Reviewer ’s report  
 
Title:  Changes in microbiota composition, bile and fatty acid metabo lism, in successful faecal 
microbiota transplantation for Clostridioides difficile infection.  
 
Version: 0 Date: 08 May 2018 
 
Reviewer:  Jonna  Jalanka  
 
Reviewer’s report:  
 
The manuscript entitled" Changes in microbiota, bile and fatty acid metabolism in successful 
faecal microbiota transplantation for Clostridioides difficile infect ion" by Brown et al., describes 
a small cohort of recurrent CDI patients treated with FMT. They determined the patients' 
intestinal microbiota composition, faecal bile and fatty acid composition and levels of 
methanogenic archaea and attempted to find asso ciations between the different analytic methods. 
Although finding these association is novel, and interesting there were several weaknesses in this 
manuscript.  
 
The main concern is the quality of the 16S sequencing. The microbiota composition can not be 
reliably described with this shallow sequencing, making the compositional analysis and 
correlational analysis unreliable. The statistical methods utilized to analyse the microbiota 
compositional changes is not optimal (or described in the methods section) an d should be revised 
for the next round of submission.  
 
The manuscript should be revised for grammar as well as reordering of the text. e.g. the results 
section is lacking several p -values and is discussing the results in the results section (but failing 
to provide to correct reference or the actual result).  
 
The figures are not self -explanatory and there are mistakes in the tables. The main critique is that 
the because the microbiota sequencing is of poor quality, the novelty in this study, the correlation  
of the bile and fatty acids with the microbiota changes is unreliable. For this publication to be 
published, the microbiota composition should be re -analysed.  
 
Are the methods appropriate and well described?  
If not, please specify what is required in your comments to the authors.  
 
No 
 
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:  
 
Needs some language corrections before being published  
 
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.  
 
I have no computing interes ts 
 
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 au thors' 
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:  Changes in microbiota composition, bile and fatty acid metabo lism, in successful faecal 
microbiota transplantation for Clostridioides difficile infection.  
 
Version: 0 Date: 08 May 2018 
 
Reviewer:  Jonna  Jalanka  
 
Reviewer’s report:  
 
The manuscript entitled" Changes in microbiota, bile and fatty acid metabolism in successful 
faecal microbiota transplantation for Clostridioides difficile infect ion" by Brown et al., describes 
a small cohort of recurrent CDI patients treated with FMT. They determined the patients' 
intestinal microbiota composition, faecal bile and fatty acid composition and levels of 
methanogenic archaea and attempted to find asso ciations between the different analytic methods. 
Although finding these association is novel, and interesting there were several weaknesses in this 
manuscript.  
 
The main concern is the quality of the 16S sequencing. The microbiota composition can not be 
reliably described with this shallow sequencing, making the compositional analysis and 
correlational analysis unreliable. The statistical methods utilized to analyse the microbiota 
compositional changes is not optimal (or described in the methods section) an d should be revised 
for the next round of submission.  
 
The manuscript should be revised for grammar as well as reordering of the text. e.g. the results 
section is lacking several p -values and is discussing the results in the results section (but failing 
to provide to correct reference or the actual result).  
 
The figures are not self -explanatory and there are mistakes in the tables. The main critique is that 
the because the microbiota sequencing is of poor quality, the novelty in this study, the correlation  
of the bile and fatty acids with the microbiota changes is unreliable. For this publication to be 
published, the microbiota composition should be re -analysed.  
 
Are the methods appropriate and well described?  
If not, please specify what is required in your comments to the authors.  
 
No 
 
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:  
 
Needs some language corrections before being published  
 
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.  
 
I have no computing interes ts 
 
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 au thors' 
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:  Changes in microbiota composition, bile and fatty acid metabo lism, in successful faecal 
microbiota transplantation for Clostridioides difficile infection.  
 
Version: 0 Date: 08 May 2018 
 
Reviewer:  Jonna  Jalanka  
 
Reviewer’s report:  
 
The manuscript entitled" Changes in microbiota, bile and fatty acid metabolism in successful 
faecal microbiota transplantation for Clostridioides difficile infect ion" by Brown et al., describes 
a small cohort of recurrent CDI patients treated with FMT. They determined the patients' 
intestinal microbiota composition, faecal bile and fatty acid composition and levels of 
methanogenic archaea and attempted to find asso ciations between the different analytic methods. 
Although finding these association is novel, and interesting there were several weaknesses in this 
manuscript.  
 
The main concern is the quality of the 16S sequencing. The microbiota composition can not be 
reliably described with this shallow sequencing, making the compositional analysis and 
correlational analysis unreliable. The statistical methods utilized to analyse the microbiota 
compositional changes is not optimal (or described in the methods section) an d should be revised 
for the next round of submission.  
 
The manuscript should be revised for grammar as well as reordering of the text. e.g. the results 
section is lacking several p -values and is discussing the results in the results section (but failing 
to provide to correct reference or the actual result).  
 
The figures are not self -explanatory and there are mistakes in the tables. The main critique is that 
the because the microbiota sequencing is of poor quality, the novelty in this study, the correlation  
of the bile and fatty acids with the microbiota changes is unreliable. For this publication to be 
published, the microbiota composition should be re -analysed.  
 
Are the methods appropriate and well described?  
If not, please specify what is required in your comments to the authors.  
 
No 
 
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:  
 
Needs some language corrections before being published  
 
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.  
 
I have no computing interes ts 
 
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 au thors' 
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