Title: Comparison of Sampling Methods in Assessing the Microbiomefrom Patients with
Ulcerative Colitis
Version: 1 Date: 20 Jul 2021
Reviewer's report:
In this work the authors investigate the microbiome differences in luminal lavage, mucosal
biopsies and stool samples. The addition of luminal lavage is interesting. In general I find the
paper well written without major drawbacks and want to congratulate the authors on their work.
What I would like to see, though, is some more focus on different taxonomic levels and not
just on Phylum which is generally not a very good marker and is generally quite stable without
huge variation.
Also, it would be interesting to see a more explanatory ML approach for the LASSO method to
highlight the factors which are most important. Especially since the stool samples appear to be
performing better than the lavage samples (better AUC).
Also i would suggest the authors cite more recent works which are relevant such as:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7160452/
https://pubmed.ncbi.nlm.nih.gov/32328469/
Title: Comparison of Sampling Methods in Assessing the Microbiomefrom Patients with
Ulcerative Colitis
Version: 1 Date: 20 Jul 2021
Reviewer's report:
In this work the authors investigate the microbiome differences in luminal lavage, mucosal
biopsies and stool samples. The addition of luminal lavage is interesting. In general I find the
paper well written without major drawbacks and want to congratulate the authors on their work.
What I would like to see, though, is some more focus on different taxonomic levels and not
just on Phylum which is generally not a very good marker and is generally quite stable without
huge variation.
Also, it would be interesting to see a more explanatory ML approach for the LASSO method to
highlight the factors which are most important. Especially since the stool samples appear to be
performing better than the lavage samples (better AUC).
Also i would suggest the authors cite more recent works which are relevant such as:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7160452/
https://pubmed.ncbi.nlm.nih.gov/32328469/
Please review this paper.
user
Title: Comparison of Sampling Methods in Assessing the Microbiomefrom Patients with
Ulcerative Colitis
Version: 1 Date: 20 Jul 2021
Reviewer's report:
In this work the authors investigate the microbiome differences in luminal lavage, mucosal
biopsies and stool samples. The addition of luminal lavage is interesting. In general I find the
paper well written without major drawbacks and want to congratulate the authors on their work.
What I would like to see, though, is some more focus on different taxonomic levels and not
just on Phylum which is generally not a very good marker and is generally quite stable without
huge variation.
Also, it would be interesting to see a more explanatory ML approach for the LASSO method to
highlight the factors which are most important. Especially since the stool samples appear to be
performing better than the lavage samples (better AUC).
Also i would suggest the authors cite more recent works which are relevant such as:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7160452/
https://pubmed.ncbi.nlm.nih.gov/32328469/
assistant