Hi,

16S rDNA is the most used conserved region to identify bacteria. Have a look to these articles:

Article A Universal Method for the Identification of Bacteria Based ...

Article 16S rRNA Gene Sequencing for Bacterial Identification in the...

You may also consider other genes such as elongation factor T, gyrases and heat shock proteins, as pointed by:

Article Detection and Identification of Microorganisms by Gene Ampli...

Hello Legesse,

we usually use these primers:

91e: 5'- gga att caa a(gt) g aat tga cgg ggg c-3'

13b: 5'- cgg gat ccc agg ccc ggg aac gta ttc ac-3'

Amplification product ca. 550bp

Literature: Relman D A, Schmidt T M, MacDermott R P, Falkow S. Identification of the uncultured bacillus of Whipple’s disease. N Engl J Med. 1992;327:293–301

or:

DG 74: 5-' agg agg tga tcc aac cgc a-3'

RW01: 5'- aac tgg agg aag gtg ggg at-3'

Amplification product ca. 300-350bp

Literature: Greisen K, Loeffelholz M, Purohit A, Leong D. PCR primers and probes for the 16S rRNA gene of most species of pathogenic bacteria, including bacteria found in cerebrospinal fluid. J Clin Microbiol. 1994;32:335–351

Best regards

I always use universal primers of 16s rRNA (27F, 1492R).