Reviewer's report
Title:Comparison of the Gut Microbiota Composition between Obese and
Non-obese Individuals in a Japanese Population, as Analyzed by Terminal
Restriction Fragment Length Polymorphism and Next-generation Sequencing
Version:3Date:11 May 2015
Reviewer: Gopanandan Parthasarathy
Reviewer's report:
(i) Major Compulsory Revisions
1. It is mentioned that 21 of 56 participants had a normal diagnosis on
colonoscopy. It is important to describe what diagnosis the other 35 participants
received, as it may be a major confounding factor.
2. It is essential to include the average (or median) number of reads/sample
obtained in the Illumina sequencing to give a measure of quality and depth of
analyses.
3. False discovery rate correction is required in the statistical analyses in order to
correct for multiple testing. Consider including FDR corrected P values for both
T-RFLP and next-generation sequencing.
(ii) Minor Essential Revisions
1. In the abstract, it is probably not appropriate to term the study of gut
microbiota in obesity as "recent" (Ley et al's landmark paper came in 2006).
2. In the abstract, it is not appropriate to suggest that gut microbiota is related to
the "development" of obesity. This study has only demonstrated an association,
and an experiment with perturbation of one or both elements would be required
to reach that conclusion.
3. It may be better to include your reasoning for why a different BMI classification
was chosen in the methods section, rather than in the discussion.
4. It may not be correct to use the term "predicted" to describe the results of the
T-RFLP analysis.
5. In Table 2, consider reordering the bacteria per taxonomic hierarchy. As of
now, it is confusing to see order followed by genus followed by phylum.
6. In the figure legends, the term "microbiome" has been used instead of
"microbiota". Per Morgan et al. PLOS Computational Biology 2012, "microbiome"
refers to the total microbial community and biomolecules within a defined
environment. As simultaneous assessment of other biomolecules has not been
performed, the use of "microbiota" is more appropriate.
(iii) Discretionary Revisions
1. May be useful to elaborate on the use of T-RFLP in microbiota analysis. This
method is not as well known as next generation 16s rRNA based sequencing.
Therefore, its validity may need to be further supported by appropriate references
(for eg. Sjoberg et al. JOURNAL OF MICROBIOLOGICAL METHODS 2013)
2. As you have already noted, the relationship between microbiota and age is
particularly relevant only with respect to the early years of age. Consider
removing the paragraph about microbiota and age in the discussion.
3. Interesting as it is, the part of the discussion that focuses on the functional role
of the bacterial species that have been observed in this study is conjecture. For
example, without simultaneous analysis of stool SCFA levels, one cannot infer
that these organisms may be playing a metabolic role in obesity. Further, it is
important to note (as you have, in the conclusion) that we do not know the
direction of this association i.e. does obesity lead to alterations in gut microbiota
or vice versa?
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Needs some language corrections before being
published
Statistical review: Yes, and I have assessed the statistics in my report.
Declaration of competing interests:
I declare that I have no competing interests
Reviewer's report
Title:Comparison of the Gut Microbiota Composition between Obese and
Non-obese Individuals in a Japanese Population, as Analyzed by Terminal
Restriction Fragment Length Polymorphism and Next-generation Sequencing
Version:3Date:11 May 2015
Reviewer: Gopanandan Parthasarathy
Reviewer's report:
(i) Major Compulsory Revisions
1. It is mentioned that 21 of 56 participants had a normal diagnosis on
colonoscopy. It is important to describe what diagnosis the other 35 participants
received, as it may be a major confounding factor.
2. It is essential to include the average (or median) number of reads/sample
obtained in the Illumina sequencing to give a measure of quality and depth of
analyses.
3. False discovery rate correction is required in the statistical analyses in order to
correct for multiple testing. Consider including FDR corrected P values for both
T-RFLP and next-generation sequencing.
(ii) Minor Essential Revisions
1. In the abstract, it is probably not appropriate to term the study of gut
microbiota in obesity as "recent" (Ley et al's landmark paper came in 2006).
2. In the abstract, it is not appropriate to suggest that gut microbiota is related to
the "development" of obesity. This study has only demonstrated an association,
and an experiment with perturbation of one or both elements would be required
to reach that conclusion.
3. It may be better to include your reasoning for why a different BMI classification
was chosen in the methods section, rather than in the discussion.
4. It may not be correct to use the term "predicted" to describe the results of the
T-RFLP analysis.
