Reviewer ’s report  
 
Title: Small intestinal microbiota composition and the prog nosis of infants with ileostomy 
resulting from distinct primary diseases  
 
Version: 2 Date: 03 Mar 2 020 
 
Reviewer: Stephanie Ganal -Vonarburg  
 
Reviewer's report:  
 
The authors have tried to address most of my comments and I am pleased with their replies on 
the 16S microbiome analysis as well as with the curations on the manuscript regarding language 
and figure legends. Both have  sufficiently improved. I can also understand that longitudinal 
sampling of the infants is difficult and the authors' reasoning for difficulties in interpretation due 
to changing conditions are plausible.  
 
However, I still think that statistical analyses w ithin the manuscript are weak. It would help the 
reader to better interpret the data if error bars were included in Figure 1B. In addition, although 
statistical analysis (T -test) has been performed on the data in Table 2, the resulting p -values do 
not fit the interpretation of the data in the text. For example, while colitis is significantly reduced 
in the breast -feeding group, sepsis is not. Likewise, the claimed increase in Streptococcus is not 
underlined by the statistical analysis. The authors should ad just the manuscript accordingly and 
highlight the limitations of their data resulting from a limited sample size. Some of the 
observations are pure trends instead of firm results. The best would be to increase the cohort.  
 
Are the methods appropriate and well desc ribed?  
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 conclusions drawn adequately supported by the data shown?  
If not, please explain in your comments to the authors.  
 
No 
 
 
 
 
 
 
Are you able to assess any statistics in the manus cript or would you recommend an 
additional statistical review?  
If an additional statistical review is recommended, please speci fy what aspects require further 
assessment in your comments to the editors.  
 
I recommend additional statistical  review  
 
Quality of written English  
Please indicate the quality of language in the manuscr ipt: 
 
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, f ees, funding, or salary from an 
organisation that may  in any way gain or lose financial ly from the publication of this 
manuscript, either now or in the future?  
 
2. Do you hold any stocks or shares in an organisation t hat may in any way gain or lose 
financially from the publication of this manuscript, either n ow 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 t o 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 int erests' 
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 understan d that my name will be included 
on my report to the authors and, if the ma nuscript is accepted f or 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://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 in cluded 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: Small intestinal microbiota composition and the prog nosis of infants with ileostomy 
resulting from distinct primary diseases  
 
Version: 2 Date: 03 Mar 2 020 
 
Reviewer: Stephanie Ganal -Vonarburg  
 
Reviewer's report:  
 
The authors have tried to address most of my comments and I am pleased with their replies on 
the 16S microbiome analysis as well as with the curations on the manuscript regarding language 
and figure legends. Both have  sufficiently improved. I can also understand that longitudinal 
sampling of the infants is difficult and the authors' reasoning for difficulties in interpretation due 
to changing conditions are plausible.  
 
However, I still think that statistical analyses w ithin the manuscript are weak. It would help the 
reader to better interpret the data if error bars were included in Figure 1B. In addition, although 
statistical analysis (T -test) has been performed on the data in Table 2, the resulting p -values do 
not fit the interpretation of the data in the text. For example, while colitis is significantly reduced 
in the breast -feeding group, sepsis is not. Likewise, the claimed increase in Streptococcus is not 
underlined by the statistical analysis. The authors should ad just the manuscript accordingly and 
highlight the limitations of their data resulting from a limited sample size. Some of the 
observations are pure trends instead of firm results. The best would be to increase the cohort.  
 
Are the methods appropriate and well desc ribed?  
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 conclusions drawn adequately supported by the data shown?  
If not, please explain in your comments to the authors.  
 
No 
 
 
 
 
 
 
Are you able to assess any statistics in the manus cript or would you recommend an 
additional statistical review?  
If an additional statistical review is recommended, please speci fy what aspects require further 
assessment in your comments to the editors.  
 
I recommend additional statistical  review  
 
Quality of written English  
Please indicate the quality of language in the manuscr ipt: 
 
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, f ees, funding, or salary from an 
organisation that may  in any way gain or lose financial ly from the publication of this 
manuscript, either now or in the future?  
 
2. Do you hold any stocks or shares in an organisation t hat may in any way gain or lose 
financially from the publication of this manuscript, either n ow 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 t o 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 int erests' 
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 understan d that my name will be included 
on my report to the authors and, if the ma nuscript is accepted f or 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://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 in cluded 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: Small intestinal microbiota composition and the prog nosis of infants with ileostomy 
resulting from distinct primary diseases  
 
Version: 2 Date: 03 Mar 2 020 
 
Reviewer: Stephanie Ganal -Vonarburg  
 
Reviewer's report:  
 
The authors have tried to address most of my comments and I am pleased with their replies on 
the 16S microbiome analysis as well as with the curations on the manuscript regarding language 
and figure legends. Both have  sufficiently improved. I can also understand that longitudinal 
sampling of the infants is difficult and the authors' reasoning for difficulties in interpretation due 
to changing conditions are plausible.  
 
However, I still think that statistical analyses w ithin the manuscript are weak. It would help the 
reader to better interpret the data if error bars were included in Figure 1B. In addition, although 
statistical analysis (T -test) has been performed on the data in Table 2, the resulting p -values do 
not fit the interpretation of the data in the text. For example, while colitis is significantly reduced 
in the breast -feeding group, sepsis is not. Likewise, the claimed increase in Streptococcus is not 
underlined by the statistical analysis. The authors should ad just the manuscript accordingly and 
highlight the limitations of their data resulting from a limited sample size. Some of the 
observations are pure trends instead of firm results. The best would be to increase the cohort.  
 
Are the methods appropriate and well desc ribed?  
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 conclusions drawn adequately supported by the data shown?  
If not, please explain in your comments to the authors.  
 
No 
 
 
 
 
 
 
Are you able to assess any statistics in the manus cript or would you recommend an 
additional statistical review?  
If an additional statistical review is recommended, please speci fy what aspects require further 
assessment in your comments to the editors.  
 
I recommend additional statistical  review  
 
Quality of written English  
Please indicate the quality of language in the manuscr ipt: 
 
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, f ees, funding, or salary from an 
organisation that may  in any way gain or lose financial ly from the publication of this 
manuscript, either now or in the future?  
 
2. Do you hold any stocks or shares in an organisation t hat may in any way gain or lose 
financially from the publication of this manuscript, either n ow 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 t o 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 int erests' 
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 understan d that my name will be included 
on my report to the authors and, if the ma nuscript is accepted f or 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://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 in cluded as confidential comments 
to the editors, which will not be published.  
 
I agree to the open peer review policy of the journal  
assistant