16S questions

Diane Stothard dstothar at magnus.acs.ohio-state.edu
Wed Jul 12 17:10:25 EST 1995


In article <wblank.1155972325B at news.srv.ualberta.ca>,
Walter Blank <wblank at gpu.srv.ualberta.ca> wrote:
>A friend of mine asked me a couple of questions that I don't know if there
>are any hard-and-fast answers to:
>
>>Q1: For identification of an organism by 16s rRNA is there a "rule" that
>>would tell you how much identity you need to classify an organism within a
>>certain species?
>>
>>Q2: How much difference would you need to classify it as a new species?
>
>Maybe someone out there can help us out?
>
>Thanks bunches!
>
>Wally
>
>It's all much appreciated.  Out!

In my experience, there is no hard and fast rule...Ah, that life would be so 
simple! However, I have done extensive literature searches on this very topic 
and found that most species that are considered as belonging to the same genus 
are rarely more than 10% different based on the 16S rRNA gene. There are 
examples, though, of species belonging to different genera that are less than 
10% (e.g., E. coli and Proteus vulgaris are 7% different). I think the 
judgement must be made based on the precendent that is currently set in the 
genus and/or species. PLus, it is unwise to base a classification solely on 
sequence data. You should have some other data, either sequences from other 
genes or some phenotypic/morpholoical/physiological/immunological data that 
will help strengthen your position on the classification of a novel strain.

Good luck!
Diane



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