Identification des
microorganismes.
Identification of microbes.
State of the art (I hope :-)
Zuckerkandl and Pauling
(Zuckerkandl
and Pauling, 1965) were the first to consider that macro-molecules
were depositary of the history of evolution. Since their first
publication, proteins and then nucleic acid sequences have been widely
used to study the evolutionnary history of microbes, and then to
identify them (Fox
et col., 1980), using genes such as the rRNA gene sequences
(unicellular) and also cytochrome b (animals) and ribulose (plants).
More recently, other ubiquitous genes have also been used to increase
the resolving taxonomic power (they are more divergent than the rRNA
sequences).
Use of rRNA sequences was pionnered by Woese (Woese, 1990). This
"slowly" evolving genes are strongly constrained, present in every
cellular organism and is mostly protected from the changes in the
environment. It is almost a good evolutionnary clock (Kimura,
1983) -but there are exceptions- and is little affected by lateral
transferts. The major problems are that is is often present in several
copies (making it difficult to use its numbers to assess how many cells
are present in a sample) and its slow evolution makes it possible that
two different species have the same sequence (Achenbach et
col.,
2001). Its major advantage is that is has been sequenced for most
validly describe species.
ITS (Internal Transcribed Spacer) or house keeping gene sequences
should be considered as an alternative when one wants to describe
biodiversity at the genus, species and sub-species levels.
The following documents are available for more precisions (some are
presently in french, but scientic french and english documents use much
common words):
Case studies
-
Alveolata, analyzing diversity of protists BIOPRO
- Identification
of a bacterial species from its 16S rRNA gene sequences. (a
new strain clearly included in a genus)
- 16S rRNA analysis of bacterial biodiversity.
- As of may 2006 (EMBL release 86), Bacterial and Archaeal sequences are contained into two different sets of files:
- pro01.dat -> pro05.dat, 235 532 entries.
- env01.dat -> env05.dat, 215 780 entries usually derived from PCR and cloning analyses of environmental sequences.
- Taking into account both sets of files, it is possible to identify:
- 578 056 described features (see below)
- 229 427 16S rRNA gene sequences for Bacteria, among which
11 064 subsequences (16S rRNA sequences contained in an entry that
contains more than the 16S sequence itself).
- How to retrieve such sequences using ACNUC, three tutorials
in french for protists but similar for bacteria :-), waiting
translation. ACNUC is much better than SRS for such retrieval (Entrez
is worse than SRS).
- Each "entry", as identified by an accession (SV) number can contain:
- The complete sequence of a gene.
- The partial sequence of "something"
- A large sequence encompassing some part of a bacterial chromosome, without up to thousands of genes.
- Some entries contain a very precise FT section, that describes exactly where each gene is located, what it codes for...
- Some entries contain no FT section, you have no idea of which genes are encoded by the sequence.
- Some entries are updated after their publication, make sure you have the latest version.
Références.
- Achenbach, L. A., J. Carey, and M. T. Madigan. 2001.
Photosynthetic and
Phylogenetic Primers for Detection of Anoxygenic Phototrophs in Natural
Environments. Appl. Environ. Microbiol. 67:2922-2926.
- Fox, G., E. Stackebrandt, R. B. Hespell, J. Gibson, J.
Maniloff, T. A.
Dyer, R. S. Wolfe, W. E. Balch, R. S. Tanner, L. J. Magrum, L. B.
ZaBlen, R. Blakemore, R. Gupta, L. Bonen, B. J. Lewis, D. A. Stahl, K.
R. Luehrsen, K. N. Chen, C. R. Woese. 1980. The Phylogeny of
Prokaryotes. Science. 209:457-463.
- Kimura, (1983). Prokaryote Systematics: The Evolution of a
Science. Prokaryotes 2nd Edition vol. 1, ch.1 pgs. 3-18.
- Zuckerkandl and Pauling. 1965. Prokaryote Systematics: The
Evolution of
a Science. Prokaryotes 2nd Edition vol. 1, ch.1 pgs. 3-18.
- Woese C., 1990. Prokaryote Systematics: The Evolution of a
Science. Prokaryotes 2nd Edition vol. 1, ch.1 pgs. 3-18.
Richard Christen. June 2006