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There have recently been several papers on using 16S rRNA as a way of identifying species (here, and here). I'm wondering if it's possible to sequence either just that subunit of the ribosome or just the sequence of DNA that it comes from (probably not, I know). That way you can use only the sequence you need to compare against other 16S rRNA sequences to test for novel species.

If so, what is the process involved?

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Maybe I am just over-reading your question, but why would you think sequencing 16S would be more complicated that sequencing any other gene? –  nico Jun 27 '12 at 5:30
Well I think that the simple answer is yes and in fact it is commonly done. –  bobthejoe Jun 27 '12 at 5:50
@nico & bobthejoe well I'm unfamiliar with the process of sequencing genes, so I don't have any idea of how it's done. Could you explain the process? I'll edit the question. –  ohblahitsme Jun 27 '12 at 7:04
you should probably just read about colony PCR. that is the simplest method... –  shigeta Jun 27 '12 at 16:35

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Basically, all 16S genes are highly conserved, i.e., they share much identical bases. This means one can bind the 16S gene piece (after DNA was cut) to a specific other piece of DNA, even if you don't know exactly the 16S gene bases. Everything else is discarded then. Now finally, using PCR the rest is amplified and sequenced. Sequencing 16S only is much less work, so that's how they did it years ago. Today, whole microbiomes are sequenced by professional labs.

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Is it possible to look at the actual rRNA molecule and get the sequence of rRNA rather than sequencing the DNA the encodes for it? –  ohblahitsme Jul 18 '12 at 3:00
I don't know but I think it would make a good question. 8) –  rwst Jul 18 '12 at 16:28

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