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: 03 Dec 2017 
 
Reviewer:  Rita Busuttil  
 
Reviewer’s report:  
 
In this manuscript the authors seek to identify the differe nt gut microbiota present in H.pylori 
infected patients with and without concurrent  dyspepsia. The premise itself is not novel but the 
methodology/strategy is. It does however seem that the results section is extremely brief and that 
the authors have miss ed the opportunity to further refine their analysis.  
 
1. In the introduction the authors describe a longitudinal study that found that incidence of 
GC is decreased in patients who have had an unsuccessful course of treatment to 
eradicate H. pylori. They p ropose that this might be due to successful eradication, during 
treatment of non -H. pylori bacteria that might contribute to the development of GC. Is it 
also possible that treatment to eradicate H. pylori may be specifically eradicating 
pathogenic strains ? 
 
2. Table 1: Staphylococcus percentage. Please check calculations - 19/21 patients is not 
42.8%  
 
3. Also Table 1 - make sure numbers are rounded correctly. Example Micrococcus 1 patient 
of 21= 4.8%  
 
4. The results section is very brief and the authors hav e missed an opportunity to perform a 
more detailed analysis of their findings and thus several questions remained unanswered:  
 
a. Are the bacterial counts different in patients with and without dyspepsia?  
 
b. It appears the authors did not analyse strains of  H.pylori? Why not?  
 
c. Were there differences in the types of bacteria found between men and women?  
 
d. It appears that the authors did not separately analyse the bacterial contribution separately 
in the antrum and body specimens. This decision was based on  a previous publication by 
Bik et al. In the same publication these Bik et al found no difference in H. pylori in 
bacterial diversity. Given that the current authors hypothesised that there IS a difference 
it would have made more sense to analyse these ind ependently. Can the authors screen a 
small number of additional patients to either prove or refute this?  
 
e. What is the distribution of the microflora amongst individiduals? Did some patients have 
much more representation than others?  
 
f. Findings in the n on-dyspeptic groups analysed in terms of their clinical indications? Why 
not? 
 
5. Did the authors explore potential pathogencity of the bacterial types? This should also be 
mentioned in the discussion?  
 
6. Can the authors clarify what they mean by colony c haracter study Pg 9 line 4.  
 
7. Why is table 2 not represented in terms of percentages?  
 
8. Page 12 lines 28 -40 appear to be duplicate sentences with the same information  
 
9. Can the authors comment on the future clinical ramifications of this work?  
 
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.  
 
No 
 
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 t he 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 co ntent 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 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 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: 03 Dec 2017 
 
Reviewer:  Rita Busuttil  
 
Reviewer’s report:  
 
In this manuscript the authors seek to identify the differe nt gut microbiota present in H.pylori 
infected patients with and without concurrent  dyspepsia. The premise itself is not novel but the 
methodology/strategy is. It does however seem that the results section is extremely brief and that 
the authors have miss ed the opportunity to further refine their analysis.  
 
1. In the introduction the authors describe a longitudinal study that found that incidence of 
GC is decreased in patients who have had an unsuccessful course of treatment to 
eradicate H. pylori. They p ropose that this might be due to successful eradication, during 
treatment of non -H. pylori bacteria that might contribute to the development of GC. Is it 
also possible that treatment to eradicate H. pylori may be specifically eradicating 
pathogenic strains ? 
 
2. Table 1: Staphylococcus percentage. Please check calculations - 19/21 patients is not 
42.8%  
 
3. Also Table 1 - make sure numbers are rounded correctly. Example Micrococcus 1 patient 
of 21= 4.8%  
 
4. The results section is very brief and the authors hav e missed an opportunity to perform a 
more detailed analysis of their findings and thus several questions remained unanswered:  
 
a. Are the bacterial counts different in patients with and without dyspepsia?  
 
b. It appears the authors did not analyse strains of  H.pylori? Why not?  
 
c. Were there differences in the types of bacteria found between men and women?  
 
d. It appears that the authors did not separately analyse the bacterial contribution separately 
in the antrum and body specimens. This decision was based on  a previous publication by 
Bik et al. In the same publication these Bik et al found no difference in H. pylori in 
bacterial diversity. Given that the current authors hypothesised that there IS a difference 
it would have made more sense to analyse these ind ependently. Can the authors screen a 
small number of additional patients to either prove or refute this?  
 
e. What is the distribution of the microflora amongst individiduals? Did some patients have 
much more representation than others?  
 
f. Findings in the n on-dyspeptic groups analysed in terms of their clinical indications? Why 
not? 
 
5. Did the authors explore potential pathogencity of the bacterial types? This should also be 
mentioned in the discussion?  
 
6. Can the authors clarify what they mean by colony c haracter study Pg 9 line 4.  
 
7. Why is table 2 not represented in terms of percentages?  
 
8. Page 12 lines 28 -40 appear to be duplicate sentences with the same information  
 
9. Can the authors comment on the future clinical ramifications of this work?  
 
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.  
 
No 
 
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 t he 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 co ntent 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 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 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: 03 Dec 2017 
 
Reviewer:  Rita Busuttil  
 
Reviewer’s report:  
 
In this manuscript the authors seek to identify the differe nt gut microbiota present in H.pylori 
infected patients with and without concurrent  dyspepsia. The premise itself is not novel but the 
methodology/strategy is. It does however seem that the results section is extremely brief and that 
the authors have miss ed the opportunity to further refine their analysis.  
 
1. In the introduction the authors describe a longitudinal study that found that incidence of 
GC is decreased in patients who have had an unsuccessful course of treatment to 
eradicate H. pylori. They p ropose that this might be due to successful eradication, during 
treatment of non -H. pylori bacteria that might contribute to the development of GC. Is it 
also possible that treatment to eradicate H. pylori may be specifically eradicating 
pathogenic strains ? 
 
2. Table 1: Staphylococcus percentage. Please check calculations - 19/21 patients is not 
42.8%  
 
3. Also Table 1 - make sure numbers are rounded correctly. Example Micrococcus 1 patient 
of 21= 4.8%  
 
4. The results section is very brief and the authors hav e missed an opportunity to perform a 
more detailed analysis of their findings and thus several questions remained unanswered:  
 
a. Are the bacterial counts different in patients with and without dyspepsia?  
 
b. It appears the authors did not analyse strains of  H.pylori? Why not?  
 
c. Were there differences in the types of bacteria found between men and women?  
 
d. It appears that the authors did not separately analyse the bacterial contribution separately 
in the antrum and body specimens. This decision was based on  a previous publication by 
Bik et al. In the same publication these Bik et al found no difference in H. pylori in 
bacterial diversity. Given that the current authors hypothesised that there IS a difference 
it would have made more sense to analyse these ind ependently. Can the authors screen a 
small number of additional patients to either prove or refute this?  
 
e. What is the distribution of the microflora amongst individiduals? Did some patients have 
much more representation than others?  
 
f. Findings in the n on-dyspeptic groups analysed in terms of their clinical indications? Why 
not? 
 
5. Did the authors explore potential pathogencity of the bacterial types? This should also be 
mentioned in the discussion?  
 
6. Can the authors clarify what they mean by colony c haracter study Pg 9 line 4.  
 
7. Why is table 2 not represented in terms of percentages?  
 
8. Page 12 lines 28 -40 appear to be duplicate sentences with the same information  
 
9. Can the authors comment on the future clinical ramifications of this work?  
 
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.  
 
No 
 
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 t he 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 co ntent 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 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 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