The human immune system only kills off foreign bacteria that the body does not naturally recognize; the human body is full of friendly bacteria that it needs to function, particularly in our digestive system. Occasionally, a bacteria that is harmful to a certain part of the body will be found, flagged as an invasive species, and killed. Viruses, on the other hand, function parasitically, and are always destructive. Your immune system will try to keep them at a minimum. Many bacteria, on the other hand, live symbiotically with the human body, and are necessary for survival.