Review for 10.1186/s12876-020-01195-1 (2020)

Reviewer ’s report  
 
Title: Intestinal fl ora imbalance affects bile acid metabolism a nd is associated with gallstone 
formation.  
 
Version: 1 Date: 19 Dec 2019  
 
Reviewer: Joseph Pierre  
 
Reviewer's report:  
The revision by Wang et al has improved several editor and reviewer comments. I have several 
minor points remaining.  
1) The figures are all poor re solution. While this may be due to uploading, it is almost not 
possible to rea d the figures panels and axis labels.  
2) I may have missed it, but I do not see a statistical reference in the methods for the core 
microbiome analysis displayed in figure 1.  
3) Similarly, within the methods, the authors should state what sequencing dept h was used for 
rarefaction curves of alpha diversity and other analysis. In fact, this reviewer does not find the 
total reads per sample obtained or other information pertaining to the sequencing depth or quality 
used. Please address.  
 
 
 
Are the methods appropriate and well described?  
If not, please specify what is re quired 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, plea se explain in your comments to the authors.  
 
Yes 
 
Are you able to assess any statistics in the manus cript 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, f ees, funding, or salary from an 
organisation that may in any way gain or lose financially from the publicat ion 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 current ly 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 ot her 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 giv e details below.  
 
I declare that I have no competing interests.  
 
I agree to the open peer review policy of the journal. I understan d that my name will be included 
on my report to the authors and, if the manuscript is accepted f or 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 in cluded as confidential comments 
to the editors, which will not be published.  
 
I agree to the open peer review policy of the journal