We have bacteria covering our entire bodies, inside and out. To say you're going to kill all of them is insane. A lot of it is beneficial. An interesting thing I learned in my biology/life science class though is that a recent study showed that a certain type of bacteria is the cause of heartburn.

As far as those other creatures go... lol try not eating pork, they carry eggs of certain worms that wallow in their cess pools. Also, try not eating raw meat (or rare) because if a cow or whatever else it is you're eating is carrying eggs of anything, it will be given to you.