What kind of DNA do you want to target?

Human cell DNA?

Cell free DNA?

Microbiome DNA?

One of the possible solution is to use commercial kit to extract the DNA first before doing PCR. 

From

http://www.sciencedirect.com/science/article/pii/S0163445313000984

McAuliffe GN, Anderson TP, Stevens M, Adams J, Coleman R, Mahagamasekera P, Young S, Henderson T, Hofmann M, Jennings LC, Murdoch DR. Systematic application of multiplex PCR enhances the detection of bacteria, parasites, and viruses in stool samples. Journal of Infection. 2013 Aug 31;67(2):122-9.

They use STAR buffer to store the stools for extraction. 

You can try QIAamp DNA Stool Mini Kit DNA for DNA isolation. This kit is specific for metagenomic DNA isolation from stool sample and also contain PCR inhibitor remover.

Good luck.

There are different DNA extraction kits from stool samples that treat the sample to remove non specific inhibitors. We normally use QIAamp DNA Stool Mini Kit (Qiagen) and we are getting good results.

we used the biomerieux with magnetic silica (MiniMAG) to extract DNA and RNA for infectious diseases diagnostics in stool. When the PCR was inhibited, most of the time a dilution (1/10 - 1/100) in nuclease free water was enough to eliminate the effect of PCR inhibitors in the sample (after being extracted of course).

I use Mobio DNA power soil to fecal samples from animals and I had good results. Other option (if your DNA concentration in good) is dilute your DNA or to use BSA in PCR mix

Hi Elizabeth. As Isabel, we normally use QIAamp DNA Stool Mini Kit (Qiagen) and we are getting good results.I use an internal control (home made) to detect inhibition problems. We do the PCR with pure sample (stools from patients). If we detect inhibition problems, we repete the PCR with an 1/10 dilution of the sample to overcome the inhibitor problems, and normally its works. Good luck. Alicia

Thank for your help, but I can not use DNA extraction kits from stool samples because is very expensive and we have not foreign exchange actually, in Venezuela we have Currency control, is impossible for us have $$$ or E. We used protocols of DNA extractions made in home, and we also tried using several dilutions of the DNA but it did not run.

Try to use the method citated by my colleague Silva et al. (Parasitol Res, 2010, 107:271–277). DOI 10.1007/s00436-010-1858-2

It is not too expensive and it works pretty well.

you can use some DNA extraction kits that contain remover for PCR inhibitors

Hello Elizabeth!!!!.  I  normally use QIAamp Fast DNA Stool Mini Kit (Qiagen) . It is good for to remove non specific inhibitors in the human stool samples. In addition, as Alicia Moreno tell you if we detect inhibition problems, we repete the PCR with an 1/10 dilution of the sample to overcome the inhibitor problems and we are getting good results I  normally use QIAamp Fast DNA Stool Mini Kit (Qiagen) . It is good for to remove non specific inhibitors in the human stool samples.

Thanks Esperanza, Thank for your help, but I can not use DNA extraction kits from stool samples because is very expensive and we have not foreign exchange actually, in Venezuela we have Currency control, is impossible for us have $$$ or E. We used protocols of DNA extractions made in home, and we also tried using several dilutions of the DNA but it did not run.

stool and soil are one of the toughest samples, that contain substantial number of inhibitors of enzymatic reactions (such as PCR) that tend to co-purify with DNA. try PureLink microbiome kit (Invitrogen)- it has a very efficient inhibitor depletion step, yet very high DNA yield