New Bacteria Criteria
Name: Aleksandra S.
What is the standard on determining a new bacteria
species? More specifically, when the highly variable rRNA is sequenced
and the sequence entered into BLAST or some other
database, what % sequence difference is considered sequencing
error, otherwise what is the standard % difference between sequences that
warrants a new species classification. I've heard 5% and I've also heard
10%, is there a setstandard?
According to my knowledge, the 'official' criteria for
new species is not the rRNA identity, but the degree
of overall DNA similarity, as determined by the
temperature required to separate two DNA strands (the
melting temperature, Tm). In a publication of the
ad-hoc committee on Reconciliation of Approaches to
Bacterial Systematics, in 1987 (Wayne et al,
International Journal of Systematic Bacteriology
37:463-464) a bacterial species was defined as a group
of strains (including the type strain) sharing 70% or
greater DNA-DNA relatedness with 5 degrees C or less
difference of melting temperature (Delta Tm).
The rRNA genes are so strongly conserved that they do
no vary significantly within a species. In other
words, the rest of the DNA will mutate and vary
stronger than the rRNA, so that the Tm will have
changed considerably by the time rRNA would no longer
'fit the species'. However, the degree of variation of
rRNA genes may be different from species to species.
So if you would compare the rRNA within a species,
this may vary 1% in one, and 5% in another. Without
the back-up data on DNA-DNA hybridization one can not
define if an isolate should be incorporated in an
existing species or not. In practice,
biochemical/bacteriological tests, often representing
certain phenotypes, are combined Tm data. Novel
species are constantly being discovered and defined,
sometimes because they are isolated and/or
characterized for the first time, or by reanalysis of
pre-existing (and pre-classified) organisms.
Peer-reviewed publication in the J. Bact. Syst. is
generally seen as an important step for a novel
species to be accepted.
Dr. Trudy Wassenaar
Click here to return to the Molecular Biology Archives
Update: June 2012