Reviewer ’s report  
Title:  Small intestinal bacterial overgrowth is associated with irritable bowel syndrome and is 
independent of proton pump inhibitor usage  
 
Version:  0 Date : 10 Mar 2016  
 
Reviewer:  Lindsey  G. Albenberg  
 
Reviewer's report:  
This is overall a well done study which adds to our current knowledge of SIBO and IBS and the 
role of PPI therapy. The number of endoscopie s performed with duodenal aspirates was 
impressive, however, the subgroups (IBS, PPI use) were relatively small which is a limitation. 
Additionally, the data on PPI use seemed limited, however, how this data was collected was not 
well described and needs t o be addressed. Comments by section:  
 
Abstract: Only the total number of endoscopies was described in the abstract. However, the 
abstract should also include the n in the subgroups including number of subjects with SIBO and 
IBS and number of subjects with SIBO and IBS plus PPI intake especially because this relates 
directly to the primary outcome. Also, in the conclusion of the abstract, the last sentence is too 
strong particularly because gastric pH was not measured in this study.  
 
Introduction: The first sentence of the first paragraph should have references. Also, I found the 
term "colonic type bacteria" confusing even after looking at reference number 5. How do you 
differentiate between colonic type bacteria and bacteria normally found in the small bowel  based 
on aerobic culture? The majority of the bacteria in the colon are anaerobes and we do know that 
there are aerotolerant bacteria normally present in the small bowel. This needs to be clarified. 
Also, please clarify whether the 904 patients in the pro spective cohort included the previously 
published 320 subjects.  
  
Methods:  
Study design: Please clarify whether antibiotic use was an exclusion. It appears as an exclusion 
in figure 1, but is not mentioned in the text. It is also important to disclose what cut-off was used 
in terms of time frame. It would also be helpful to give additional details in regards to the sample 
collection method. Was anything done to limit contamination? If not, this should be mentioned 
as a study limitation. Also, occasionally, w hen the duodenum is intubated there is very little fluid 
if any present. What was done in this situation? Were there any situations when a wash was 
required? When describing IBS classification, Rome criteria should be referenced.  
Statistical analysis: Plea se describe method for obtaining PPI data. Was this based on chart 
review? Patient questionnaires? Did you have accurate start and stop dates? Was adherence 
assessed?  
Finally, the manuscript is statistics heavy. Would recommend statistical review.  
 
Results:  
Primary study endpoint:  
Recommend reordering this section to improve the flow. The current flow is difficult to read. 
Would recommend discussing table 1 all at once. Right now, table 1 is discussed, then table 2, 
and then back to table 1. Would r ecommend discussing subjects with and without SIBO and all 
of the clinical metadata, then the analysis between presence of SIBO and presence of IBS, and 
then the PPI discussion. At the top of page 7 would mention in the text the percentage of SIBO at 
all 3 thresholds.  
Secondary endpoints:  
Again, the method for capture of PPI data needs to be described in detail. I do not think that table 
4 adds very much to the manuscript because it does not have anything to do with SIBO. I 
interpret it as patients with IBS  are frequently prescribed PPIs. This manuscript to me is more 
about SIBO and IBS and the relationship to PPI use. Similarly, table 5 would be more relevant if 
you described the type of bacteria in IBS with and without SIBO and with and without PPI. 
Again,  this paper seems to be more about IBS and SIBO.  
 
Discussion:  
At the top of page 10, a weak association is made between SIBO, T2DM, and dysmotility. I 
would omit this. I also do not think that the second paragraph on page 10 is needed or relevant. 
It's not  relevant to the aims of the study. We again need more information on how the PPI data 
was acquired. Particularly, how was time acquired?  
Conclusions:  
Similar to the abstract, the last sentence is too strong as pH was not measured.  
 
Table 2: It is implie d that the remainder of the endoscopies (40%) were normal, is this true? The 
ones where gastritis or ulcers were not found. Please clarify.  
 
