Q: Gram +/- and bacterial systematics

[Keith Robison]

Henrik Nielsen (hnielsen at rna) wrote:
: 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.
: --

Two very useful resources for prokaryote classification are:

The Ribosomal Database Project at University of Illinois,
	gopher://rdpgopher.life.uiuc.edu
		You can download a PostScript file of the current tree,
	or a plaintext file (more useful for searching).
		An article describing RDP was published in one of the 
	January issues of J.Bacteriology.

NCBI's Entrez database/software incorporates a full taxonomy of living
things now, with a nice tree-oriented browser of the taxonomy.  If your
Entrez software doesn't have this, time for an upgrade.

	Entrez software is available via ftp from ncbi.nlm.nih.gov.

	There is also a WWW version of Entrez available at
		http://www.ncbi.nlm.nih.gov

Both of these taxonomies use a much broader model than Gram+/Gram-.


Good luck!

Keith Robison
Harvard University
Department of Cellular and Developmental Biology
Department of Genetics / HHMI

robison at mito.harvard.edu