I'm new to 16s RNA-Seq analysis, and I have a question after using QIIME here.
For example, I have 2 samples from leaves with treatment of rain water collected at different time. QIIME results have shown that these 2 samples have similar bio-diversity of one bacteria family. Taxonomy assignments are done by clustering representative sequences with OTUs hence a threshold of distance allowing differences exists, in this case, is it reasonable for me to compare (BLASTN) the representative sequences of the 2 samples to see if they have the same (100% identity) representative sequences so that I can conclude that, say, Bacteria A from sample 1 is the same with Bacteria A from sample 2.
Thanks for responding. I would appreciate any answer or reference.
Let me try to clarify my question a little more:
I want to see if one the microbiome community member of my 2 samples share the same origin (treated by different rain water). So I extracted the representative sequences clustered to the OTU of that bacteria species, and want to perform pairwise BLASTN to check the similarity of them. But I'm not sure if it makes sense.