I just spotted this on the Fankhauser site with regard to bubbly cheese, which is probably what Jen was referring to, but I bring it up again because of his point about aging to make the cheese safe:
The bacteria which form bubbles may be a form of Escherichia. However, it does not necessarily ruin the cheese, but does make it iffy. Many CO2 formers are non-pathogenic. Indeed, you might WANT bubbles in your finished cheese. Think about Swiss cheese... However, to be safe, age your cheese for at least two months because pathogens do not survive this extended aging.