Or does this high quantity of human DNA not affect PCR applications targetting the bacteria DNA where I am using 16s rRNA primers.
No, this is no problem, given your primers are specific for the bacterial 16s rRNA.
They should not produce a PCR product when only human DNA is used as template; you can easily check this (run a PCR with only "sterile" human DNA as template). In the unexpected case that they will unfortunately give some product(s), this may interfere with the amplification of the specific bacterial target sequence.
In the worst case the bacterial target sequence might not be amplified up to detectable amounts, you the rate of false-negatives will increase. If false-negatives are not a concern, then you are save anyway. However, this relativates when you are doing a quantitative PCR. Here, the influence of the amplification of uncepcific products on the amplification efficiency of the specific product will make a reliable quantification impossible. Again it is sufficient to chek if there are any unspecific products occuring when only human DNA is used as template (if they occur only very late, after 35 and more cycles, even this may be neglected since it won't have any significant influence on the quantification based on ct values below 30).
In the very unexpected and unfortunate case that the primers give a product of a very similar length like the specific product, they won't be distinguishable in a standard (agarose) gel electrophoresis. This would produce false-positive results. In this case you should really design new primers. If you use a sequence-specific detection system (like real-time PCR with sequence-specific fluorescent probes or a Southern-blot) this is also not a problem.
I taked with a collegue with the same porblem: actually one might think 18S does not disturb but it does, thinking of stoichiometry.
She played a lot with PCR settings, sometimes with tiny bands, sometimes not.
She than used a Kit to concentrate bacterial DNA - Looxster was the one that resolved her problem.
Maybe you can try this, if playing with PCR settings will not help you.
Hello,
I have the same problem here and I am asking if you find a propriate method to amplify only the bacterial 16s RNA?
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