Reviewer ’s report  
 
Title: Taurocholic acid is an active promoting factor, not just a biomarker of progression of liver 
cirrhosis: evidence from a human metabolomic study and in vitro experiments  
 
Version: 0 Date: 17 Apr 2018  
 
Reviewer: Abhishek Agnihotri  
 
Reviewer's report:  
 
The authors present an  interesting and little explored aspect of cirrhosis pathogenesis. Bile acids 
along with interaction with microbiome have been postulated to play a key role in pathogenesis 
of cirrhosis. It is unknown if bile acids could be therapeutic targets in altering the disease course.  
The aim and methodology is clear. The manuscript requires major grammatical corrections.  
There also needs to be a detailed discussion of the limitations of this study. It is unclear if sample 
size was adequate or if study was adequately  powered to measure the effects seen in the study.  
1) Last paragraph of Background is redundant and should be removed.  
 
2) Please provide a flowchart figure of bile acid synthesis mechanism. It will be easier to follow 
than text description.  
 
3) Please explain if sample size estimation was done prior to initiation of the study. Since 
authors reference the article by Wang, et al. (J. Proteome Res., 2016, 15 (4), pp 1126 -1134) 
and other studies have shown some correlation between TCA levels and d ecompensation of 
cirrhosis, did the authors predict at the start of the study the sample size required to 
demonstrate a significant correlation between certain bile acids and severity of cirrhosis.  
 
4) Authors mention PBS solution as control for cell proli feration assay. I assume this is 
phosphate buffered saline, please mention this in list of abbreviations. Moreover it would 
have been interesting to compare this with DCA or CA as control to validate the hypothesis 
that serum level of TCA is indeed a valua ble biomarker compared to DCA or CA as they are 
the least elevated bile acids. Please mention this in discussion.  
 
5) Please discuss the limitation of sample size and possible lack of power in discussions.  
 
6) Please suggest future directions based on thes e results in discussion.  
 
 
Some grammatical errors - 
Page 2 Line marker 27: Background: First line is grammatically flawed, please change it. Uncler 
what "accumulation of chronic liver diseas" mean.  
Page 2 Line marker 44: Background: Please change to "li ver cirrhosis was over 1 million"  
Page 4 Line marker 33: Metabolome is not a research method.  
Page 4 Line marker 58: Spelling correction: metabolome  
Page 5 Line marker 33: Remove the word have before fasted.  
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 a n 
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:  
 
Not suitable for publication unless extensively edited  
 
Declaration of competing interests  
Please complete a declaration of competing interests, considering the following questions:  
 
1. Have you in t he 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 organisat ion 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 reimbursemen ts, 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 t his 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.  
 
None  
 
I agree to the open peer review policy of the journal. I understand that my name w ill 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 u nder 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 b e published.  
 
I agree to the open peer review policy of the jou rnal 
Reviewer ’s report  
 
Title: Taurocholic acid is an active promoting factor, not just a biomarker of progression of liver 
cirrhosis: evidence from a human metabolomic study and in vitro experiments  
 
Version: 0 Date: 17 Apr 2018  
 
Reviewer: Abhishek Agnihotri  
 
Reviewer's report:  
 
The authors present an  interesting and little explored aspect of cirrhosis pathogenesis. Bile acids 
along with interaction with microbiome have been postulated to play a key role in pathogenesis 
of cirrhosis. It is unknown if bile acids could be therapeutic targets in altering the disease course.  
The aim and methodology is clear. The manuscript requires major grammatical corrections.  
There also needs to be a detailed discussion of the limitations of this study. It is unclear if sample 
size was adequate or if study was adequately  powered to measure the effects seen in the study.  
1) Last paragraph of Background is redundant and should be removed.  
 
2) Please provide a flowchart figure of bile acid synthesis mechanism. It will be easier to follow 
than text description.  
 
3) Please explain if sample size estimation was done prior to initiation of the study. Since 
authors reference the article by Wang, et al. (J. Proteome Res., 2016, 15 (4), pp 1126 -1134) 
and other studies have shown some correlation between TCA levels and d ecompensation of 
cirrhosis, did the authors predict at the start of the study the sample size required to 
demonstrate a significant correlation between certain bile acids and severity of cirrhosis.  
 
