Reviewer's report
Title:Lactobacillus acidophilus CRL 1014 improved gut health in the SHIME
reactor
Version: 3Date:17 February 2013
Reviewer: Alexandra Meziti
Reviewer's report:
Major comments
Point 1. Although the authors made most of the corrections suggested, I still find
unacceptable to present results (l.28-29, p.9) such as 'the band marked ‘‘lac 3’’
revealed 81% of similarity to Lactobacillus johnsonii (GI,AB6343.1).'. My
comment at the first MS was whether this (81%) is a typing error and the answer
was that this was due to bad sequencing. It is definite that bad sequences
(e.g.chimeras, bad chromatograms) should not be further used in any molecular
analysis. Especially in 16S, as done here, they drive in biased conclusions. I
suggest that the sequencing should be done again since the authors have DNA
left from their experiments.
Point 2. I insist that all sequences obtained in this study should be submitted in
Genbank before publishing.
Point 3. I do not understand and I find inadequate the explanation the authors
provided in point 6 of the first revision
[Point 6: Why were only four bands successfully sequenced. Was there any
problem
with sequencing or you suggest it was not needed? Please clarify.
Answer 6: Our objective in this paper was showed the ecological microbial
changes,
no specified bands. According Possemiers et al (2004), when using in vitro
simulators, before influencing the microbial ecosystem, it is crucial to start from a
stable community, which is more or less representative to the in vivo human
situation. Otherwise specific shifts can’t be related to a specific in vitro treatment.
As
DGGE patterns offer a more accurate view on the species distribution and
composition in a microbial community, PCR-DGGE was applied to monitor
changes
in the in vitro microbial community composition during the start-up period of the
SHIME reactor system.]
The answer provided does not answer the question "why only four bands were
SUCCESSFULLY sequenced?". How did you select these bands?
Level of interest: An article of importance in its field
Quality of written English: Needs some language corrections before being
published
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:Lactobacillus acidophilus CRL 1014 improved gut health in the SHIME
reactor
Version: 3Date:17 February 2013
Reviewer: Alexandra Meziti
Reviewer's report:
Major comments
Point 1. Although the authors made most of the corrections suggested, I still find
unacceptable to present results (l.28-29, p.9) such as 'the band marked ‘‘lac 3’’
revealed 81% of similarity to Lactobacillus johnsonii (GI,AB6343.1).'. My
comment at the first MS was whether this (81%) is a typing error and the answer
was that this was due to bad sequencing. It is definite that bad sequences
(e.g.chimeras, bad chromatograms) should not be further used in any molecular
analysis. Especially in 16S, as done here, they drive in biased conclusions. I
suggest that the sequencing should be done again since the authors have DNA
left from their experiments.
Point 2. I insist that all sequences obtained in this study should be submitted in
Genbank before publishing.
Point 3. I do not understand and I find inadequate the explanation the authors
provided in point 6 of the first revision
[Point 6: Why were only four bands successfully sequenced. Was there any
problem
with sequencing or you suggest it was not needed? Please clarify.
Answer 6: Our objective in this paper was showed the ecological microbial
changes,
no specified bands. According Possemiers et al (2004), when using in vitro
simulators, before influencing the microbial ecosystem, it is crucial to start from a
stable community, which is more or less representative to the in vivo human
situation. Otherwise specific shifts can’t be related to a specific in vitro treatment.
As
DGGE patterns offer a more accurate view on the species distribution and
composition in a microbial community, PCR-DGGE was applied to monitor
changes
in the in vitro microbial community composition during the start-up period of the
SHIME reactor system.]
The answer provided does not answer the question "why only four bands were
SUCCESSFULLY sequenced?". How did you select these bands?
Level of interest: An article of importance in its field
Quality of written English: Needs some language corrections before being
published
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:Lactobacillus acidophilus CRL 1014 improved gut health in the SHIME
reactor
Version: 3Date:17 February 2013
Reviewer: Alexandra Meziti
Reviewer's report:
Major comments
Point 1. Although the authors made most of the corrections suggested, I still find
unacceptable to present results (l.28-29, p.9) such as 'the band marked ‘‘lac 3’’
revealed 81% of similarity to Lactobacillus johnsonii (GI,AB6343.1).'. My
comment at the first MS was whether this (81%) is a typing error and the answer
was that this was due to bad sequencing. It is definite that bad sequences
(e.g.chimeras, bad chromatograms) should not be further used in any molecular
analysis. Especially in 16S, as done here, they drive in biased conclusions. I
suggest that the sequencing should be done again since the authors have DNA
left from their experiments.
Point 2. I insist that all sequences obtained in this study should be submitted in
Genbank before publishing.
Point 3. I do not understand and I find inadequate the explanation the authors
provided in point 6 of the first revision
[Point 6: Why were only four bands successfully sequenced. Was there any
problem
with sequencing or you suggest it was not needed? Please clarify.
Answer 6: Our objective in this paper was showed the ecological microbial
changes,
no specified bands. According Possemiers et al (2004), when using in vitro
simulators, before influencing the microbial ecosystem, it is crucial to start from a
stable community, which is more or less representative to the in vivo human
situation. Otherwise specific shifts can’t be related to a specific in vitro treatment.
As
DGGE patterns offer a more accurate view on the species distribution and
composition in a microbial community, PCR-DGGE was applied to monitor
changes
in the in vitro microbial community composition during the start-up period of the
SHIME reactor system.]
The answer provided does not answer the question "why only four bands were
SUCCESSFULLY sequenced?". How did you select these bands?
Level of interest: An article of importance in its field
Quality of written English: Needs some language corrections before being
published
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
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