16S rDNA - Bacteria identification (Jan/06/2011 )

Hi, everybody I’m new here and have some questions . Soon I will have a presentation about 16s rDNA so I desperately need some help . I know that you can use 16s rDNA for the identification of unknown bacteria .But what I don’t understand is what your using to sequence the unknown bacteria . Is it the DNA of a bacteria cell or is it just the ribosome of the bacterial cell??
Thank you in advance !

Hi NPY -- welcome to the BioFourm!

To identify bacteria by 16s, you (typically) amplify 16s rDNA from the bacterial chromosome using universal primers (ones that match "all" bacteria), sequence the amplicon, and use this sequence to identify the organism by similarity to other 16s sequences, using a database like the one at the Ribosomal Database Project (see here).

There is a common misunderstanding -- there is usually more than one 16s rDNA gene in the chromosome of bacteria (see, for example, here), so speaking of "the 16s rDNA gene" is usually incorrect. Moreover, sometimes not all the 16s genes in a particular organism are the same sequence, so classification can be a bit tricky with the ones that have multiple 16s genes with heterologous sequence...