Can I use universal primers of rpoB, gyrB, etc. for species level identification of bacterial strains? How much is the efficiency of the technique of using degenerate primers?
You can identify different bacterial isolates up to species level using 16S rRNA gene sequence analysis method. Refer weisburg et al you may find different primer which you can use as universal primers.
You can identify different bacterial isolates up to species level using 16S rRNA gene sequence analysis method. Refer weisburg et al you may find different primer which you can use as universal primers.
I agree to Nilmini opinion. It is better to find the genus of bacteria by 16S rRNA analysis first, and use genus specific MLST primers. You will get more valuable data and have better comparison to the current databases.
If you like to limit your research by 2-3 universal genes like gyrB or rpoB and use universal primers, I would recommend to sequence the PCR fragments after cloning only.
Alex
There is a very good paper suggesting primers for this sort of thing that has worked for me; Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins by SR Santos, H Ochman - Environmental Microbiology, 2004. I've used the rpoB and gyrA primers (within a genus) to differentiate species to the ecotype level.
http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2004.00617.x/abstract
Thank you @Nilmini Kumari, @Alex Ignatov, @Sarah Kopac for your kind help.
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