Hello Everybody,
I have a mixture of DNA isolated directly from a product containing seven bacterial specie? I want to ask that other than NGS, what can be the best ideal and accurate method to quickly validate all of the bacterial specie? Will targeting specific gene sequence for each species in a simple PCR reaction will be valid enough?
Thanks
MJ
PCR is enough if you are having specific gene sequence for each species
Hi,
PCR is a better option other than NGS, wherein the PCR product of 16S rDNA or 16S rRNA gene has to be obtained,sequenced and aligned against the bacterial DNA .The band from PCR at 35-40 isolates can be compared in BLAST to identify genus or species.But it does have some limitation that it cannot distinguish some taxa like Bacillus cereus and B.anthracis are same in genomic DNA only the plasmid is virulent. RT PCR and qPCR gives reliable results for species identification.
So,you can also try with rpoB gene that is a gene target and codes for β-subunit of bacterial RNA polymerase . It is precise within species,especially rapidly dividing species like Mycobacterium.
All the best....
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