Reviewer ’s report  
 
Title: Small intestinal microbiota composition and the prog nosis of infants with ileostomy 
resulting from distinct primary diseases  
 
Version: 1 Date: 10 Jan 2020  
 
Reviewer: Stephanie Ganal -Vonarburg  
 
Reviewer's report:  
 
The presented study is of high interest to the filed of gastroenterology and microbiome research 
as it tries to characterize the small intestinal microbial community in neonates. It covers 30 
infants with different gastrointestinal  disorders that had undergone surgery for ileostomy. The 
presence of different diseases and underlying different gestational ages at birth may affect the 
outcome of the study. It is nevertheless valuable as the small intestinal microbiota is otherwise 
largely inaccessible. In addition, it is of great interest especially in diseased children to 
understand if and how the microbiota may contribute to the disease/recovery. However, I have 
major concerns regarding the publication in the current status. Please, s ee my detailed comments 
below:  
 
1. Throughout the manuscript, I largely miss statistical analyses. This accounts especially for 
Figures 1A,B, 2 and Table 2.  
 
2. Connected to my first comment, how representative are the measurements in one patient? 
Were the y sampled at different time points/multiple times after surgery? It will be impossible to 
resample the patients, but maybe frozen samples are available from another time point that could 
be included? Otherwise, could one repeat with a few patients a longit udinal sampling in order to 
see reproducibility of the results at different collection times?  
 
3. Was there a cut -off for the read number per sample? Were samples with low read number (e.g. 
under 1000) excluded from the analysis?  
 
4. If the data of Figure 1 would be presented in a PCoA plot, is there any clustering according to 
disease or any other external factor visible?  
 
5. The quality of all plots in the available pdf is very low. Especially Figure 3 is unsharp and I 
was unable to review it correctly. It s eems that some legends in the figure itself are missing as 
well.  
 
6. The figure legends are very short and miss important information.  
 
7. Minor comment: the English would have to be revised throughout the manuscript.  
 
 
 
 
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.  
 
No 
 
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 re view  
 
Quality of written English  
Please indicate the quality of language in the manuscr ipt: 
 
Needs some language corrections before being published  
 
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: 1 Date: 10 Jan 2020  
 
Reviewer: Stephanie Ganal -Vonarburg  
 
Reviewer's report:  
 
The presented study is of high interest to the filed of gastroenterology and microbiome research 
as it tries to characterize the small intestinal microbial community in neonates. It covers 30 
infants with different gastrointestinal  disorders that had undergone surgery for ileostomy. The 
presence of different diseases and underlying different gestational ages at birth may affect the 
outcome of the study. It is nevertheless valuable as the small intestinal microbiota is otherwise 
largely inaccessible. In addition, it is of great interest especially in diseased children to 
understand if and how the microbiota may contribute to the disease/recovery. However, I have 
major concerns regarding the publication in the current status. Please, s ee my detailed comments 
below:  
 
1. Throughout the manuscript, I largely miss statistical analyses. This accounts especially for 
Figures 1A,B, 2 and Table 2.  
 
2. Connected to my first comment, how representative are the measurements in one patient? 
Were the y sampled at different time points/multiple times after surgery? It will be impossible to 
resample the patients, but maybe frozen samples are available from another time point that could 
be included? Otherwise, could one repeat with a few patients a longit udinal sampling in order to 
see reproducibility of the results at different collection times?  
 
3. Was there a cut -off for the read number per sample? Were samples with low read number (e.g. 
under 1000) excluded from the analysis?  
 
4. If the data of Figure 1 would be presented in a PCoA plot, is there any clustering according to 
disease or any other external factor visible?  
 
5. The quality of all plots in the available pdf is very low. Especially Figure 3 is unsharp and I 
was unable to review it correctly. It s eems that some legends in the figure itself are missing as 
well.  
 
6. The figure legends are very short and miss important information.  
 
7. Minor comment: the English would have to be revised throughout the manuscript.  
 
 
 
 
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.  
 
No 
 
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 re view  
 
Quality of written English  
Please indicate the quality of language in the manuscr ipt: 
 
Needs some language corrections before being published  
 
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: 1 Date: 10 Jan 2020  
 
Reviewer: Stephanie Ganal -Vonarburg  
 
Reviewer's report:  
 
The presented study is of high interest to the filed of gastroenterology and microbiome research 
as it tries to characterize the small intestinal microbial community in neonates. It covers 30 
infants with different gastrointestinal  disorders that had undergone surgery for ileostomy. The 
presence of different diseases and underlying different gestational ages at birth may affect the 
outcome of the study. It is nevertheless valuable as the small intestinal microbiota is otherwise 
largely inaccessible. In addition, it is of great interest especially in diseased children to 
understand if and how the microbiota may contribute to the disease/recovery. However, I have 
major concerns regarding the publication in the current status. Please, s ee my detailed comments 
below:  
 
1. Throughout the manuscript, I largely miss statistical analyses. This accounts especially for 
Figures 1A,B, 2 and Table 2.  
 
2. Connected to my first comment, how representative are the measurements in one patient? 
Were the y sampled at different time points/multiple times after surgery? It will be impossible to 
resample the patients, but maybe frozen samples are available from another time point that could 
be included? Otherwise, could one repeat with a few patients a longit udinal sampling in order to 
see reproducibility of the results at different collection times?  
 
3. Was there a cut -off for the read number per sample? Were samples with low read number (e.g. 
under 1000) excluded from the analysis?  
 
4. If the data of Figure 1 would be presented in a PCoA plot, is there any clustering according to 
disease or any other external factor visible?  
 
5. The quality of all plots in the available pdf is very low. Especially Figure 3 is unsharp and I 
was unable to review it correctly. It s eems that some legends in the figure itself are missing as 
well.  
 
6. The figure legends are very short and miss important information.  
 
7. Minor comment: the English would have to be revised throughout the manuscript.  
 
 
 
 
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.  
 
No 
 
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 re view  
 
Quality of written English  
Please indicate the quality of language in the manuscr ipt: 
 
Needs some language corrections before being published  
 
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