Review for 10.1186/s12876-021-01885-4 (2021)

Reviewer’s report
Title: 
Study protocol P-MAPS: Microbiome As Predictor of Severity in Acute
Pancreatitis: A prospective multicentre translational study
Version: 
0 
Date: 
25 Apr 2021
Reviewer's report:
This is an interesting study which is also pertinent in view of the scarcity of
literature on the microbiome in clinical acute pancreatitis. 
The strength of the
study is the sample size (n=400) and recruitment of the patient early in the
disease course. Having said so, I also have a few concerns.
1. The language and grammar of the manuscript has to be substantially
improved.
2. I am a little skeptical on the sampling method, i.e. authors proposed to collect
only a buccal and a rectal swab. I am not sure if this would yield a substantially
homogeneous bacterial load. Moreover, just rectal swab may not necessarily
represent the entire gut bacteriome. At best, use of stool samples (or jejunal
aspirates or small intestinal/colonic biopsy) would have been superior ways to
get higher quality and better representative sample.
3. I don't see any description on how the Nanopore sequence data will be handled
and processed (data trimming, quality assessment etc). There are also no
descriptions on key aspects such as the method of annotation, reference database
that will be used, depth of taxonomic assignment, etc.
4. Authors also need to describe how will they represent the visualizations of
their data.
5. There should also be descriptions on how the authors will make the data
publicly available post publication.
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Is the study design appropriate to answer the research question (including the use
of appropriate controls), and are the conclusions supported by the evidence
presented?
Yes
Are the methods sufficiently described to allow the study to be repeated?
No
Is the use of statistics and treatment of uncertainties appropriate?
Yes
Is the presentation of the work clear?
Yes
Are the images in this manuscript (including electrophoretic gels and blots) free
from apparent manipulation?
Yes