I am trying to isolate DNA from cervical swabs while also maintaining the microbiome. Our collaborators want the swabs processed in a sterile environment, which rules out using a kit that exposes any of the samples to each other. We've been testing the QIAmp Fast DNA Stool Mini Kit on our pilot samples and modifying the protocol for cervical swabs instead of stool. We've been working in a biosafety hood and basically just spinning down and collecting liquid off the swabs.
Our DNA concentration yields are low and inconsistent. In other discussions I've seen complaints that the InhibitEX buffer in this kit doesn't work as well as the tablets, but I am not sure if that is our problem. Has anyone found a good protocol for extracting DNA from cervical swabs? If so, can it be modified to maintain a sterile environment?
Hi, try DNA stool kit (without Fast). Qiagen stool kit is quite good for me for 16S metagenomics, but in the case of your sample type I am not sure.
Hi,
Qiaamp Power FecalPro is the newest generaiton in this product line with improved mechanical lysis and inhibitor removal, therefore giving you more consistent abundancies especially also for hard to lzye bacteria and Funghi. I have used the kit to extract DNA from buccal swabs which work really well and easy (and had no background in blank extractions)
Sven
I have some stuff that should be able to help you out here. I'm on the bioinformatics team at Zymo and do a fair amount with microbiome (I also used to work in the department of Medicine at UCLA when I was more wet lab and can definitely understand the issues you bring up).
For a collection device, I would recommend this: https://www.zymoresearch.com/products/dna-rna-shield-collection-tube-w-swab The swabs are good quality and shield reagent can then be put through our microbiome extraction methods. Since you are also saying that you are having issues with low biomass of sample (not surprising with a cervical swab), you might also want to try out our microprep to maximize your recovery and concentration at https://www.zymoresearch.com/products/zymobiomics-dna-microprep-kit .
If you want to try some of these out, send me a ping and I can probably arrange to get you a pack or two for testing out.
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