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: 09 May 2018 
 
Reviewer:  Patrizia  Kump  
 
Reviewer’s report:  
 
Please include all comments for the authors in this box rather than uploading your report as an 
attachment. Please only upl oad as attachments annotated versions of manuscripts, graphs, 
supporting materials or other aspects of your report which cannot be included in a text format.  
 
Please overwrite this text when adding your comments to the authors.  
 
Drs Brown, Flemer, Joyce and  O`Toole studied bile and fatty acid metabolism after FMT in C. 
diff. infection in 10 patients. They found a restoration of secondary and tertiary bile acid 
production. The effect on fatty acids has been demonstrated to be less clear.  
 
 
Major comments:  
 
-) Page 13 line 271: the patient with pre -existing ulcerative colitis has to be excluded. Alteration 
of microbiota in IBD is a well known pathogenetic factor, the mechanisms of FMT or bile acid 
metabolism in IBD is still not well understood.  
 
-) page 15 line 305: SI Fig 1A Shows only nine dots for donor samples, but 10 are reported in the 
text (page 14, line 297)!!  
 
-) page 16 line 329:  4 Co -Abundance Groups are reported. CAG 4 is not further mentioned in 
the study. If not relevant for the evaluation, it shoul d be removed from the text as well as from 
exploratory figure 1. Why was not it relevant?  
 
-) page 13 line 279: Was the patient, who relapsed after FMT, treated with the Open Biome 
transplant? Did the authors see any differences in primary bile acids, micro biota, FA etc after 
FMT compared to responders? Detailed results and discussion are missing!  
 
 
Minor comments:  
 
-)The authors used a combination of upper and lower stool application for FMT (via gastroscopy 
in the duodenum as well as via colonoscopy in the d istal ileum and right colon). What is the 
rational for such a protocol as FMT as each of the application routes is effective and 
recommended in international guidelines?  
-)How many day or hours was antibiotic treatment stopped before FMT?  
 
-) Why were onl y 7 "RF" samples acquired after FMT and at different time points? Where all 
patients in clinical remission at time of sample collection?  
 
-) Recently Solbach et al (PLoS one 13(5): e0196977) reported a significantly lower prevalence 
of BaiCD gene Cluster i n rCDI patients, 1/2 patient turned positive after FMT. This paper could 
be used for discussion  
 
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.  
 
Unable to assess  
 
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 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, 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 declare that I have not 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 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: 09 May 2018 
 
Reviewer:  Patrizia  Kump  
 
Reviewer’s report:  
 
Please include all comments for the authors in this box rather than uploading your report as an 
attachment. Please only upl oad as attachments annotated versions of manuscripts, graphs, 
supporting materials or other aspects of your report which cannot be included in a text format.  
 
Please overwrite this text when adding your comments to the authors.  
 
Drs Brown, Flemer, Joyce and  O`Toole studied bile and fatty acid metabolism after FMT in C. 
diff. infection in 10 patients. They found a restoration of secondary and tertiary bile acid 
production. The effect on fatty acids has been demonstrated to be less clear.  
 
 
Major comments:  
 
-) Page 13 line 271: the patient with pre -existing ulcerative colitis has to be excluded. Alteration 
of microbiota in IBD is a well known pathogenetic factor, the mechanisms of FMT or bile acid 
metabolism in IBD is still not well understood.  
 
-) page 15 line 305: SI Fig 1A Shows only nine dots for donor samples, but 10 are reported in the 
text (page 14, line 297)!!  
 
-) page 16 line 329:  4 Co -Abundance Groups are reported. CAG 4 is not further mentioned in 
the study. If not relevant for the evaluation, it shoul d be removed from the text as well as from 
exploratory figure 1. Why was not it relevant?  
 
-) page 13 line 279: Was the patient, who relapsed after FMT, treated with the Open Biome 
transplant? Did the authors see any differences in primary bile acids, micro biota, FA etc after 
FMT compared to responders? Detailed results and discussion are missing!  
 
 
Minor comments:  
 
-)The authors used a combination of upper and lower stool application for FMT (via gastroscopy 
in the duodenum as well as via colonoscopy in the d istal ileum and right colon). What is the 
rational for such a protocol as FMT as each of the application routes is effective and 
recommended in international guidelines?  
-)How many day or hours was antibiotic treatment stopped before FMT?  
 
-) Why were onl y 7 "RF" samples acquired after FMT and at different time points? Where all 
patients in clinical remission at time of sample collection?  
 
-) Recently Solbach et al (PLoS one 13(5): e0196977) reported a significantly lower prevalence 
of BaiCD gene Cluster i n rCDI patients, 1/2 patient turned positive after FMT. This paper could 
be used for discussion  
 
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.  
 
Unable to assess  
 
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 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, 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 declare that I have not 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 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: 09 May 2018 
 
Reviewer:  Patrizia  Kump  
 
Reviewer’s report:  
 
Please include all comments for the authors in this box rather than uploading your report as an 
attachment. Please only upl oad as attachments annotated versions of manuscripts, graphs, 
supporting materials or other aspects of your report which cannot be included in a text format.  
 
Please overwrite this text when adding your comments to the authors.  
 
Drs Brown, Flemer, Joyce and  O`Toole studied bile and fatty acid metabolism after FMT in C. 
diff. infection in 10 patients. They found a restoration of secondary and tertiary bile acid 
production. The effect on fatty acids has been demonstrated to be less clear.  
 
 
Major comments:  
 
-) Page 13 line 271: the patient with pre -existing ulcerative colitis has to be excluded. Alteration 
of microbiota in IBD is a well known pathogenetic factor, the mechanisms of FMT or bile acid 
metabolism in IBD is still not well understood.  
 
-) page 15 line 305: SI Fig 1A Shows only nine dots for donor samples, but 10 are reported in the 
text (page 14, line 297)!!  
 
-) page 16 line 329:  4 Co -Abundance Groups are reported. CAG 4 is not further mentioned in 
the study. If not relevant for the evaluation, it shoul d be removed from the text as well as from 
exploratory figure 1. Why was not it relevant?  
 
-) page 13 line 279: Was the patient, who relapsed after FMT, treated with the Open Biome 
transplant? Did the authors see any differences in primary bile acids, micro biota, FA etc after 
FMT compared to responders? Detailed results and discussion are missing!  
 
 
Minor comments:  
 
-)The authors used a combination of upper and lower stool application for FMT (via gastroscopy 
in the duodenum as well as via colonoscopy in the d istal ileum and right colon). What is the 
rational for such a protocol as FMT as each of the application routes is effective and 
recommended in international guidelines?  
-)How many day or hours was antibiotic treatment stopped before FMT?  
 
-) Why were onl y 7 "RF" samples acquired after FMT and at different time points? Where all 
patients in clinical remission at time of sample collection?  
 
-) Recently Solbach et al (PLoS one 13(5): e0196977) reported a significantly lower prevalence 
of BaiCD gene Cluster i n rCDI patients, 1/2 patient turned positive after FMT. This paper could 
be used for discussion  
 
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.  
 
Unable to assess  
 
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 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, 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 declare that I have not 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 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