Reviewer ’s report  
 
Title: Impact of nutrition and rotavirus infection on the infant gut microbiota in a humanized pig 
model  
 
Version: 0 Date: 11 Dec 2017  
 
Revi ewer: Pallavi Singh  
 
Reviewer's report:  
 
The present study by Kumar et. al., investigates effect of rotavirus infection in humanized pig 
model beyond mouse  models to closely mimic human conditions. This is an important and well -
designed study attempting to understand impact of infant microbioata and diet in relation to HRV 
infection. However, the human Infant microbiota is dynamic and changing unlike human a dult 
microbiome. It is also known that the mode of delivery and diet plays an important role in the 
shaping the gut microbiome of an infant. Nevertheless, the role of malnutrition in HRV infection 
and disease progression is an important study.  
 
Specific C omments:  
1. Introduction: Lines: 120 - 122. The statement on hypotheses though good may be a bit 
misleading. The pigs upon transplantation with HIFM are fed with the diet specified for the 
group. The microbial community trying to settle will be in response to diet fed and will not 
be "perturbed". It will be different from that of the ones fed with a nutritious diet which is 
introduced to the piglets before the microbioata is. Additionally, the immune system 
development is in response to commensals and microb iota introduced.  
 
2. Lines 186 -187.  
 
a. How were the diarrheal scores determined?  
 
b. Please include supporting data in Supplemental information for data not shown. Similarly, 
for lines 234 and 236.  
 
3. The increase in microbial community di versity is counter intuitive to increased diarrheal 
severity post HRV infection. Previous studies have shown that diverse microbial community 
is helpful in preventing disease progression. It will be helpful if the authors could elaborate 
on this trend. Add itionally, alpha rarefactions can determine the change in diversity and they 
have not been included to support this statement.  
 
4. Studies have also linked to increased bodyweight to increase in Firmicutes:Bacteroidetes 
ratio in several species including p igs. However, in this study no difference is seen between 
the pigs with significantly higher bodyweight on PCD=0. It will be helpful to elaborate on 
this point in result as well as discussion. In HRV infected result section (lines 244 -259), 
such a trend ma y be visible, but I am unable to infer that based on the results.  
 
5. It is also important to stress in the discussion that the microbial community in GF pigs were 
responsible for less severe infections in both protein rich and deficient diet. According to the 
results the diet has some effect, but major response is due to presence of a diverse 
community and be included in conclusion and/or discussion.  
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 ar e 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 qua lity 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 years received reimbursements, fees, funding, or salar y 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 publicati on 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 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 C reative 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: 0 Date: 11 Dec 2017  
 
Revi ewer: Pallavi Singh  
 
Reviewer's report:  
 
The present study by Kumar et. al., investigates effect of rotavirus infection in humanized pig 
model beyond mouse  models to closely mimic human conditions. This is an important and well -
designed study attempting to understand impact of infant microbioata and diet in relation to HRV 
infection. However, the human Infant microbiota is dynamic and changing unlike human a dult 
microbiome. It is also known that the mode of delivery and diet plays an important role in the 
shaping the gut microbiome of an infant. Nevertheless, the role of malnutrition in HRV infection 
and disease progression is an important study.  
 
Specific C omments:  
1. Introduction: Lines: 120 - 122. The statement on hypotheses though good may be a bit 
misleading. The pigs upon transplantation with HIFM are fed with the diet specified for the 
group. The microbial community trying to settle will be in response to diet fed and will not 
be "perturbed". It will be different from that of the ones fed with a nutritious diet which is 
introduced to the piglets before the microbioata is. Additionally, the immune system 
development is in response to commensals and microb iota introduced.  
 
2. Lines 186 -187.  
 
a. How were the diarrheal scores determined?  
 
b. Please include supporting data in Supplemental information for data not shown. Similarly, 
for lines 234 and 236.  
 
3. The increase in microbial community di versity is counter intuitive to increased diarrheal 
severity post HRV infection. Previous studies have shown that diverse microbial community 
is helpful in preventing disease progression. It will be helpful if the authors could elaborate 
on this trend. Add itionally, alpha rarefactions can determine the change in diversity and they 
have not been included to support this statement.  
 
4. Studies have also linked to increased bodyweight to increase in Firmicutes:Bacteroidetes 
ratio in several species including p igs. However, in this study no difference is seen between 
the pigs with significantly higher bodyweight on PCD=0. It will be helpful to elaborate on 
this point in result as well as discussion. In HRV infected result section (lines 244 -259), 
such a trend ma y be visible, but I am unable to infer that based on the results.  
 
5. It is also important to stress in the discussion that the microbial community in GF pigs were 
responsible for less severe infections in both protein rich and deficient diet. According to the 
results the diet has some effect, but major response is due to presence of a diverse 
community and be included in conclusion and/or discussion.  
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 ar e 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 qua lity 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 years received reimbursements, fees, funding, or salar y 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 publicati on 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 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 C reative 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: 0 Date: 11 Dec 2017  
 
Revi ewer: Pallavi Singh  
 
Reviewer's report:  
 
The present study by Kumar et. al., investigates effect of rotavirus infection in humanized pig 
model beyond mouse  models to closely mimic human conditions. This is an important and well -
designed study attempting to understand impact of infant microbioata and diet in relation to HRV 
infection. However, the human Infant microbiota is dynamic and changing unlike human a dult 
microbiome. It is also known that the mode of delivery and diet plays an important role in the 
shaping the gut microbiome of an infant. Nevertheless, the role of malnutrition in HRV infection 
and disease progression is an important study.  
 
Specific C omments:  
1. Introduction: Lines: 120 - 122. The statement on hypotheses though good may be a bit 
misleading. The pigs upon transplantation with HIFM are fed with the diet specified for the 
group. The microbial community trying to settle will be in response to diet fed and will not 
be "perturbed". It will be different from that of the ones fed with a nutritious diet which is 
introduced to the piglets before the microbioata is. Additionally, the immune system 
development is in response to commensals and microb iota introduced.  
 
2. Lines 186 -187.  
 
a. How were the diarrheal scores determined?  
 
b. Please include supporting data in Supplemental information for data not shown. Similarly, 
for lines 234 and 236.  
 
3. The increase in microbial community di versity is counter intuitive to increased diarrheal 
severity post HRV infection. Previous studies have shown that diverse microbial community 
is helpful in preventing disease progression. It will be helpful if the authors could elaborate 
on this trend. Add itionally, alpha rarefactions can determine the change in diversity and they 
have not been included to support this statement.  
 
4. Studies have also linked to increased bodyweight to increase in Firmicutes:Bacteroidetes 
ratio in several species including p igs. However, in this study no difference is seen between 
the pigs with significantly higher bodyweight on PCD=0. It will be helpful to elaborate on 
this point in result as well as discussion. In HRV infected result section (lines 244 -259), 
such a trend ma y be visible, but I am unable to infer that based on the results.  
 
5. It is also important to stress in the discussion that the microbial community in GF pigs were 
responsible for less severe infections in both protein rich and deficient diet. According to the 
results the diet has some effect, but major response is due to presence of a diverse 
community and be included in conclusion and/or discussion.  
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 ar e 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 qua lity 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 years received reimbursements, fees, funding, or salar y 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 publicati on 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 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 C reative 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