Of course, it depends on your DNA extraction method. If you use a kit designed to remove the PCR inhibitors from soil or stool, such as the MoBio Powersoil kit, then there should not be much inhibitor present. In any case, if you have a high enough yield of DNA, you can also dilute the sample considerably, at least 1/20 or 1/100 to obtain a PCR product. But whether this is useful also depends on the experimental application.

I would suggest using a kit specifically designed to remove PCR inhibitors from the stool. As David above mentioned, it depends on how much starting DNA you have also. However, I think you will get a much cleaner product if your extraction method was designed for stool.

I've used Stool extraction kit for the past few years and it proves to be effective when added with BSA.. but when i switch to Analytik Jena Stool Extraction Kit, I don't have to use BSA during extraction and the results is just as good as with previous kit+BSA.. however, it still largely depend on the quality of DNA in stool sample collected..

Thank you for all of the suggestions given. It would be my first time extracting DNA from stool and I guess practice makes perfect to gain the best result. Anyone have the experience using the stool extraction kit from Qiagen? How well it could remove the PCR inhibitors? If I am going to extract stool from premature babies, BSA might come in handy I think. I doubted babies stool has high quality DNA.

i have used Qiagen dna extraction kit, but unfortunately for plant DNA, but the kit always give me a good result both in quality and quantity, so maybe stool kit from Qiagen will give you a good result too. i hope :).

The best way to overcome the effect of inhibitors is of course to utilize a DNA extraction kit that removes as many as possible and leaves you with pure DNA. An alternative is to use a more robust polymerase than the off-the-shelf taq. You could find some inspiration here: http://www.sciencedirect.com/science/article/pii/S1875176811001752