As we know, there's limitation in DGGE that we can only use short number of basepairs. If we want to distinguish bacteria from some sample until the genus level with DGGE, what gene can we use aside of 16S rRNA? I hear that this traditional gene can harbor some arbitrary point mutations.
Hi Elisa,
Some authors use the rpoB gene as a novel molecular marker to infer phylogeny, but the big truth is the most of databases still use the 16S rRNA gene as the standard for classification and identification of bacteria, so you need to be clear on your goals and to do the best choice for your work.
Best,
Alejandra
Hi Elisa
I think you can work with 16S rRNA , it is better choice than rpoB as the later one is more prone to mutations.
Good luck
YK Negi
You can use 16S-23S ITS as described in http://aem.asm.org/content/69/11/6634 and in some other works.
In theory, 23S rRNA would be better, but nobody has tried it.
Hi,
Some people use the gyrB gene. This gene encodes DNA gyrase β-subunit and it is, as a phylogenetic marker, supposedly good enough to differentiate even strains of a single species (perhaps not always, but in some cases). Some articles suggest that a phylogenetic tree based on gyrB results could have one order of magnitude higher resolution than a tree based on 16S rRNA gene.
unfortunately, even consensus rpoD and gyrB primers can amplify genes in rather narrow taxonomic groups and you have to apply many primers pairs to characterize any natural sample.
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