I am extracting DNA from fish gut to characterise the microbial community. I have found that DNA yields are usually low (between 50 and 300ng/ul using nanodrop/qubit). I am curious to know the yields that others are deeming as acceptable to use for NGS approaches when characterising microbial communities of similar samples to mine.
Thank you
Depends how you wish to proceed if using kits like Nextera, its good enough.
But for amplicon, yes if you get good enough amplicons that you think reflect a close approximation of the community membership it should be ok.
Hi,
I have done the same with environmental samples and my DNA conc. ranged from 25 to 400 ng/µL and everything went fine. They told me that the purity of the DNA (removal of RNA, ...) is more important than the DNA conc..
So, your DNA conc. should be good enough for NGS.
Greetings
Hi Bastian and Jay, thank you for your answers. Bastian - were your measurements of conc and purity with nanodrop or qubit? Thank you
I guess you want to amplify a variable region of the 16S, in that case it is more than enough. When we do this, we dilute all the samples to have 50 ng/ul and the we amplify. It work nicely. Just have a good quality DNA (>1.7).
In our lab, we are able to successfully amplify 16S rDNA below 10 ng/ul (sometimes even below 5 ng/ul ) by NanoDrop. Once the purity is OK, it will not be a big problem. For NanoDrop reading, if you can see a little peak at 260 nm, that means the reading and purity are probably OK and make sure that the 260/230 ratio is at least 1.0. This is especially the case when your DNA concentration is low.
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