Reviewer’s report  
 
Title:  Gastric Bacterial Flora in Patients Harbouring Helicobacter pylori With or Without 
Chronic Dyspepsia: Analysis with Matrix -assisted Laser Desorption Ionization Time -of-Flight 
Mass Spectroscopy  
 
Version: 0 Date: 13 Nov 2017 
 
Reviewer:  Annalisa  Schiepatti  
 
Reviewer’s report:  
 
In this paper the Authors aimed at characterizing the gastric microbiota of patients with H.Pylori  
infection with or without chronic dyspepsia and absence of organic disease. The paper is globally 
well structured and the results show a substantial difference in the gastric microbiota 
composition between these two groups.  
 
I have the following minor co ncerns/considerations:  
 
- Although the study of microbiota is a topic of interest, I am not sure that these results 
could impact clinical decisions, since it is very difficult to understand whether microbiota 
differences could anticipate H. Pylori infection or be the consequence of the presence of 
H. Pylori itself. This point is described in the discussion, but  
 
- Rome III criteria have been updated to Rome IV criteria in 2016. Although Rome III 
definition of "functional gastro -duodenal disorders" has been lar gely confirmed, the 
Authors should refer to Rome IV criteria  
 
- Could the Authors provide information about smoking and NSAIDs use in their patients?  
 
- I am a little bit puzzled by the fact that gastric biopsies were not performed in the group 
of patients und ergoing a gastroscopy because of dyspepsia. I think that this is a limitation 
of the study, because we do not have information about the presence of a chronic 
gastritis. The Authors are conscious of this point, but I think that this should be further 
highl ighted.  
 
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 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 quality 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 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 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, fee s, 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 websi te 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 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:  Gastric Bacterial Flora in Patients Harbouring Helicobacter pylori With or Without 
Chronic Dyspepsia: Analysis with Matrix -assisted Laser Desorption Ionization Time -of-Flight 
Mass Spectroscopy  
 
Version: 0 Date: 13 Nov 2017 
 
Reviewer:  Annalisa  Schiepatti  
 
Reviewer’s report:  
 
In this paper the Authors aimed at characterizing the gastric microbiota of patients with H.Pylori  
infection with or without chronic dyspepsia and absence of organic disease. The paper is globally 
well structured and the results show a substantial difference in the gastric microbiota 
composition between these two groups.  
 
I have the following minor co ncerns/considerations:  
 
- Although the study of microbiota is a topic of interest, I am not sure that these results 
could impact clinical decisions, since it is very difficult to understand whether microbiota 
differences could anticipate H. Pylori infection or be the consequence of the presence of 
H. Pylori itself. This point is described in the discussion, but  
 
- Rome III criteria have been updated to Rome IV criteria in 2016. Although Rome III 
definition of "functional gastro -duodenal disorders" has been lar gely confirmed, the 
Authors should refer to Rome IV criteria  
 
- Could the Authors provide information about smoking and NSAIDs use in their patients?  
 
- I am a little bit puzzled by the fact that gastric biopsies were not performed in the group 
of patients und ergoing a gastroscopy because of dyspepsia. I think that this is a limitation 
of the study, because we do not have information about the presence of a chronic 
gastritis. The Authors are conscious of this point, but I think that this should be further 
highl ighted.  
 
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 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 quality 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 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 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, fee s, 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 websi te 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 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:  Gastric Bacterial Flora in Patients Harbouring Helicobacter pylori With or Without 
Chronic Dyspepsia: Analysis with Matrix -assisted Laser Desorption Ionization Time -of-Flight 
Mass Spectroscopy  
 
Version: 0 Date: 13 Nov 2017 
 
Reviewer:  Annalisa  Schiepatti  
 
Reviewer’s report:  
 
In this paper the Authors aimed at characterizing the gastric microbiota of patients with H.Pylori  
infection with or without chronic dyspepsia and absence of organic disease. The paper is globally 
well structured and the results show a substantial difference in the gastric microbiota 
composition between these two groups.  
 
I have the following minor co ncerns/considerations:  
 
- Although the study of microbiota is a topic of interest, I am not sure that these results 
could impact clinical decisions, since it is very difficult to understand whether microbiota 
differences could anticipate H. Pylori infection or be the consequence of the presence of 
H. Pylori itself. This point is described in the discussion, but  
 
- Rome III criteria have been updated to Rome IV criteria in 2016. Although Rome III 
definition of "functional gastro -duodenal disorders" has been lar gely confirmed, the 
Authors should refer to Rome IV criteria  
 
- Could the Authors provide information about smoking and NSAIDs use in their patients?  
 
- I am a little bit puzzled by the fact that gastric biopsies were not performed in the group 
of patients und ergoing a gastroscopy because of dyspepsia. I think that this is a limitation 
of the study, because we do not have information about the presence of a chronic 
gastritis. The Authors are conscious of this point, but I think that this should be further 
highl ighted.  
 
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 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 quality 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 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 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, fee s, 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 websi te 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 included as confidential comments 
to the editors, which will not be published . 
 
I agree to the open peer review policy of the journal  
assistant