>I need to classify some sequence entries from databases into
>Gram-positive (single-membraned, such as B.subtilis) and Gram-negative
>(double-membraned, such as E.coli) bacteria. SWISSPROT, however, does
>not use those terms in the classification, instead it divides
>PROKARYOTA into FIRMICUTES, GRACILICUTES (including ANOXYPHOTOBACTERIA,
>OXYPHOTOBACTERIA, and SCOTOBACTERIA), MENDOSICUTES (= ARCHAEBACTERIA),
>and TENERICUTES (= MYCOPLASMA). Do these groups relate to the Gram +/-
>concept, and if so, how?
>>Would it e.g. be safe to say that FIRMICUTES = Gram+ and GRACILICUTES
>(or maybe SCOTOBACTERIA) = Gram- ???
>>Answers will be greatly appreciated.
>--
>>Henrik Nielsen
>>Center for Biological Sequence Analysis (CBS)
>Department of Physical Chemistry (FKI)
>The Technical University of Denmark (DTU)
>Building 206
>DK-2800 Lyngby, Denmark
>>phone: +45 4288 2222 ext. 2470 (operator)
>phone: +45 4593 1222 ext. 2470 (tone)
> fax: +45 4593 4808
>e-mail: hnielsen at cbs.dth.dk
Henrik,
In the last edition of 'Bergey's Manual of Systematic Bacteriology'
(Krieg, N., ed., Williams and Wilkins, Baltimore, 1984.),
the prokaryotes are divided in these four 'divisions'.
1. Gracilicutes: Gram-negative eubacteria that have complex cell walls,
(consisting of outer lipopolysaccharide membrane and a thin peptidoglycan
layer)
2. Firmicutes: Gram-positive eubacteria that have cell walls (without
lipopolysaccharide layer, but with thick peptidoglycan)
3. Tenericutes: Eubacteria lacking cell walls
4. Mendosicutes: Archaeobacteria
Concerning the first two divisions, some Gracilicutes may actually
stain Gram-positive, and some Firmicutes Gram-negative, but apart
from these exceptions, I assume it is correct to say
Gracilicutes = Gram-negative eubacteria
Firmicutes = Gram-positive eubacteria
As a final remark: Bergey's taxonomy is based on phenotypic properties.
Increasingly, bacteria are being classified on the basis of properties
which reflect their phylogenetic relationship (e.g. rRNA sequences).
The latter approach has shown, for instance, that the Gram-negative bacteria
are not a phylogenetically coherent group.
Chris Michiels
