Reviewer's report
Title:Microbial community analysis reveals high level phylogenetic alterations in
the overall gastrointestinal microbiota of diarrhoea-predominant irritable bowel
syndrome sufferers
Version: 4Date:17 November 2009
Reviewer: Petra Louis
Reviewer's report:
Minor Essential Revisions
1. I was referring to the diversity indices in my 1. comment on revision 1 and had
requested that the discussion would include a statement that mentions that the
Simpson index was very similar between the 2 libraries at lower OTU cut-offs,
which suggests little difference between the 2 libraries.
Discretionary Revisions
2. 2. comment on revision 1: For clarification, I was referring to a 7-fold difference
in DNA concentration between fractions based on additional file 1. If I interpret
the additional data given for the calculation of non-proportional to proportional
amounts of sequences correctly, the authors have ignored the different clone
numbers obtained for the different fractions. If the clones per fraction are very
similar this would not really matter, but the total clone numbers ranged from 272
to 355. The absolute clone numbers should be converted into proportions before
relating them to the amount of DNA. This does not lead to dramatic changes and
I agree with the authors that the results are similar for non-proportional and
proportional data at this phylogenetic level, however, it is mathematically
incorrect. I would assume that there may be more striking differences at a finer
phylogenetic level if proportional and non-proportional data are compared, but
am satisfied that the comment added to the discussion addresses this.
3. 4. comment on revision 1: As differences between analyses of single and
combined libraries are due to differences in the alignments, which is a technical
issue rather than reflecting real phylogenetic differences, I would use only one
alignment generated from all sequences for the analyses. However, the additions
to the manuscript have clarified how the data were generated and I am happy to
leave it to the authors to decide whether to keep the analyses separate.
4. Minor comment 3 on revision 1: I believe the requested information on primer
design is provided in the new reference 5. Otherwise, please include as
requested previously.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests
Reviewer's report
Title:Microbial community analysis reveals high level phylogenetic alterations in
the overall gastrointestinal microbiota of diarrhoea-predominant irritable bowel
syndrome sufferers
Version: 4Date:17 November 2009
Reviewer: Petra Louis
Reviewer's report:
Minor Essential Revisions
1. I was referring to the diversity indices in my 1. comment on revision 1 and had
requested that the discussion would include a statement that mentions that the
Simpson index was very similar between the 2 libraries at lower OTU cut-offs,
which suggests little difference between the 2 libraries.
Discretionary Revisions
2. 2. comment on revision 1: For clarification, I was referring to a 7-fold difference
in DNA concentration between fractions based on additional file 1. If I interpret
the additional data given for the calculation of non-proportional to proportional
amounts of sequences correctly, the authors have ignored the different clone
numbers obtained for the different fractions. If the clones per fraction are very
similar this would not really matter, but the total clone numbers ranged from 272
to 355. The absolute clone numbers should be converted into proportions before
relating them to the amount of DNA. This does not lead to dramatic changes and
I agree with the authors that the results are similar for non-proportional and
proportional data at this phylogenetic level, however, it is mathematically
incorrect. I would assume that there may be more striking differences at a finer
phylogenetic level if proportional and non-proportional data are compared, but
am satisfied that the comment added to the discussion addresses this.
3. 4. comment on revision 1: As differences between analyses of single and
combined libraries are due to differences in the alignments, which is a technical
issue rather than reflecting real phylogenetic differences, I would use only one
alignment generated from all sequences for the analyses. However, the additions
to the manuscript have clarified how the data were generated and I am happy to
leave it to the authors to decide whether to keep the analyses separate.
4. Minor comment 3 on revision 1: I believe the requested information on primer
design is provided in the new reference 5. Otherwise, please include as
requested previously.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests
Please review this paper.
user
Reviewer's report
Title:Microbial community analysis reveals high level phylogenetic alterations in
the overall gastrointestinal microbiota of diarrhoea-predominant irritable bowel
syndrome sufferers
Version: 4Date:17 November 2009
Reviewer: Petra Louis
Reviewer's report:
Minor Essential Revisions
1. I was referring to the diversity indices in my 1. comment on revision 1 and had
requested that the discussion would include a statement that mentions that the
Simpson index was very similar between the 2 libraries at lower OTU cut-offs,
which suggests little difference between the 2 libraries.
Discretionary Revisions
2. 2. comment on revision 1: For clarification, I was referring to a 7-fold difference
in DNA concentration between fractions based on additional file 1. If I interpret
the additional data given for the calculation of non-proportional to proportional
amounts of sequences correctly, the authors have ignored the different clone
numbers obtained for the different fractions. If the clones per fraction are very
similar this would not really matter, but the total clone numbers ranged from 272
to 355. The absolute clone numbers should be converted into proportions before
relating them to the amount of DNA. This does not lead to dramatic changes and
I agree with the authors that the results are similar for non-proportional and
proportional data at this phylogenetic level, however, it is mathematically
incorrect. I would assume that there may be more striking differences at a finer
phylogenetic level if proportional and non-proportional data are compared, but
am satisfied that the comment added to the discussion addresses this.
3. 4. comment on revision 1: As differences between analyses of single and
combined libraries are due to differences in the alignments, which is a technical
issue rather than reflecting real phylogenetic differences, I would use only one
alignment generated from all sequences for the analyses. However, the additions
to the manuscript have clarified how the data were generated and I am happy to
leave it to the authors to decide whether to keep the analyses separate.
4. Minor comment 3 on revision 1: I believe the requested information on primer
design is provided in the new reference 5. Otherwise, please include as
requested previously.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests
assistant