Not all E. coli are disease causing. There are many strains. You have E. coli in your body already and it is actually necessary for good health. It's the bad strains that cause illness, or strains your body is not used to like traveling and getting sick. Microbial coagulant also doesn't actually contain the bacteria that makes it. The microbial rennet is produced by the bacteria and then removed and purified. If you have concerns with genetically modified organisms, you may want to consider how that relates to microbial rennet. The bacteria are modified so that they produce the rennet.
Susan