Hi,
I am working with cyanobacteria and want do Whole genome sequencing of Pseudanabaena (a cyanobacteria). I cannot get axenic culture of it , it is contaminated with other bacteria. Every time i extract DNA and run PCR i will get other bacteria and even fungus. I have used antibiotics like Penicillin G and streptomycin (120 microgm/ml) and end up killing cyanobacteria too. I used cycloheximide to kill green algae and it works quite well. But still i am suffering to get axenic culture.
So my question is, does the presence of bacterial genome will effect whole genome sequencing of my cyanobacteria? another, how to get axenic culture of cyanobacteria.
Thank you!!!!
On one side, if you plan to sequence at a company, they will never accept contaminated DNA. On other side if you do the sequencing by yourself, you end up with a mixture of genomes. That great for some aspects if you plan to study metagenomics (as example) but useless if you want to screen for specifics clusters.
Sometimes, the contamination is not limited to the culture however to the wet lab material as pipettes, flasks, original strain, ect. Check all these parameters before launching a new culture and try to cultivate many flasks in parallel. It should work out.
Good luck.
Loub.
perhaps contam not from culture , from lab environment , from instruments, you can try in another lab
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