Reviewer's report
Title:Ulcerative colitis and irritable bowel patients exhibit distinct abnormalities of
the gut microbiota
Version: 1Date:25 January 2010
Reviewer: Gunnar Loh
Reviewer's report:
The manuscript submitted by Narbad and co-workers describes the differences in
intestinal microbiota composition between patients suffering from ulerative colitis
(UC) or irritable bowel syndrome (IBS) and healthy controls. PCR-Denaturing
Gradient Gel Electrophoresis (DGGE) with universal and Bacteroides specific
primers was used to analyze dominant bacteria in fecal samples obtained from
the study subjects. Data was evaluated using a newly developed or adapted
statistical method. Prominent bands were cut out of the gel and sequenced in
order to identify important bacterial species.
The authors report a decreased microbiota diversity and a higher variability of
dominant bacteria in both IBS and UC patients in remission as compared to
healthy controls. Diversity of Bacteroides spp. was lower in UC compared to IBS
and healthy subjects. From sequencing prominant bands, the authors conclude
that the absence of Bacteroides vulgatus, B. ovatus, B. uniformis, and
Parabacteroides distasonis is an important feature in UC and IBS.
The most important finding of the study are largely of confirmative nature.
Changes in gut microbiota composition have been demonstrated by
culture-independent methods for IBD (e.g.Krogius-Kurikka et al. BMC
Gastroenterology 2009, 9:95) and UC patients in remission (e.g. Martinez et al.
Am J Gastroenterol. 2008, 103(3):643). A depletion of Bacteroides spp. in UC
has also been shown previously (e.g. Frank et al. Proc Natl Acad Sci U S A.
2007, 104(34):13780).
It has to been mentioned that the role of the individual Bacteroides spp. in IBS
and UC has possibly been over-interpreted because the similarities of the
sequences to sequneces in databases is -with the exception of B. vulgatus- too
low for valid identifcation.
However, an improvement of DGGE profil analysis is not without merits. One of
the major limitations of DGGE is the fact that different gels cannot easily be
compared and that the number of samples that can be loaded on one single gel
is limited. If it is now possible to compare different DGGE gels with an improved
method for gel alignment, this method can be used to analyze and compare
microbiota communities in larger study groups. By confirming the results of
studies (see above) in which more cutting-edge but also much more costly and
laborious methods have been used, the validity of this new method can nicely be
demonstrated.
I recommend to better work out the technical improvement of DGGE data anlysis
and to re-submit the manuscript to be published in the "Tecnical Advances"
section of the journal. The novelty of the improved technique must become clear.
Thus, in such a revision, the decisions made to improve gel and data handling
must be comprehensible to the reader (section "DGGE profil analysis"). Please
state shortly the advances in data interpretation that can be achieved by using
PLS-DA or CVA and the consequences for further data evaluation and
interpretation.
Check the figure numbering.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Acceptable
Statistical review: Yes, but I do not feel adequately qualified to assess the
statistics.
Declaration of competing interests:
I declare that I have no competing interests
Reviewer's report
Title:Ulcerative colitis and irritable bowel patients exhibit distinct abnormalities of
the gut microbiota
Version: 1Date:25 January 2010
Reviewer: Gunnar Loh
Reviewer's report:
The manuscript submitted by Narbad and co-workers describes the differences in
intestinal microbiota composition between patients suffering from ulerative colitis
(UC) or irritable bowel syndrome (IBS) and healthy controls. PCR-Denaturing
Gradient Gel Electrophoresis (DGGE) with universal and Bacteroides specific
primers was used to analyze dominant bacteria in fecal samples obtained from
the study subjects. Data was evaluated using a newly developed or adapted
statistical method. Prominent bands were cut out of the gel and sequenced in
order to identify important bacterial species.
The authors report a decreased microbiota diversity and a higher variability of
dominant bacteria in both IBS and UC patients in remission as compared to
healthy controls. Diversity of Bacteroides spp. was lower in UC compared to IBS
and healthy subjects. From sequencing prominant bands, the authors conclude
that the absence of Bacteroides vulgatus, B. ovatus, B. uniformis, and
Parabacteroides distasonis is an important feature in UC and IBS.
The most important finding of the study are largely of confirmative nature.
Changes in gut microbiota composition have been demonstrated by
culture-independent methods for IBD (e.g.Krogius-Kurikka et al. BMC
Gastroenterology 2009, 9:95) and UC patients in remission (e.g. Martinez et al.
