I see two areas of difficulty that you are encountering.
First, by working with dichotomous schemes you are expecting
a "definitive" answer. Dichotomous schemes
give yes/no answers -- but sometimes identification requires "judgement"
as to what the most likely or reasonable or sensible ID is. You just don't get
a clear cut results.
You need to acquire the ability to perform a range of tests and accept
that in some instances the IDs will be in the form of a probability... or
your personal judgement about the organism.
Second, PCR identification schemes are still very much in their infancy.
In some ways they can suffer from the same limitations that dichotomous
schemes have. That is, the gene is there or it is not there!! Yes/No
But what happens when you have a perfectly fine specimen of an organism
with a significant modification of a gene or gene sequence? What happens
when something is not quite right with the complex technology?
Identifying beasties requires a broad look at an array of characteristics
and sound microbiological judgement. You must develop an ability to accept
answers in terms of probability.
If there is some legal reason why the ID must be accurate, then use
standardized procedures such as those in BAMA and AOAC. At least you will be
able to defend your result.
In article <8ngd8m$am5$1 at nnrp1.deja.com>, riyazandrabi at my-deja.com says...
>I am working on DETECTION OF FOOD PATHOGENS BY PCR.My work requires me
>to isolate and identify microorganisms from food.Presently I have got
>some dichotomous keys downloaded from internet and schemes from some
>mannuals for this purpose.I particularly follow the Microbiology Mannual
>by Cappiccino and Sherman.I want to know if this mannual is sufficient
>for the purpose.If not please help me in finding a reliable scheme of
>identification.I have faced many problems during identification of some
>microorganisms.Presently,I'll mention one.In the above mentioned mannual
>the identification scheme recognises only three species of Bacillus
>viz,B.cereus,B.subtilis and B.megatherium.Further,the scheme shows that
>all mannitol negative are B.cereus.I took all the mannitol -ve Bacillus
>species and ran a PCR reaction using the primers specific for
>B.cereus.Do you know what was the result,only some of them showed
>positive results.So please guide me.Thanks in advance.
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