Be sure to keep up the probiotics while on PPIs, because taking them could increase the risk of c-diff. Stomach acid keeps c-diff down. PPIs keep stomach acid below the level of protection against c-diff.
My experience with this: dd started with GERD in Nov 2010. Doctor put her on prevacid in December. I had a conversation with the owner of Custom Probiotics who suggested that my daughter should probably not take prevacid due to her history of c-diff in 2006. He said you need some acid to balance out the good/bad bugs. I went back and asked the doctor, who said there is no relation to the prevacid. In April 2010, she got c-diff while still on it. FWIW.