Am J Gastroenterol. 2008, 103(3):643). A depletion of Bacteroides spp. in UC
has also been shown previously (e.g. Frank et al. Proc Natl Acad Sci U S A.
2007, 104(34):13780).
It has to been mentioned that the role of the individual Bacteroides spp. in IBS
and UC has possibly been over-interpreted because the similarities of the
sequences to sequneces in databases is -with the exception of B. vulgatus- too
low for valid identifcation.
However, an improvement of DGGE profil analysis is not without merits. One of
the major limitations of DGGE is the fact that different gels cannot easily be
compared and that the number of samples that can be loaded on one single gel
is limited. If it is now possible to compare different DGGE gels with an improved
method for gel alignment, this method can be used to analyze and compare
microbiota communities in larger study groups. By confirming the results of
studies (see above) in which more cutting-edge but also much more costly and
laborious methods have been used, the validity of this new method can nicely be
demonstrated.
I recommend to better work out the technical improvement of DGGE data anlysis
and to re-submit the manuscript to be published in the "Tecnical Advances"
section of the journal. The novelty of the improved technique must become clear.
Thus, in such a revision, the decisions made to improve gel and data handling
must be comprehensible to the reader (section "DGGE profil analysis"). Please
state shortly the advances in data interpretation that can be achieved by using
PLS-DA or CVA and the consequences for further data evaluation and
interpretation.
Check the figure numbering.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Acceptable
Statistical review: Yes, but I do not feel adequately qualified to assess the
statistics.
Declaration of competing interests:
I declare that I have no competing interests
Please review this paper.
user
Reviewer's report
Title:Ulcerative colitis and irritable bowel patients exhibit distinct abnormalities of
the gut microbiota
Version: 1Date:25 January 2010
Reviewer: Gunnar Loh
Reviewer's report:
The manuscript submitted by Narbad and co-workers describes the differences in
intestinal microbiota composition between patients suffering from ulerative colitis
(UC) or irritable bowel syndrome (IBS) and healthy controls. PCR-Denaturing
Gradient Gel Electrophoresis (DGGE) with universal and Bacteroides specific
primers was used to analyze dominant bacteria in fecal samples obtained from
the study subjects. Data was evaluated using a newly developed or adapted
statistical method. Prominent bands were cut out of the gel and sequenced in
order to identify important bacterial species.
The authors report a decreased microbiota diversity and a higher variability of
dominant bacteria in both IBS and UC patients in remission as compared to
healthy controls. Diversity of Bacteroides spp. was lower in UC compared to IBS
and healthy subjects. From sequencing prominant bands, the authors conclude
that the absence of Bacteroides vulgatus, B. ovatus, B. uniformis, and
Parabacteroides distasonis is an important feature in UC and IBS.
The most important finding of the study are largely of confirmative nature.
Changes in gut microbiota composition have been demonstrated by
culture-independent methods for IBD (e.g.Krogius-Kurikka et al. BMC
Gastroenterology 2009, 9:95) and UC patients in remission (e.g. Martinez et al.
Am J Gastroenterol. 2008, 103(3):643). A depletion of Bacteroides spp. in UC
has also been shown previously (e.g. Frank et al. Proc Natl Acad Sci U S A.
2007, 104(34):13780).
It has to been mentioned that the role of the individual Bacteroides spp. in IBS
and UC has possibly been over-interpreted because the similarities of the
sequences to sequneces in databases is -with the exception of B. vulgatus- too
low for valid identifcation.
However, an improvement of DGGE profil analysis is not without merits. One of
the major limitations of DGGE is the fact that different gels cannot easily be
compared and that the number of samples that can be loaded on one single gel
is limited. If it is now possible to compare different DGGE gels with an improved
method for gel alignment, this method can be used to analyze and compare
microbiota communities in larger study groups. By confirming the results of
studies (see above) in which more cutting-edge but also much more costly and
laborious methods have been used, the validity of this new method can nicely be
demonstrated.
I recommend to better work out the technical improvement of DGGE data anlysis
and to re-submit the manuscript to be published in the "Tecnical Advances"
section of the journal. The novelty of the improved technique must become clear.
Thus, in such a revision, the decisions made to improve gel and data handling
must be comprehensible to the reader (section "DGGE profil analysis"). Please
state shortly the advances in data interpretation that can be achieved by using
PLS-DA or CVA and the consequences for further data evaluation and
interpretation.
Check the figure numbering.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Acceptable
Statistical review: Yes, but I do not feel adequately qualified to assess the
statistics.
Declaration of competing interests:
I declare that I have no competing interests
assistant