Reviewer ’s report  
 
Title: Effects of Proton Pump Inhibitor Use on the Esophageal Microbial Community  
 
Version: 0 Date: 05 Aug 2020  
 
Reviewer's report:  
 
My major concern relates to the methodology of the study.  
Ideally this study should compare microbiota in patients befor e and after PPI therapy. Please 
rationale why you did not have chosen this study design.   
The authors should add inclusion and exclusion criteria for both groups.  
There is a significant discrepancy between the numbers of PPI users and non -users (52 vs 6 
patients) - it raises concerns about significance of the results  
Clinical characteristics should be more detailed and include for example history of surgeries and 
chronic disease, use of drugs other than PPI, smoking  
Please discuss the role of alteration o f the esophageal microbiota in Barrett's esophagus -how it 
may affect the results in the study  
There is lack of interpretation of the main findings of the study. The aithors should answer on the 
question what result from the finding that PPI use does not s ignificantly change the lower 
esophageal microbial composition.  
 
Publons Reviewer Recognition . Springer Nature can send verifica tion of this review directly to 
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Publons and you as a reviewer, carefully considering the sensi tivity of such information. For 
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webservice if you have registered for such service or help editors t o identify candidate reviewers. 
Please find the details of processing in Publons ’ privacy policy https://publons.com/about/terms  
 
Yes 
 
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 financially from the publi cation 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 now or in the future?  
 
3. Do you hold or are you curr ently 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  
 
Reviewer Publication Consent. 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 ) if this 
manuscript  is accepted for publication. Any comments that I do not wish to be included in the 
published report have been included as confidential comments to the editor, which will not be 
published.  If you are not happy for us to publish this report, please contact th e edi torial office 
before completing the review.  If you wish, you can include your name in your publish ed report. 
Please note you must decide whether to include your name at the start of the process and  confirm 
this decision whenever prompted. If you change  your decision later, we will not be able to publish 
your name.  
 
I agree to the terms of the CC -BY 4.0 license; please do not publish my name with my report.  
(default)  
Is the study design appropriate to answer the research question (i ncluding the use of appropriate 
controls), and are the conclusions supported by t he evidence presented?  
 
No 
 
Are the methods sufficiently described to allow the study to be repeated?  
 
Yes 
 
Is the use of statistics and treatment of uncertainties appropriate?  
 
Yes 
 
Is the presentation of the work clear?  
 
Yes 
 
Are the images in this manuscript (i ncluding electrophoretic gel s and blots) free from apparent 
manipulation?  
 
Yes 
Reviewer ’s report  
 
Title: Effects of Proton Pump Inhibitor Use on the Esophageal Microbial Community  
 
Version: 0 Date: 05 Aug 2020  
 
Reviewer's report:  
 
My major concern relates to the methodology of the study.  
Ideally this study should compare microbiota in patients befor e and after PPI therapy. Please 
rationale why you did not have chosen this study design.   
The authors should add inclusion and exclusion criteria for both groups.  
There is a significant discrepancy between the numbers of PPI users and non -users (52 vs 6 
patients) - it raises concerns about significance of the results  
Clinical characteristics should be more detailed and include for example history of surgeries and 
chronic disease, use of drugs other than PPI, smoking  
Please discuss the role of alteration o f the esophageal microbiota in Barrett's esophagus -how it 
may affect the results in the study  
There is lack of interpretation of the main findings of the study. The aithors should answer on the 
question what result from the finding that PPI use does not s ignificantly change the lower 
esophageal microbial composition.  
 
Publons Reviewer Recognition . Springer Nature can send verifica tion of this review directly to 
Publons (a subsidiary of Clarivate Analytics). If you would like to take advantage of this service, 
please click on the “Yes” option below. Your name, email  address, title of the reviewed 
manuscript, name of the journal, and date of your review submission (the “Review Data ”) will 
then be transmitted to Publons upon publication of the manuscript.  If you have already registered 
at Publons, they will notify you of the receipt of this review and  update your profile as per your 
settings and their policy. If you are not registered with Publons,  you will receive an email from 
them asking you to register in order for them to be able to re cognize your review on your new 
profile page. Publons may use t he Review Data to generate derivat ive metadata for  the benefit of 
Publons and you as a reviewer, carefully considering the sensi tivity of such information. For 
example, Publons may verify your record as a reviewer by updatin g your profile published on its 
webservice if you have registered for such service or help editors t o identify candidate reviewers. 
Please find the details of processing in Publons ’ privacy policy https://publons.com/about/terms  
 
Yes 
 
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 financially from the publi cation 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 now or in the future?  
 
