Reviewer’s report
Title: 
Gut microbiota composition and functional prediction in diarrhea-
predominant irritable bowel syndrome
Version: 
3 
Date: 
27 Jan 2021
Reviewer's report:
"PEER REVIEWER ASSESSMENTS: 
OBJECTIVE - Full research articles: is there a clear objective that addresses one
or several testable research questions? (Brief or other article types: is there a
clear objective?)
Yes - there is a clear objective
DESIGN - Is the current approach (including controls and analysis protocols)
appropriate for the objective?
No - there are minor issues
EXECUTION - Are the experiments and analyses performed with sufficient
technical rigor to allow confidence in the results?
Yes - experiments and analyses were performed appropriately
STATISTICS - Is the use of statistics in the manuscript appropriate?
Yes - appropriate statistical analyses have been used in the study
INTERPRETATION - Is the current interpretation/discussion of the results
reasonable and not overstated?
Yes - the author's interpretation is reasonable
OVERALL MANUSCRIPT POTENTIAL - Has the author addressed your
concerns sufficiently for you to now recommend the work as a technically sound
contribution? If not, can further revisions be made to make the work technically
sound?
Probably - with minor revisions
PEER REVIEWER COMMENTS: 
GENERAL COMMENTS: 2021 01 25 
Gut microbiota paper
Comments by Reviewer No. 3:
To the authors: This is a detailed, well organized ,and well implemented study.
You have addressed the concerns of both reviewers adequately, and the
manuscript has been modified accordingly in most cases. However there are a
few concerns, once these have been addressed, I would recommend publication
of this study.
Reviewer 1
Comment 1) Requested a flow chart. This was done (S9).
Comment 2) Requested discussions being shortened into a table. Authors
responded with reasons why this could not be done. 
I concur.
Comment 3) Limited number of patients. Author justified this, as indicated in
line 290, no it was indicated in line 270.
Reviewer 2:
Comment 1): Determination of sample size. The author justified this in lines 86-
87
Comment 2) Antibiotics have a long term effect on the gut microbiome. 
Author
addressed this in 
lines 86-87.
Comment 3) Define organic heart disease. 
Implied in line 86..""taking
antibiotics, probiotics or 
other treatments"". 
Organic heart disease should be added as the 6th item in line
89.
Comment 4) ""psychopath is not appropriate"" psychiatric comorbidity has been
substituted in line 89.
Comment 5) Obesity. Author indicated their comment was modified in line 291,
no it was line 271.
Comment 6) Discussion , recommend adding a paragraph of limitations. Done in
line 271 not 291
as the authors indicated. 
Conclusion summarizes several major points.
Comment 7) ""Change to four subtypes"" 
Done on line 38.
Comment 8 ) Figure 4 Legend is missing. 
This was not done. The author on line
155 states"" as shown in Figure 5"" Which is it? Figure 4 or Figure 5? 
If Figure 4
is redundant, it should be removed, if not, then a legend must be added to Figure
4. Text must be altered accordingly.
Comment 9) ""This study is the first to analyze"" deleted from line 224.
Comment 10) ""China has undergone"" deleted from text as requested.
Comment 11) Line 292 As this section of the mss. has been redacted, the ""thin
body""comment is gone.
I would suggest that you read, and possibly comment on this paper in your
manuscript:
Scallan Walter, E J, Crim SM, Bruce BB, et al Postinfectious Irritable Bowel
Syndrome After Campylobacter Infection 
Am J Gastroenterol 
2019
Oct;114(10):1649-1656. 
doi: 10.14309/ajg.0000000000000408. 
These authors conclude that persons with a Campylobacter infection have a
much higher risk of developing IBS compared with those not diagnosed with
Campylobacter infection. 
This finding supports your finding of the increased presence of Proteobacteria
i.e. Campylobacter in IBD patients compared to normal controls. 
Table S1; Sex is indicated by 1 or 2 which is male and which is female? This
information must be available. 
Why not use M for male and F for female?
REQUESTED REVISIONS: 
All issues have been resolved."
Publons Reviewer Recognition
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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.
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a reviewer by updating your profile published on its webservice if you have
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find the details of processing in Publons’ privacy policy
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No
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, 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.
This reviewer has been recruited by a partner organization, Research Square.
Reviewers with declared or apparent competing interests are not utilized for
these reviews. This reviewer has agreed to publication of their comments online
under a Creative Commons Attribution License attributed to Research Square
and was paid a small honorarium for completing the review within a specified
timeframe. Honoraria for reviews such as this are paid regardless of the reviewer
recommendation.
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 the editorial
office before completing the review.
If you wish, you can include your name in your published 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 (including the use
of appropriate controls), and are the conclusions supported by the evidence
presented?
Yes
Are the methods sufficiently described to allow the study to be repeated?
No
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 (including electrophoretic gels and blots) free
from apparent manipulation?
Yes
Reviewer’s report
Title: 
Gut microbiota composition and functional prediction in diarrhea-
predominant irritable bowel syndrome
Version: 
3 
Date: 
27 Jan 2021
Reviewer's report:
"PEER REVIEWER ASSESSMENTS: 
OBJECTIVE - Full research articles: is there a clear objective that addresses one
or several testable research questions? (Brief or other article types: is there a
clear objective?)
