We have been using the QIAmp DNA Stool kit to extract total DNA from the gut of the Solea senegalensis larvae (2 dph to 60 dph), but when we do the amplification of the 16S RNA variable regions we do not have any results.
I suppose this is primarily the problem of the amount of bacterial DNA is very less due to very little starting material in extraction. Try increased starting material and if possible make replicates during extraction and pool them for the quantification. I suppose you are taking whole gut for the DNA extraction and in quantification you probably get amount/quantity (qubit/nanodrop) or band (gel) from the host DNA. [needless to mention, to use correct combination of primers with preferred temp. as mentioned in literature]
Any kit would supposed to work unless there is not unusual high amount of inhibitors, and as the samples are coming from larvae, it should not be a problem.
In conclusion, increased amount of gut microbial material would give you good result.
Thanks for your answer.
I will follow your recommendations increasing amount of larval gut.
What do you mean with "no result"? You get no product in the PCR, that is, no band in the gel?
I would try to purify the DNA, and then do a new PCR. Also, try more universal primers. In my experience, with 16S primers you always get something, even if you don't want to!
I agree that any kit would do, or even salt-extarction etc. I have worked with smaller samples (different taxa, but DNA is DNA), and the 3 compared methods worked. See this: Article Pellets of proof: First glimpse of the dietary composition o...
And keep in mind, that you may have a little bit of DNA even though not visible on the gel. Hope you get it done! :- )
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