Identification of new species
Posted 22 November 2012 - 09:16 AM
I isolated bacteria from a dog, sequeneced the 16S rRNA gene and aligned it (similarity after manual correction and BLAST search ~96%). Then, I sequenced two other protein coding genes yielding a homology of <90% to the closest relative. I did the whole procedure twice. A few month ago, I isolated bacteria, selected one single colony and sequenced it. Now, I isolated again and selected three colonies. I streaked them on plate several times and again sequenced the genes.
I am wondering why all the sequences from all the colonies are 100% identical. Shouldn't there be slight differences, i.e. different strains?
Will people believe that I isolated twices if the sequences are fully identical?
Thanks a lot!
Posted 22 November 2012 - 09:30 AM
One must presume that long and short arguments contribute to the same end. - Epicurus
...except casandra's that belong to the funniest, most interesting and imaginative (or over-imaginative?) ones, I suppose.
Posted 22 November 2012 - 04:05 PM
Did you isolate the second time from dog too? Same medium?
Some species have a plethora of closely related strains or within the same species, almost like a gradient of similarity based on 16S. Others however, may have the exact same 16 S or maybe just one bp different and being different species. The last case is not very common but there are some cases that need extra sequencing of some other genes to confirm.
Posted 06 December 2012 - 03:25 AM
yes, I did everything the same way.
16S was completely the same for all isolates. Then, I sequenced gyrA and rpoB but the sequences were again 100% identical. Okay, if your samples from Australia and China did not show any differences for ITS, this might also be the case for my isolates.
I will conduct ERIC fingerprinting, maybe yielding bands of different length. What do you think of this approach?
Another question concerning the identification of new species:
I read a lot of papers and the authors only sequenced the 16S rRNA gene. In addition, they conducted a lot of biochemical tests and also cell wall murein analysis and lipid analysis. Are the latter two essential when describing a new species from Corynebacterium genus?
The method papers mentioned in the publications are very old. For example, they use paper chromatography and to be honest, it will be very hard for me to reproduce the methods since I have never done this before.
Can I replace these analyses by sequence data of 4 genes instead of only one (16S rRNA)? I will add results from API Coryne but I have no idea about cell wall and lipid analysis.
Edited by czernobill, 06 December 2012 - 03:42 AM.
Posted 06 December 2012 - 05:23 AM
Posted 06 December 2012 - 02:57 PM