Yes - there is a clear objective
DESIGN - Is the current approach (including controls and analysis protocols)
appropriate for the objective?
No - there are minor issues
EXECUTION - Are the experiments and analyses performed with sufficient
technical rigor to allow confidence in the results?
Yes - experiments and analyses were performed appropriately
STATISTICS - Is the use of statistics in the manuscript appropriate?
Yes - appropriate statistical analyses have been used in the study
INTERPRETATION - Is the current interpretation/discussion of the results
reasonable and not overstated?
Yes - the author's interpretation is reasonable
OVERALL MANUSCRIPT POTENTIAL - Has the author addressed your
concerns sufficiently for you to now recommend the work as a technically sound
contribution? If not, can further revisions be made to make the work technically
sound?
Probably - with minor revisions
PEER REVIEWER COMMENTS: 
GENERAL COMMENTS: 2021 01 25 
Gut microbiota paper
Comments by Reviewer No. 3:
To the authors: This is a detailed, well organized ,and well implemented study.
You have addressed the concerns of both reviewers adequately, and the
manuscript has been modified accordingly in most cases. However there are a
few concerns, once these have been addressed, I would recommend publication
of this study.
Reviewer 1
Comment 1) Requested a flow chart. This was done (S9).
Comment 2) Requested discussions being shortened into a table. Authors
responded with reasons why this could not be done. 
I concur.
Comment 3) Limited number of patients. Author justified this, as indicated in
line 290, no it was indicated in line 270.
Reviewer 2:
Comment 1): Determination of sample size. The author justified this in lines 86-
87
Comment 2) Antibiotics have a long term effect on the gut microbiome. 
Author
addressed this in 
lines 86-87.
Comment 3) Define organic heart disease. 
Implied in line 86..""taking
antibiotics, probiotics or 
other treatments"". 
Organic heart disease should be added as the 6th item in line
89.
Comment 4) ""psychopath is not appropriate"" psychiatric comorbidity has been
substituted in line 89.
Comment 5) Obesity. Author indicated their comment was modified in line 291,
no it was line 271.
Comment 6) Discussion , recommend adding a paragraph of limitations. Done in
line 271 not 291
as the authors indicated. 
Conclusion summarizes several major points.
Comment 7) ""Change to four subtypes"" 
Done on line 38.
Comment 8 ) Figure 4 Legend is missing. 
This was not done. The author on line
155 states"" as shown in Figure 5"" Which is it? Figure 4 or Figure 5? 
If Figure 4
is redundant, it should be removed, if not, then a legend must be added to Figure
4. Text must be altered accordingly.
Comment 9) ""This study is the first to analyze"" deleted from line 224.
Comment 10) ""China has undergone"" deleted from text as requested.
Comment 11) Line 292 As this section of the mss. has been redacted, the ""thin
body""comment is gone.
I would suggest that you read, and possibly comment on this paper in your
manuscript:
Scallan Walter, E J, Crim SM, Bruce BB, et al Postinfectious Irritable Bowel
Syndrome After Campylobacter Infection 
Am J Gastroenterol 
2019
Oct;114(10):1649-1656. 
doi: 10.14309/ajg.0000000000000408. 
These authors conclude that persons with a Campylobacter infection have a
much higher risk of developing IBS compared with those not diagnosed with
Campylobacter infection. 
This finding supports your finding of the increased presence of Proteobacteria
i.e. Campylobacter in IBD patients compared to normal controls. 
Table S1; Sex is indicated by 1 or 2 which is male and which is female? This
information must be available. 
Why not use M for male and F for female?
REQUESTED REVISIONS: 
All issues have been resolved."
Publons Reviewer Recognition
. Springer Nature can send verification 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 after the final decision on the manuscript has been made. 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 recognize your review on your new
profile page. Publons may use the Review Data to generate derivative metadata
for the benefit of Publons and you as a reviewer, carefully considering the
sensitivity of such information. For example, Publons may verify your record as
a reviewer by updating your profile published on its webservice if you have
registered for such service or help editors to identify candidate reviewers. Please
find the details of processing in Publons’ privacy policy
https://publons.com/about/terms
No
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, 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.
This reviewer has been recruited by a partner organization, Research Square.
Reviewers with declared or apparent competing interests are not utilized for
these reviews. This reviewer has agreed to publication of their comments online
under a Creative Commons Attribution License attributed to Research Square
and was paid a small honorarium for completing the review within a specified
timeframe. Honoraria for reviews such as this are paid regardless of the reviewer
recommendation.
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 the editorial
office before completing the review.
If you wish, you can include your name in your published 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 (including the use
of appropriate controls), and are the conclusions supported by the evidence
presented?
Yes
Are the methods sufficiently described to allow the study to be repeated?
No
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 (including electrophoretic gels and blots) free
from apparent manipulation?
