Hi,

I would advise you an alignment of type strains' 16S/ 23S rRNA gene sequences. Probably you will find some conservative motifs. But prior to this make sure that nobody permormed it before. That will spare your time. Designing new primers you should confirm  species-specificity but also exclude non-specific binding (consider closely related genera , e.g. Pseudomonas).

Good luck!

Hi Carlos,

There are only 129 16S-23S ITS sequences of Burkholderia spp. in the GeneBank, and over 5800 sequences of recA gene. I would advise to use recA.

just as an example:

Cesarini S, Bevivino A, Tabacchioni S, Chiarini L, Dalmastri C. RecA gene sequence and Multilocus Sequence Typing for species-level resolution of Burkholderia cepacia complex isolates. Lett Appl Microbiol. 2009 Nov;49(5):580-8.

Hi Magdalena,

I will order primers for that region. You confirmed my suspicions.

Thanks for your answer.