Bacterial Systematics

[B. J. Tindall]

Hi Scott,
Since we have discussed this problem before in an e-mail exchange I would
like to point out that I was not trying to play down your efforts. One of
the major problems is that in prokyrotes we have largely turned our
attention to genera and species. Anything above that is either non-existent
or out of date (with certain exceptions) - but you know that anyway. At
present I do not see the point in re-arranging your system since Bergey's
Manual will fill in the gaps in the next edition, which you will probably
follow: perhaps you should contact Bergey's Trust. Having said that I still
do not think that this is the final state of affairs. In many cases the
groups are based solely on 16S rDNA data ("phylogenetic" in microbiological
terms - no zoologists should not complain to me about misuse of the term!)
and the problem of "unstable" trees is a problem most of us are familiar with.
I have also pointed this out before; it would help if you listed not only
the "latest" name of species but the synonyms - Dr.Euzeby's website:
 http://www-sv.cict.fr/bacterio/
does this quite well - but then we exchange ideas. You should also check
whether or not names have been validly published. I know this is a lot of
work, but this is an area where there should be much closer co-operation
between those who administer databases and taxonomists. There are OECD
initiative running at present in this direction. I would also refer you to
BJ Tindall
Misunderstanding the Bacteriological Code
Int J Syst Bacteriol 1999 49: 1313-1316
(sorry I did write this, but it does help to explain the problem - check
out http://ijs.sgmjournals.org/)
One of the major problems we have is that modern prokaryotic taxonomy uses
methods developed within the last 50 years. On top of this is the fact that
we have entered into an era of an ever growing list of new species, many of
which are in new genera. We are also appreciating the diversity of taxa
such the genera Clostridium and Bacillus, which means there will continue
to be taxonomic re-arrangements over the next decades. I have my problems
following everything and my job is prokaryotic taxonomy, so I pity those
who are doing this as a fringe activity. Enough said - if NCBI would like
to sit down and discuss the problem (this directly effects EMBL and DDBJ)
we should meet directly - we might not be able to solve all the problems
but we might be able to iron out a few of the difficulties.
Best wishes
Brian


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