Yes
Please review this paper.
user
Reviewer’s report
Title: 
Gut microbiota composition and functional prediction in diarrhea-
predominant irritable bowel syndrome
Version: 
3 
Date: 
27 Jan 2021
Reviewer's report:
"PEER REVIEWER ASSESSMENTS: 
OBJECTIVE - Full research articles: is there a clear objective that addresses one
or several testable research questions? (Brief or other article types: is there a
clear objective?)
Yes - there is a clear objective
DESIGN - Is the current approach (including controls and analysis protocols)
appropriate for the objective?
No - there are minor issues
EXECUTION - Are the experiments and analyses performed with sufficient
technical rigor to allow confidence in the results?
Yes - experiments and analyses were performed appropriately
STATISTICS - Is the use of statistics in the manuscript appropriate?
Yes - appropriate statistical analyses have been used in the study
INTERPRETATION - Is the current interpretation/discussion of the results
reasonable and not overstated?
Yes - the author's interpretation is reasonable
OVERALL MANUSCRIPT POTENTIAL - Has the author addressed your
concerns sufficiently for you to now recommend the work as a technically sound
contribution? If not, can further revisions be made to make the work technically
sound?
Probably - with minor revisions
PEER REVIEWER COMMENTS: 
GENERAL COMMENTS: 2021 01 25 
Gut microbiota paper
Comments by Reviewer No. 3:
To the authors: This is a detailed, well organized ,and well implemented study.
You have addressed the concerns of both reviewers adequately, and the
manuscript has been modified accordingly in most cases. However there are a
few concerns, once these have been addressed, I would recommend publication
of this study.
Reviewer 1
Comment 1) Requested a flow chart. This was done (S9).
Comment 2) Requested discussions being shortened into a table. Authors
responded with reasons why this could not be done. 
I concur.
Comment 3) Limited number of patients. Author justified this, as indicated in
line 290, no it was indicated in line 270.
Reviewer 2:
Comment 1): Determination of sample size. The author justified this in lines 86-
87
Comment 2) Antibiotics have a long term effect on the gut microbiome. 
Author
addressed this in 
lines 86-87.
Comment 3) Define organic heart disease. 
Implied in line 86..""taking
antibiotics, probiotics or 
other treatments"". 
Organic heart disease should be added as the 6th item in line
89.
Comment 4) ""psychopath is not appropriate"" psychiatric comorbidity has been
substituted in line 89.
Comment 5) Obesity. Author indicated their comment was modified in line 291,
no it was line 271.
Comment 6) Discussion , recommend adding a paragraph of limitations. Done in
line 271 not 291
as the authors indicated. 
Conclusion summarizes several major points.
Comment 7) ""Change to four subtypes"" 
Done on line 38.
Comment 8 ) Figure 4 Legend is missing. 
This was not done. The author on line
155 states"" as shown in Figure 5"" Which is it? Figure 4 or Figure 5? 
If Figure 4
is redundant, it should be removed, if not, then a legend must be added to Figure
4. Text must be altered accordingly.
Comment 9) ""This study is the first to analyze"" deleted from line 224.
Comment 10) ""China has undergone"" deleted from text as requested.
Comment 11) Line 292 As this section of the mss. has been redacted, the ""thin
body""comment is gone.
I would suggest that you read, and possibly comment on this paper in your
manuscript:
Scallan Walter, E J, Crim SM, Bruce BB, et al Postinfectious Irritable Bowel
Syndrome After Campylobacter Infection 
Am J Gastroenterol 
2019
Oct;114(10):1649-1656. 
doi: 10.14309/ajg.0000000000000408. 
These authors conclude that persons with a Campylobacter infection have a
much higher risk of developing IBS compared with those not diagnosed with
Campylobacter infection. 
This finding supports your finding of the increased presence of Proteobacteria
i.e. Campylobacter in IBD patients compared to normal controls. 
Table S1; Sex is indicated by 1 or 2 which is male and which is female? This
information must be available. 
Why not use M for male and F for female?
REQUESTED REVISIONS: 
All issues have been resolved."
Publons Reviewer Recognition
. Springer Nature can send verification 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 after the final decision on the manuscript has been made. 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 recognize your review on your new
profile page. Publons may use the Review Data to generate derivative metadata
for the benefit of Publons and you as a reviewer, carefully considering the
sensitivity of such information. For example, Publons may verify your record as
a reviewer by updating your profile published on its webservice if you have
registered for such service or help editors to identify candidate reviewers. Please
find the details of processing in Publons’ privacy policy
https://publons.com/about/terms
No
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, 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.
This reviewer has been recruited by a partner organization, Research Square.
Reviewers with declared or apparent competing interests are not utilized for
these reviews. This reviewer has agreed to publication of their comments online
under a Creative Commons Attribution License attributed to Research Square
and was paid a small honorarium for completing the review within a specified
timeframe. Honoraria for reviews such as this are paid regardless of the reviewer
recommendation.
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 the editorial
office before completing the review.
If you wish, you can include your name in your published 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 (including the use
of appropriate controls), and are the conclusions supported by the evidence
presented?
Yes
Are the methods sufficiently described to allow the study to be repeated?
No
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 (including electrophoretic gels and blots) free
from apparent manipulation?
Yes
assistant