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PCR/cloning of bacterial communities

Bill Burnett bbur at dml.ac.uk
Mon Feb 10 05:57:35 EST 1997

Hi All....

I've been working on bacterial symbionts for a while now, in "simple" 
systems with single bacterial strains within a host.  This all works 
quite nicely...  extract DNA from host, amplify with bacterial specific 
primers, clone, sequence and in situ hybridise...  voila.

However, I'm moving on to more complex systems with multiple symbionts 
with different morphologies, which may or may not represent different 
strains within the same host.  These morphologies are present in varying 
proportions, and might represent very closely or more distantly related 
bugs within the purple bacteria....

What I'd like to know, from anyone with similar sorts of experience of 
characterising mixed bacterial communities, is how well comparatively 
rare strains show up among a population of clones after PCR and cloning, 
and how many clones I'm likely to have to sequence in order to find a 
reasonable percentage of the different strains present.  

Any thoughts or suggestions for approaches greatly appreciated....


Bill Burnett             bbur at dml.ac.uk
Scottish Association for Marine Science
P.O.Box 3, Oban, Argyll, Scotland

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