We are working with different fermentation times of silage, when extracted DNA at time 0 yield >100ng/ul but at time 140 days yield
What kind of extraction procedure do you use??. Is it a commercial kit?. I think you should try for both Gram positive and negative protocols. As far as I know, Propionibacteriaceae members are gram positive. Therefore It will be little difficult to get good DNA amount as usually we get with Gram negatives.
We are using the Quick DNA Fecal/Soil Microbe MiniPrep™ by Zymoresearch and used FastPrep®-24 Classic -MP Biomedicals to physical break.
I think the normal concentration should be > 100ng/ul just like what you observed during t = 0. There must be something that makes the dna yield at t = 140 days low, maybe because there are many metabolites after fermentation that might interfere(?) Anyway, what I know is different growth conditions may affect dna yield, and maybe the conditions during fermentation affects them. Actually dna concentration of 10 ng/ul still can be used (depends on what you intend to use it for), but you can try using different extraction method if you still want to try to get higher dna concentration.
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