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 requi re further 
assessment in your comments to the editors.  
I recommend additional statistical review  
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, 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 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 recei ved 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 co mpeting 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 website along with the authors' 
responses. I agree for my report to be made available under an Open Access Creative Commons 
CC-BY licens e (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 polic y of the journal  
Reviewer ’s report  
Title:  Small intestinal bacterial overgrowth is associated with irritable bowel syndrome and is 
independent of proton pump inhibitor usage  
 
Version:  0 Date : 10 Mar 2016  
 
Reviewer:  Lindsey  G. Albenberg  
 
Reviewer's report:  
This is overall a well done study which adds to our current knowledge of SIBO and IBS and the 
role of PPI therapy. The number of endoscopie s performed with duodenal aspirates was 
impressive, however, the subgroups (IBS, PPI use) were relatively small which is a limitation. 
Additionally, the data on PPI use seemed limited, however, how this data was collected was not 
well described and needs t o be addressed. Comments by section:  
 
Abstract: Only the total number of endoscopies was described in the abstract. However, the 
abstract should also include the n in the subgroups including number of subjects with SIBO and 
IBS and number of subjects with SIBO and IBS plus PPI intake especially because this relates 
directly to the primary outcome. Also, in the conclusion of the abstract, the last sentence is too 
strong particularly because gastric pH was not measured in this study.  
 
Introduction: The first sentence of the first paragraph should have references. Also, I found the 
term "colonic type bacteria" confusing even after looking at reference number 5. How do you 
differentiate between colonic type bacteria and bacteria normally found in the small bowel  based 
on aerobic culture? The majority of the bacteria in the colon are anaerobes and we do know that 
there are aerotolerant bacteria normally present in the small bowel. This needs to be clarified. 
Also, please clarify whether the 904 patients in the pro spective cohort included the previously 
published 320 subjects.  
  
Methods:  
Study design: Please clarify whether antibiotic use was an exclusion. It appears as an exclusion 
in figure 1, but is not mentioned in the text. It is also important to disclose what cut-off was used 
in terms of time frame. It would also be helpful to give additional details in regards to the sample 
collection method. Was anything done to limit contamination? If not, this should be mentioned 
as a study limitation. Also, occasionally, w hen the duodenum is intubated there is very little fluid 
if any present. What was done in this situation? Were there any situations when a wash was 
required? When describing IBS classification, Rome criteria should be referenced.  
Statistical analysis: Plea se describe method for obtaining PPI data. Was this based on chart 
review? Patient questionnaires? Did you have accurate start and stop dates? Was adherence 
assessed?  
Finally, the manuscript is statistics heavy. Would recommend statistical review.  
 
Results:  
Primary study endpoint:  
Recommend reordering this section to improve the flow. The current flow is difficult to read. 
Would recommend discussing table 1 all at once. Right now, table 1 is discussed, then table 2, 
and then back to table 1. Would r ecommend discussing subjects with and without SIBO and all 
of the clinical metadata, then the analysis between presence of SIBO and presence of IBS, and 
then the PPI discussion. At the top of page 7 would mention in the text the percentage of SIBO at 
all 3 thresholds.  
Secondary endpoints:  
Again, the method for capture of PPI data needs to be described in detail. I do not think that table 
4 adds very much to the manuscript because it does not have anything to do with SIBO. I 
interpret it as patients with IBS  are frequently prescribed PPIs. This manuscript to me is more 
about SIBO and IBS and the relationship to PPI use. Similarly, table 5 would be more relevant if 
you described the type of bacteria in IBS with and without SIBO and with and without PPI. 
Again,  this paper seems to be more about IBS and SIBO.  
 
Discussion:  
At the top of page 10, a weak association is made between SIBO, T2DM, and dysmotility. I 
would omit this. I also do not think that the second paragraph on page 10 is needed or relevant. 
It's not  relevant to the aims of the study. We again need more information on how the PPI data 
was acquired. Particularly, how was time acquired?  
Conclusions:  
Similar to the abstract, the last sentence is too strong as pH was not measured.  
 
Table 2: It is implie d that the remainder of the endoscopies (40%) were normal, is this true? The 
ones where gastritis or ulcers were not found. Please clarify.  
 
