I'm trying to extract DNA from tomato fruit in order to study the bacterial microbiota found inside the fruit using NGS. I have tried using a CTAB protocol, but the precipitate is highly charged in polysaccharides. I have also tried using the QIAamp Powerfecal DNA extraction kit, which gave even worse results than the CTAB protocol.
Any ideas of protocols/extraction kits that could work?
I think that the inside of a healthy fruit suppose to be sterile and can't get any
foreign DNA , might you get the DNA of the fruit it self
best wishes
Hi Zahra,
Thanks for your reply. However, numerous studies have shown that bacteria can effectively colonise fruits and vegetables. Here are a few examples:
Article Distribution of Bacteria within the Tissue of Healthy Tomatoes
Article Internal Colonization of Salmonella enterica Serovar Typhimu...
Article Microbial Contamination of Fruit and Vegetables and the Beha...
Regards
This is probably not an answer but might help you? How are you starting the extraction? From the fresh tissue or with frozen sample? If you suggest me any indication of our protocol, there might me something I could suggest you. Do you have any particular location of fruit (juice, sub-cutaneous or pulp) where you expect to find endophytes?
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