Dear colleagues,
I’m working on illumina metabarcoding of soil fungal communities. According to the literature, the result of such study is highly dependent on the DNA extraction and it is difficult to extract DNA from soil (particularly to study fungal DNA). I have read many articles to find out which DNA extraction protocol is suitable and gives good results. some articles recommended the commercial kits such as ‘FastDNA SPIN for Soil Kit’. Others recommended ISO Standard 11063 DNA Extraction protocol and other bead beating-based protocols. Would you please share you experience in the extraction of soil DNA to be used in fungi metabarcoding studies?
Regards
I would say there would not be any recommendation regarding any particular method of DNA extraction, especially with the use of any kits. It mostly depends on the personal experience, availability and price of the kits. But for good quality of DNA and longer fragments, classical phenol-chloroform method could always be used. In general, less the fragmentation in DNA, better it would be for NGS.
did you check this from Kennedy lab:
https://cbs.umn.edu/sites/.../Kennedy%20Lab%20Illumina%20protocol%20v1.4.docx
Thanks for your comments.
Yes of course Abhijeet Singh , However some methods/kits work better than the other and give good result and that is why they are be recommended.
I found some articles that comparing soil DNA extraction methods. but i need to hear about the practical experiences that you meant.
Abhishek Kumar , the link gave me permission denied message.
Regards
Dear Dr. SK,
Please try our method and see whether you could get high molecular weight DNA.
Shaik Yazdani Basha and P. Palanivelu
Two simple non-enzymatic procedures to isolate high molecular weight DNA from fungi, Current Science, 68, 587-588 (1995)
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