5. In Table 2, consider reordering the bacteria per taxonomic hierarchy. As of
now, it is confusing to see order followed by genus followed by phylum.
6. In the figure legends, the term "microbiome" has been used instead of
"microbiota". Per Morgan et al. PLOS Computational Biology 2012, "microbiome"
refers to the total microbial community and biomolecules within a defined
environment. As simultaneous assessment of other biomolecules has not been
performed, the use of "microbiota" is more appropriate.
(iii) Discretionary Revisions
1. May be useful to elaborate on the use of T-RFLP in microbiota analysis. This
method is not as well known as next generation 16s rRNA based sequencing.
Therefore, its validity may need to be further supported by appropriate references
(for eg. Sjoberg et al. JOURNAL OF MICROBIOLOGICAL METHODS 2013)
2. As you have already noted, the relationship between microbiota and age is
particularly relevant only with respect to the early years of age. Consider
removing the paragraph about microbiota and age in the discussion.
3. Interesting as it is, the part of the discussion that focuses on the functional role
of the bacterial species that have been observed in this study is conjecture. For
example, without simultaneous analysis of stool SCFA levels, one cannot infer
that these organisms may be playing a metabolic role in obesity. Further, it is
important to note (as you have, in the conclusion) that we do not know the
direction of this association i.e. does obesity lead to alterations in gut microbiota
or vice versa?
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Needs some language corrections before being
published
Statistical review: Yes, and I have assessed the statistics in my report.
Declaration of competing interests:
I declare that I have no competing interests
Please review this paper.
user
Reviewer's report
Title:Comparison of the Gut Microbiota Composition between Obese and
Non-obese Individuals in a Japanese Population, as Analyzed by Terminal
Restriction Fragment Length Polymorphism and Next-generation Sequencing
Version:3Date:11 May 2015
Reviewer: Gopanandan Parthasarathy
Reviewer's report:
(i) Major Compulsory Revisions
1. It is mentioned that 21 of 56 participants had a normal diagnosis on
colonoscopy. It is important to describe what diagnosis the other 35 participants
received, as it may be a major confounding factor.
2. It is essential to include the average (or median) number of reads/sample
obtained in the Illumina sequencing to give a measure of quality and depth of
analyses.
3. False discovery rate correction is required in the statistical analyses in order to
correct for multiple testing. Consider including FDR corrected P values for both
T-RFLP and next-generation sequencing.
(ii) Minor Essential Revisions
1. In the abstract, it is probably not appropriate to term the study of gut
microbiota in obesity as "recent" (Ley et al's landmark paper came in 2006).
2. In the abstract, it is not appropriate to suggest that gut microbiota is related to
the "development" of obesity. This study has only demonstrated an association,
and an experiment with perturbation of one or both elements would be required
to reach that conclusion.
3. It may be better to include your reasoning for why a different BMI classification
was chosen in the methods section, rather than in the discussion.
4. It may not be correct to use the term "predicted" to describe the results of the
T-RFLP analysis.
5. In Table 2, consider reordering the bacteria per taxonomic hierarchy. As of
now, it is confusing to see order followed by genus followed by phylum.
6. In the figure legends, the term "microbiome" has been used instead of
"microbiota". Per Morgan et al. PLOS Computational Biology 2012, "microbiome"
refers to the total microbial community and biomolecules within a defined
environment. As simultaneous assessment of other biomolecules has not been
performed, the use of "microbiota" is more appropriate.
(iii) Discretionary Revisions
1. May be useful to elaborate on the use of T-RFLP in microbiota analysis. This
method is not as well known as next generation 16s rRNA based sequencing.
Therefore, its validity may need to be further supported by appropriate references
(for eg. Sjoberg et al. JOURNAL OF MICROBIOLOGICAL METHODS 2013)
2. As you have already noted, the relationship between microbiota and age is
particularly relevant only with respect to the early years of age. Consider
removing the paragraph about microbiota and age in the discussion.
3. Interesting as it is, the part of the discussion that focuses on the functional role
of the bacterial species that have been observed in this study is conjecture. For
example, without simultaneous analysis of stool SCFA levels, one cannot infer
that these organisms may be playing a metabolic role in obesity. Further, it is
important to note (as you have, in the conclusion) that we do not know the
direction of this association i.e. does obesity lead to alterations in gut microbiota
or vice versa?
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Needs some language corrections before being
published
Statistical review: Yes, and I have assessed the statistics in my report.
Declaration of competing interests:
I declare that I have no competing interests
assistant