I have done 16S rRNA sequencing for two actinobacteria isolates and when I tried the NCBI blast tool, I got hits for about 10 different species which are 100% identity, 100% query recovery and E-value of zero. I don't know what the best way to know my species as I have did blast for about 1000 base or more.
Thanks in Advance
Best Regards
You could try few things for your problem
1) Could you try SILVA or RDP for your analysis?
2) Which region did you use? could you search for the similar observations in literature?
3) try to align all those 10 species full length sequences to see if the variation is outside your variable region, and this might suggest you towards the possible change in primers for variable region
4) with isolate you mean different species or different strains
5) this can also be caused due to the limitations of database
6) it is the limitation of 16s that sometimes species level and strain level variations are not under the reach of this method.
7) full 16s amplicon sequencing might help you if the variations are outside your target region
I suggested, but I am not sure if this could help you, but now you can't do anything else too, so why not give it a try...
How can I compare with the literature? Is there any database to help?
Use only type strain hits (NCBI with type strain database) or try EZtaxon.
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