Reviewer's report
Title:Percent G+C profiling and sequence analysis reveals significant
differences in the gastrointestinal microbiota between diarrhoea-predominant
irritable bowel syndrome sufferers and healthy individuals
Version: 2Date:12 August 2009
Reviewer: John Spear
Reviewer's report:
Review of: Percent G+C profiling and sequence analysis reveals significant
differences in the gastrointestinal microbiota between diarrhoea-predominant
irritable bowel syndrome sufferers and healthy individuals
Authors: L.K. Krogius-Kurikka, et al.
Summary: Paper looks at a sequence analysis of DNA from a number of
individual fecal samples from people with diarrhoea-predominant irritable bowel
syndrome (IBS-D) as well as controls, runs those samples through a
cesium-chloride centrifugation to separate the samples into different ‘fractions’
based on %G+C content, then subjects those fractions to 16S rRNA analysis.
Authors find that this method reveals quite a bit more diversity than 16S analysis
alone, and that there are significant differences between those with IBS-D and
controls. The predominance of the Firmicute Lachnospiraceae is particularly
noteworthy. Overall, phylotype richness was lower and phylogenetic
characteristics more distinct in patient samples with IBS-D.
Critique: Overall, the paper is well written in English and has good
content—authors are to be commended for this as the paper comes out of
Finland. Authors sequenced 3267 partial 16S rRNA gene sequences (V1 and V2
regions) from G+C fractioned samples. Authors deposited ~2300 sequences in to
EMBL Nucleotide Sequence Database (not sure why they did not deposit all
sequences generated). As with previous works of these authors, this paper would
have been stronger if the authors could have done full length sequencing with all
sequences deposited into EMBL. Authors did however obtain enough sequence,
employed the right methods for analysis and covered their results with adequate
discussion.
Major Compulsory Revisions
None.
Minor Essential Revisions
Below.
Discretionary Revisions
All full length 16S rRNA gene sequences would have made this a better a paper.
As a researcher myself, we have to all think about that which follows us. In this
case, full-length sequences aid taxonomists, evolutionists, and ecologists. Even
with variable region analysis and 454 pyrosequencing approaches, we still
believe in full-length gene sequence generation.
Recommendation:
Accept, after addressing the suggested changes and additions below.
Abstract
Last sentence of Background section is awkward, as is.
First line of Results: Significant differences were found between…..
Background
Page 6, last sentence: Could draw in references of Frank et al., 2008, 2007 and
2001—all are likely worth including. This reviewer is not related to that work,
however they have put out some interesting information….
Level of interest: An article of importance in its field
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:Percent G+C profiling and sequence analysis reveals significant
differences in the gastrointestinal microbiota between diarrhoea-predominant
irritable bowel syndrome sufferers and healthy individuals
Version: 2Date:12 August 2009
Reviewer: John Spear
Reviewer's report:
Review of: Percent G+C profiling and sequence analysis reveals significant
differences in the gastrointestinal microbiota between diarrhoea-predominant
irritable bowel syndrome sufferers and healthy individuals
Authors: L.K. Krogius-Kurikka, et al.
Summary: Paper looks at a sequence analysis of DNA from a number of
individual fecal samples from people with diarrhoea-predominant irritable bowel
syndrome (IBS-D) as well as controls, runs those samples through a
cesium-chloride centrifugation to separate the samples into different ‘fractions’
based on %G+C content, then subjects those fractions to 16S rRNA analysis.
Authors find that this method reveals quite a bit more diversity than 16S analysis
alone, and that there are significant differences between those with IBS-D and
controls. The predominance of the Firmicute Lachnospiraceae is particularly
noteworthy. Overall, phylotype richness was lower and phylogenetic
characteristics more distinct in patient samples with IBS-D.
Critique: Overall, the paper is well written in English and has good
content—authors are to be commended for this as the paper comes out of
Finland. Authors sequenced 3267 partial 16S rRNA gene sequences (V1 and V2
regions) from G+C fractioned samples. Authors deposited ~2300 sequences in to
EMBL Nucleotide Sequence Database (not sure why they did not deposit all
sequences generated). As with previous works of these authors, this paper would
have been stronger if the authors could have done full length sequencing with all
sequences deposited into EMBL. Authors did however obtain enough sequence,
employed the right methods for analysis and covered their results with adequate
discussion.
Major Compulsory Revisions
None.
Minor Essential Revisions
Below.
Discretionary Revisions
All full length 16S rRNA gene sequences would have made this a better a paper.
As a researcher myself, we have to all think about that which follows us. In this
case, full-length sequences aid taxonomists, evolutionists, and ecologists. Even
with variable region analysis and 454 pyrosequencing approaches, we still
believe in full-length gene sequence generation.
Recommendation:
Accept, after addressing the suggested changes and additions below.
Abstract
Last sentence of Background section is awkward, as is.
First line of Results: Significant differences were found between…..
Background
Page 6, last sentence: Could draw in references of Frank et al., 2008, 2007 and
2001—all are likely worth including. This reviewer is not related to that work,
however they have put out some interesting information….
Level of interest: An article of importance in its field
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:Percent G+C profiling and sequence analysis reveals significant
differences in the gastrointestinal microbiota between diarrhoea-predominant
irritable bowel syndrome sufferers and healthy individuals
Version: 2Date:12 August 2009
Reviewer: John Spear
Reviewer's report:
Review of: Percent G+C profiling and sequence analysis reveals significant
differences in the gastrointestinal microbiota between diarrhoea-predominant
irritable bowel syndrome sufferers and healthy individuals
Authors: L.K. Krogius-Kurikka, et al.
Summary: Paper looks at a sequence analysis of DNA from a number of
individual fecal samples from people with diarrhoea-predominant irritable bowel
syndrome (IBS-D) as well as controls, runs those samples through a
cesium-chloride centrifugation to separate the samples into different ‘fractions’
based on %G+C content, then subjects those fractions to 16S rRNA analysis.
Authors find that this method reveals quite a bit more diversity than 16S analysis
alone, and that there are significant differences between those with IBS-D and
controls. The predominance of the Firmicute Lachnospiraceae is particularly
noteworthy. Overall, phylotype richness was lower and phylogenetic
characteristics more distinct in patient samples with IBS-D.
Critique: Overall, the paper is well written in English and has good
content—authors are to be commended for this as the paper comes out of
Finland. Authors sequenced 3267 partial 16S rRNA gene sequences (V1 and V2
regions) from G+C fractioned samples. Authors deposited ~2300 sequences in to
EMBL Nucleotide Sequence Database (not sure why they did not deposit all
sequences generated). As with previous works of these authors, this paper would
have been stronger if the authors could have done full length sequencing with all
sequences deposited into EMBL. Authors did however obtain enough sequence,
employed the right methods for analysis and covered their results with adequate
discussion.
Major Compulsory Revisions
None.
Minor Essential Revisions
Below.
Discretionary Revisions
All full length 16S rRNA gene sequences would have made this a better a paper.
As a researcher myself, we have to all think about that which follows us. In this
case, full-length sequences aid taxonomists, evolutionists, and ecologists. Even
with variable region analysis and 454 pyrosequencing approaches, we still
believe in full-length gene sequence generation.
Recommendation:
Accept, after addressing the suggested changes and additions below.
Abstract
Last sentence of Background section is awkward, as is.
First line of Results: Significant differences were found between…..
Background
Page 6, last sentence: Could draw in references of Frank et al., 2008, 2007 and
2001—all are likely worth including. This reviewer is not related to that work,
however they have put out some interesting information….
Level of interest: An article of importance in its field
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