we have studied the bacterial diversity in Pichavaram, using one-time sampling and pyrosequencing. As because of sampling, the paper was not accepted in any journals. Editors suggest to writing the paper by comparing our study with other studies. So I need help regarding how to write this paper. Thank you
Dear Sadaiappan,
I am not sure, what editor meant with comparing with other studies. But may be he want your results to be shown as unique from other studies conducted at the same or similar sampling area. So far, if you want to publish your data with one-time sampling pyrosequencing data you have to show why you did in that particular area and what are the interesting patterns you observed there should be enough (means your question which you are going answer should be very strong). Offcourse, it is an advantage to add geochemical analysis of your samples and try to compare your diversity patterns with these analyses.
I could only suggest these things, as I don´t know what is the paper about and your goal to answer in that paper.
Best regards,
Saranya
Thanks Saranya
Actually, the work is about salinity and bacterial diversity
This is the editor review
This paper presents a preliminary amplicon analysis that reports data from one sample site using alpha diversity metrics. Ideally, this study would be greatly improved via analysis of additional samples /datasets either from this study site or from other published datasets. We feel it requires great depth in analysis to be considered for review. For example, broader beta-diversity analysis should be performed that incorporates the metadata collected in this study and additional datasets that are constantly referred to in the text.
I think the editor is asking you to think on why you went to sample a bacterial community at that site in first place. Why you did not assume that the bacterial diversity there was going to be the same than in other saline sites? if you (or whoever designed the experiment) would have thought that it was going to be same, then you would have not invested the money and the time doing that. So you had an hypothesis, that was probably that the diversity was going to be different from other similar sites. Ergo you have to prove it, and in order to do that you will need to compare your results with the results that have been obtained in other similar ecosystems.
Now, you can represent a diversity from one site with a profile. For example:
1500 sequences from species-A, 765 sequences from species-B, etc..
and if you arrange your number of species (or any other taxonomic rank of interest) in a particular order then you can have a vector like (1500, 765, ... )
You can get the same from other sites, so you will have a number of vectors that you can compare with the vector representing the profile of your site. And here you a lot of statistical methods to compare such data, for example constructing a similarity matrix with those vectors and do some cluster analysis, etc.
I hope that helps.
Best regards.
Thanks Flandes
And I have another question shall I use the data in NCBI to draw a graph in comparison with my sample is it ok or it is wrong.
Thank you
Sadaiappan, the NCBI host a number of projects with different databases of data, and normally deciding what database you should use is not so easy. Do you have sequences associated to the 16S gene, right? if so then a good starting point can be the rRNA database of sequences from RefSeq in GenBank/NCBI.
Best regards.
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