3. Do you hold or are you curr ently 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  
 
Reviewer Publication Consent. 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 ) if this 
manuscript  is accepted for publication. Any comments that I do not wish to be included in the 
published report have been included as confidential comments to the editor, which will not be 
published.  If you are not happy for us to publish this report, please contact th e edi torial office 
before completing the review.  If you wish, you can include your name in your publish ed report. 
Please note you must decide whether to include your name at the start of the process and  confirm 
this decision whenever prompted. If you change  your decision later, we will not be able to publish 
your name.  
 
I agree to the terms of the CC -BY 4.0 license; please do not publish my name with my report.  
(default)  
Is the study design appropriate to answer the research question (i ncluding the use of appropriate 
controls), and are the conclusions supported by t he evidence presented?  
 
No 
 
Are the methods sufficiently described to allow the study to be repeated?  
 
Yes 
 
Is the use of statistics and treatment of uncertainties appropriate?  
 
Yes 
 
Is the presentation of the work clear?  
 
Yes 
 
Are the images in this manuscript (i ncluding electrophoretic gel s and blots) free from apparent 
manipulation?  
 
Yes 
Please review this paper.
user
Reviewer ’s report  
 
Title: Effects of Proton Pump Inhibitor Use on the Esophageal Microbial Community  
 
Version: 0 Date: 05 Aug 2020  
 
Reviewer's report:  
 
My major concern relates to the methodology of the study.  
Ideally this study should compare microbiota in patients befor e and after PPI therapy. Please 
rationale why you did not have chosen this study design.   
The authors should add inclusion and exclusion criteria for both groups.  
There is a significant discrepancy between the numbers of PPI users and non -users (52 vs 6 
patients) - it raises concerns about significance of the results  
Clinical characteristics should be more detailed and include for example history of surgeries and 
chronic disease, use of drugs other than PPI, smoking  
Please discuss the role of alteration o f the esophageal microbiota in Barrett's esophagus -how it 
may affect the results in the study  
There is lack of interpretation of the main findings of the study. The aithors should answer on the 
question what result from the finding that PPI use does not s ignificantly change the lower 
esophageal microbial composition.  
 
Publons Reviewer Recognition . Springer Nature can send verifica tion of this review directly to 
Publons (a subsidiary of Clarivate Analytics). If you would like to take advantage of this service, 
please click on the “Yes” option below. Your name, email  address, title of the reviewed 
manuscript, name of the journal, and date of your review submission (the “Review Data ”) will 
then be transmitted to Publons upon publication of the manuscript.  If you have already registered 
at Publons, they will notify you of the receipt of this review and  update your profile as per your 
settings and their policy. If you are not registered with Publons,  you will receive an email from 
them asking you to register in order for them to be able to re cognize your review on your new 
profile page. Publons may use t he Review Data to generate derivat ive metadata for  the benefit of 
Publons and you as a reviewer, carefully considering the sensi tivity of such information. For 
example, Publons may verify your record as a reviewer by updatin g your profile published on its 
webservice if you have registered for such service or help editors t o identify candidate reviewers. 
Please find the details of processing in Publons ’ privacy policy https://publons.com/about/terms  
 
Yes 
 
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 financially from the publi cation 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 now or in the future?  
 
3. Do you hold or are you curr ently 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  
 
Reviewer Publication Consent. 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 ) if this 
manuscript  is accepted for publication. Any comments that I do not wish to be included in the 
published report have been included as confidential comments to the editor, which will not be 
published.  If you are not happy for us to publish this report, please contact th e edi torial office 
before completing the review.  If you wish, you can include your name in your publish ed report. 
Please note you must decide whether to include your name at the start of the process and  confirm 
this decision whenever prompted. If you change  your decision later, we will not be able to publish 
your name.  
 
I agree to the terms of the CC -BY 4.0 license; please do not publish my name with my report.  
(default)  
Is the study design appropriate to answer the research question (i ncluding the use of appropriate 
controls), and are the conclusions supported by t he evidence presented?  
 
No 
 
Are the methods sufficiently described to allow the study to be repeated?  
 
Yes 
 
Is the use of statistics and treatment of uncertainties appropriate?  
 
Yes 
 
Is the presentation of the work clear?  
 
Yes 
 
Are the images in this manuscript (i ncluding electrophoretic gel s and blots) free from apparent 
manipulation?  
 
Yes 
assistant