4) Authors mention PBS solution as control for cell proli feration assay. I assume this is 
phosphate buffered saline, please mention this in list of abbreviations. Moreover it would 
have been interesting to compare this with DCA or CA as control to validate the hypothesis 
that serum level of TCA is indeed a valua ble biomarker compared to DCA or CA as they are 
the least elevated bile acids. Please mention this in discussion.  
 
5) Please discuss the limitation of sample size and possible lack of power in discussions.  
 
6) Please suggest future directions based on thes e results in discussion.  
 
 
Some grammatical errors - 
Page 2 Line marker 27: Background: First line is grammatically flawed, please change it. Uncler 
what "accumulation of chronic liver diseas" mean.  
Page 2 Line marker 44: Background: Please change to "li ver cirrhosis was over 1 million"  
Page 4 Line marker 33: Metabolome is not a research method.  
Page 4 Line marker 58: Spelling correction: metabolome  
Page 5 Line marker 33: Remove the word have before fasted.  
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 a n 
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:  
 
Not suitable for publication unless extensively edited  
 
Declaration of competing interests  
Please complete a declaration of competing interests, considering the following questions:  
 
1. Have you in t he 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 organisat ion 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 reimbursemen ts, 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 t his 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.  
 
None  
 
I agree to the open peer review policy of the journal. I understand that my name w ill 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 u nder 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 b e published.  
 
I agree to the open peer review policy of the jou rnal 
Please review this paper.
user
Reviewer ’s report  
 
Title: Taurocholic acid is an active promoting factor, not just a biomarker of progression of liver 
cirrhosis: evidence from a human metabolomic study and in vitro experiments  
 
Version: 0 Date: 17 Apr 2018  
 
Reviewer: Abhishek Agnihotri  
 
Reviewer's report:  
 
The authors present an  interesting and little explored aspect of cirrhosis pathogenesis. Bile acids 
along with interaction with microbiome have been postulated to play a key role in pathogenesis 
of cirrhosis. It is unknown if bile acids could be therapeutic targets in altering the disease course.  
The aim and methodology is clear. The manuscript requires major grammatical corrections.  
There also needs to be a detailed discussion of the limitations of this study. It is unclear if sample 
size was adequate or if study was adequately  powered to measure the effects seen in the study.  
1) Last paragraph of Background is redundant and should be removed.  
 
2) Please provide a flowchart figure of bile acid synthesis mechanism. It will be easier to follow 
than text description.  
 
3) Please explain if sample size estimation was done prior to initiation of the study. Since 
authors reference the article by Wang, et al. (J. Proteome Res., 2016, 15 (4), pp 1126 -1134) 
and other studies have shown some correlation between TCA levels and d ecompensation of 
cirrhosis, did the authors predict at the start of the study the sample size required to 
demonstrate a significant correlation between certain bile acids and severity of cirrhosis.  
 
4) Authors mention PBS solution as control for cell proli feration assay. I assume this is 
phosphate buffered saline, please mention this in list of abbreviations. Moreover it would 
have been interesting to compare this with DCA or CA as control to validate the hypothesis 
that serum level of TCA is indeed a valua ble biomarker compared to DCA or CA as they are 
the least elevated bile acids. Please mention this in discussion.  
 
5) Please discuss the limitation of sample size and possible lack of power in discussions.  
 
6) Please suggest future directions based on thes e results in discussion.  
 
 
Some grammatical errors - 
Page 2 Line marker 27: Background: First line is grammatically flawed, please change it. Uncler 
what "accumulation of chronic liver diseas" mean.  
Page 2 Line marker 44: Background: Please change to "li ver cirrhosis was over 1 million"  
Page 4 Line marker 33: Metabolome is not a research method.  
Page 4 Line marker 58: Spelling correction: metabolome  
Page 5 Line marker 33: Remove the word have before fasted.  
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 a n 
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:  
 
Not suitable for publication unless extensively edited  
 
Declaration of competing interests  
Please complete a declaration of competing interests, considering the following questions:  
 
1. Have you in t he 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 organisat ion 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 reimbursemen ts, 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 t his 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.  
 
None  
 
I agree to the open peer review policy of the journal. I understand that my name w ill 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 u nder 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 b e published.  
 
I agree to the open peer review policy of the jou rnal 
assistant