 
impact of malnutrition on rotavirus -induced disease severity, with a focus on microbiota 
composition. For this endeavor, they used a model of humanized pig model, in which pig born 
by C -section were colonized with human microbiota. Subsequently, dietary intervention was 
applied and animals were infected with rotavirus.  
Whil e highly descriptive in nature, this study nonetheless provide important evidence of the 
detrimental role played by malnutrition during rotavirus infection. I provide the following 
comments to the authors:  
- Figure 1 : the use of taxa summarization, for e xample at the phylum level, will be very useful 
here. Such representation can be generated through QIIME, and will help in comparing 
global microbiota composition between recipient and donor.  
 
- Figure 2: with the innovative approach used by the authors, I entirely agree that this figure is 
useful. However, I recommend to put it as figure 1.  
 
- It is not clear, in the method section, how the pig were housed following inoculation with 
human microbiota. Were they protected from environmental contamination?  
 
- Figure 3C: generating area under the curve representation will be useful here.  
 
- The authors should consider using principal coordinate analysis of the Unifrac distance in 
order to compare microbiota composition between individual (beta diversity). For examp le, 
as represented figure 6, it is impossible to appreciate inter -individual variations.  
Are the methods  appropriate and well described?  
If not, please specify what is required in your comments to the authors.  
 
Yes 
  
Does the work include the necessary controls?  
If not, please specify which controls are required in your comments to the authors.  
 
Yes 
 
Are the conc lusions 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 addit ional 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:  
 
Accept able 
 
Declaration of competing interests  
Please complete a declaration of competing interests, considering the following questions:  
 
1. Have you in the past five years 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 any way gain or lose  
financially from the publication of this manuscript, either now or in th e 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 conte nt 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 understand 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 report to be made available under an Open Access Creative Commons 
CC-BY license ( http://creativeco mmons.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