identification by 16s rRNA - (Apr/25/2012 )
We isolated several bacteria from soil. The biochemical and 16srRNA blast results didnot match with each other. How can I resolve this problem.
Maybe you made some mistakes? Maybe you found a new bacterium ? Could be many reasons why they dont match.
But by not matching: what do you mean? Its possible that it "doesnt", but that you are working with "family" (closely related) or that you get a real big difference... I mean a "real" non matching problem...
which biochemical reactions do not match with your seq?
Thanks for the answers. For eg. According to biochemical tests the bacterium is from the genus of pseudomonas but sequence blast says it is from the genus of staph or in another case bacillus.
Is your purpose to id the isolates or resolve the disparity in test results. If the frmer, you might resort to the archiac - Gram stain, oxidase, etc.
Again WHICH biochemical tests did you use? If you e.g. used API your results are probably not correct and ambigous - especially if you used the wrong system (gram -) which will by definition not be able to give you and id of bacillus or staphyloccous. or did you just use the rough tests like KOH, Oxidase etc?
However your problem can easily be solved by doing the "archaic" tests suggested by Phil especially gram staining - and they will include LOOKING at your bacteria - and microscopy will also (if you are not extremly unlucky) enable you to see a difference in the morphology of the cells (rods in case of pseudomonas, cocci for staph .....) which helps you to decide which results to trust more the DNA or the biochemistry. This will also show if you are working with a pure or mixed culture of all three - which might be the reason for your inconsistent results.