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 requi re further 
assessment in your comments to the editors.  
I recommend additional statistical review  
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, 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 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 recei ved 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 co mpeting 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 website along with the authors' 
responses. I agree for my report to be made available under an Open Access Creative Commons 
CC-BY licens e (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 polic y of the journal  
Please review this paper.
user
Reviewer ’s report  
Title:  Small intestinal bacterial overgrowth is associated with irritable bowel syndrome and is 
independent of proton pump inhibitor usage  
 
Version:  0 Date : 10 Mar 2016  
 
Reviewer:  Lindsey  G. Albenberg  
 
Reviewer's report:  
This is overall a well done study which adds to our current knowledge of SIBO and IBS and the 
role of PPI therapy. The number of endoscopie s performed with duodenal aspirates was 
impressive, however, the subgroups (IBS, PPI use) were relatively small which is a limitation. 
Additionally, the data on PPI use seemed limited, however, how this data was collected was not 
well described and needs t o be addressed. Comments by section:  
 
Abstract: Only the total number of endoscopies was described in the abstract. However, the 
abstract should also include the n in the subgroups including number of subjects with SIBO and 
IBS and number of subjects with SIBO and IBS plus PPI intake especially because this relates 
directly to the primary outcome. Also, in the conclusion of the abstract, the last sentence is too 
strong particularly because gastric pH was not measured in this study.  
 
Introduction: The first sentence of the first paragraph should have references. Also, I found the 
term "colonic type bacteria" confusing even after looking at reference number 5. How do you 
differentiate between colonic type bacteria and bacteria normally found in the small bowel  based 
on aerobic culture? The majority of the bacteria in the colon are anaerobes and we do know that 
there are aerotolerant bacteria normally present in the small bowel. This needs to be clarified. 
Also, please clarify whether the 904 patients in the pro spective cohort included the previously 
published 320 subjects.  
  
Methods:  
Study design: Please clarify whether antibiotic use was an exclusion. It appears as an exclusion 
in figure 1, but is not mentioned in the text. It is also important to disclose what cut-off was used 
in terms of time frame. It would also be helpful to give additional details in regards to the sample 
collection method. Was anything done to limit contamination? If not, this should be mentioned 
as a study limitation. Also, occasionally, w hen the duodenum is intubated there is very little fluid 
if any present. What was done in this situation? Were there any situations when a wash was 
required? When describing IBS classification, Rome criteria should be referenced.  
Statistical analysis: Plea se describe method for obtaining PPI data. Was this based on chart 
review? Patient questionnaires? Did you have accurate start and stop dates? Was adherence 
assessed?  
Finally, the manuscript is statistics heavy. Would recommend statistical review.  
 
Results:  
Primary study endpoint:  
Recommend reordering this section to improve the flow. The current flow is difficult to read. 
Would recommend discussing table 1 all at once. Right now, table 1 is discussed, then table 2, 
and then back to table 1. Would r ecommend discussing subjects with and without SIBO and all 
of the clinical metadata, then the analysis between presence of SIBO and presence of IBS, and 
then the PPI discussion. At the top of page 7 would mention in the text the percentage of SIBO at 
all 3 thresholds.  
Secondary endpoints:  
Again, the method for capture of PPI data needs to be described in detail. I do not think that table 
4 adds very much to the manuscript because it does not have anything to do with SIBO. I 
interpret it as patients with IBS  are frequently prescribed PPIs. This manuscript to me is more 
about SIBO and IBS and the relationship to PPI use. Similarly, table 5 would be more relevant if 
you described the type of bacteria in IBS with and without SIBO and with and without PPI. 
Again,  this paper seems to be more about IBS and SIBO.  
 
Discussion:  
At the top of page 10, a weak association is made between SIBO, T2DM, and dysmotility. I 
would omit this. I also do not think that the second paragraph on page 10 is needed or relevant. 
It's not  relevant to the aims of the study. We again need more information on how the PPI data 
was acquired. Particularly, how was time acquired?  
Conclusions:  
Similar to the abstract, the last sentence is too strong as pH was not measured.  
 
Table 2: It is implie d that the remainder of the endoscopies (40%) were normal, is this true? The 
ones where gastritis or ulcers were not found. Please clarify.  
 
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 requi re further 
assessment in your comments to the editors.  
I recommend additional statistical review  
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, 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 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 recei ved 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 co mpeting 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 website along with the authors' 
responses. I agree for my report to be made available under an Open Access Creative Commons 
CC-BY licens e (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 polic y of the journal  
assistant