Bacterial Taxonomy

John Ireland ireland at duke.edu
Fri Jul 9 09:00:22 EST 1999

Okay, here is a little question I would like some opinions on.  As I
understand it, at present bacteria are speciated at the level of <70%
total DNA/DNA hybridization with other known species under strict
conditions.  In addition some guidelines have been put forth dealing
with assessing speciation using the 16S RNA sequence homology data, I
think they use <95% homology.  Even with these guidelines things in the
world of bacterial taxonomy seem at times to be more arguements in
semantics rather than science.  My question for discussion is as to how
the advent of whole genome analysis is going to alter the viewpoints of
taxonomy and what would be approiate guidelines for speciation of
bacteria.  Here are two incidents to consider in this (I apologize for a
lack of references at the moment, or lab is in the process of moving
cross country and things are already in boxes, including my files). 
First, some strains of E.coli can contain up to 1 Mb of stablly
maintained DNA in addition to that which was sequenced in the original
sequencing project.  Second, certain groups of bacteria (most notably
the B. cereus/thurengensis/anthracis group) have identical 16S RNA
sequences (within experimental error) and no reliable DNA/DNA
hybridization values, yet exhibit such diverse phenotypes that it would
be hard to classically combine them in the same species (this may be the
first test of any new criteria since I think both B. anthracis and B.
cereus are being totally sequenced).

This has been a question which I have been interested in for a while and
I would like to just solicite opions on it.  Thanks for your time.

John Ireland
Ph.D. canidate
Duke University Medical Center

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