How do I identify biofilm bacteria?

fwhyde at ibm.net fwhyde at ibm.net
Tue Jun 23 08:11:15 EST 1998


Paul Taylor wrote:

> Hi,
>
> I would suggest taking the molecular approach and go for 16S rDNA
> sequencing. Extract the DNA from a sample of your slime, amplify the
> 16S
> rRNA gene using universal primers (see the Ribosomal Database Project
> for
> some sequence). the amplified product will need to be cloned into a
> suitable vector. From there it is fairly straight forward to get
> sequence
> for the rDNA and search databases for a match.

Another approach would be sequence scanning rather than full-blown
sequencing. If primers are available, you can simply PCR the 16s rRNA by
RT-PCR, then use nested PCR to get a good amp. There are kits available
that allow you to do the equivalent of T or G-ladder sequencing, much
more rapidly than dideoxy sequencing. Better for lots of samples, too.

Fred




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