Since germs are not capable of moral choices they are neither good nor bad. There is also no 'reason' for germs and their actions have the same result of all non-sentient living things - survival and reproduction. Depending on their specific requirements they may have no effect on the body, or may even protect the body from pathogens; as in the case of natural flora found in the acidic skin mantle, they may cause disease or death. It all depends on a number of factors that you seem to be unaware of.
You repeat your the naturalistic fallacy, by assuming that just because they (germs) are natural they fill a greater function. The actions that drive survival and reproduction are the 'reason' for their existence. Our death, illness just happens to be a by product of that. But again since they cannot make moral choices even our deaths would not be classified as evil.
I assume you know nothing about evolution, or more likely you are a wacky creationist. If you did know about evolution, then it would be obvious why we are not "dropping like flies". We have an adaptive immune system that has been working for us for at least 500 million years, and more if you count the innate immune system. We come from a long line of survivors, those that were not felled by diseases but could mature and live to reproduce to pass on their genetic advantage on to the next generation. But even to this day as many as 10 million people die annually from 'germs'
You are seriously deluded if you think you can find nutritional and sound medical science in the bible.