I need to extract and isolate the complete DNA from a pathogenic bacteria. The bacteria cannot be completely isolated because up until today there is no culture media and none of the media tests have worked.
If you have access to complex samples with high densities of bacteria, you could try separating bacterial cells from eukaryotic cells by density gradient centrifugation. There are several media out there, but Percoll (Fluka) works well in my hands. I routinely get >99% pure bacterial DNA from contaminated host tissue samples.
Thank you Dr. Carlier. I will try to isolate a rickettsia like organism by percoll sucrose gradients, but as I need to perform a genomic library I need to extract gDNA and make sure that such DNA is exclusively the DNA of those bacteria. But if you hace such results using percoll it may be enough for my experiment, I will double check. Thanks.
If you can disclose what you intend to do with the DNA later eg: library or sequncing, it might be easier to suggest.
If its only megaplasmids there are some protocols for insitu well lysis of bacteria for small range plasmids that you can perform in regular agarose electrophoresis units.
If the objective is to isolate megaplasmids there are some kits for BAC dna isolation might work. Alternatively you can go old school and do CsCl preps. So as you can see there are multiple methods, depends what you intend to do downstream later .
Good luck
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