I prepared a sample of anaerobic bacteria in a petri plate for scanning electron microscopy. The samples were covered with platinum. Now, I would like to extract the DNA 16S for NGS analyses. Is it possible? Thanks
Hi,
for NGS you have to have very clean DNA without visible fragmentation on agarose gel electrophoresis. It is possible to make fresh culture from your samples or do you have only those covered with platinum?
Thanks Marcela. Unfortunately, now I have just the sample covered with platinum because I stopped the reactor operation in November. I have already analysed the 16S DNA (NGS), however the results highly differed from the SEM and Gram analyses.
And what is the point of your investigation? Would you like to identify your anaerobe bacterium in Petri dish or anything else?
I would like to identify the bacterial community from an acidogenic reactor. However, I am not operating the reactor any more... The only sample I still have is that one I analysed in SEM (then, it was added glutaraldehyde and platinum).
I have found this article. It could help you with glutaraldehyde.
file:///C:/Documents%20and%20Settings/krutova96135/Dokumenty/Downloads/Overcoming-constraints-of-genomic-DNA-isolated-from-paraffin-embedded-tissue-EN.pdf
You can try some protocol and then to measure the quality of DNA. After that you can decide to do or not to do WGS.
You may check revival of the bacterium by plating on the respective nutrient medium. Or, you can try to isolate DNA from the sample treated with glutaraldehyde and covered with platinum. But I do not know studies like these. Glutaraldehyde and platinum may kill bacteria, but not DNA?
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