Review for 10.1186/1471-230X-13-100 (2013)

Reviewer's report
Title:Lactobacillus acidophilus CRL 1014 improved gut health in the SHIME
reactor
Version: 2Date:26 December 2012
Reviewer: Alexandra Meziti
Reviewer's report:
Major Compulsory Revisions
1. Methods/DGGE analysis
a. Why was a nested PCR used? Is there a specific reason or just a DGGE
directly for Lactobacillus was not successful? This has to be explained in the MS.
b. Although Lactobacilli diversity is an important factor for the characterization of
gut health, why weren’t also Bifidobacteria and Clostridia tested with DGGE?
2. Results/Plate count data
a. As mentioned in methods, samples for microbiological analysis were obtained
weekly. How did you calculate the average you present on table 2? I think you
need to include a table or graph showing your weekly results as it is done with
DGGE (T1,T2,T3,T4)
b. How do you suggest that “…no effects on the lactobacilli and bifidobacteria
counts were observed during the blank period”. There are no data shown from
the blank period.
c. I think that the significant increase of both lactobacilli/bifidobacteria and
clostridia should be mentioned in the results section written in the same way. In
the results section you present your data as they were and should not predispose
of what was expected. This will be discussed later.
2. Results/ Effects of the long-term treatment on the total microbial community
structure
a. In the manuscript you write that you have a global fingerprint for general
bacteria (1st paragraph). This is not mentioned anywhere in the results-figures or
methods. Is this a typing error or sth needs to be clarified?
b. Why were only four bands successfully sequenced. Was there any problem
with sequencing or you suggest it was not needed? Please clarify.
c. ‘…the band marked’ “lac3” revealed 81% of similarity to Lactobacillus
johnsonni…’. Is this (81%) a typing error? Because if it is not the sequence you
detected belongs to a different genus than Lactobacillus.
d. Where your sequences submitted to Genbank? This is very important for the
people who read your study and probably would like to compare their sequences
with yours.
3. Discussion
Some phrases have to be rephrased
a. 3rd paragraph: ‘however’ is not needed
b. 5th paragraph: “….were observed in terms of metabolic activity as composition
of the….” . I do not understand this phrase.
c. Last paragraph: Although your data give important hints on the positive effects
of L. acidophilus on gut health, more studies should be performed in order to
ensure the “beneficial influence on community composition” so I suggest that the
authors are not be so emphatic on that.
Minor comments
1. Italics should be used for all genera and species.
2. Lane 1991, Muyzer et al. 1993 and Sanguinetti et al. 1994 are not numbered
in the MS and do not appear at all in the references.
3. For the Genbank numbers a system as Lactobacillus casei (GB, JF520581)
would be simpler
Discretionary Revisions
DGGE with universal bacterial primers would give a better concept of how
treatment effects on gut bacterial diversity.
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