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Name: Aleksandra S.
Status: Student
Age: 20s
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Question:
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?



Replies:
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



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