different strains of the same species have same or almost same 16S

Dear Tomas,

Do you say that there could be a difference?

see http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057923

Dear Deepak

12S is extremely conserved, 16S a bit more variable but anyway don't expect more than 0.5 to 1%....if you are lucky...between strains...it means in my mind that it is not significant.....Sorry find another marker.

Good luck from Luc

Thank you Paul and Merci beaucoup Luc. Je vais l'essayer toute de suite!

But Luc,

Do microbes have a 12S rRNA?

Dear Deepak

...what do you mean by microbes???? Unicellulars or bacterias ? As soon as you've got mitochondrias you've got 12S and 16S in the nucleus you've got 18S and 23S.

Cheers from Luc

Deepak Rajendran

yes they can differ a bit, but not enough. Further, there is variability among copies of 16S within one cell. For example entorobacteria can have up to 7 copies with SNPs. These things can have hudge influence on low level phylogenetic reconstruction since sequences are very similar. Then you can virtualy compute relationship of copy lineages, not species. Another bad think is that genome sequences in genebank obtained by next generation genome sequencing virtually can not be trusted because nobody cares about 16S, all copies are assambled together, and then generally a consensus sequence is placed to the genome loci. So you cant trust these sequences. they are artificial. Nobody all resequence 16S loci via PCR to suplement a genome with exact 16S copy.