I consider bacteria and viruses to be to the human body like plugins are to software. The body is an entire organism but in fact it's a symbiosis of multiple organisms that evolved together. These organisms are so interlinked they couldn't exist separately.
Normal evolution means that the body must continually keep up with the changing environment in which it lives. Bacteria and Viruses are simply natural means to facilitate these changes. Horizontal gene transfer is part of this mechanism and there is plenty of evidence that the organisms we host talk to each other. This is just the same as software and operating systems. They all talk to each other. Lots of tiny applications and scripts slowly get incorporated into software and ultimately built into operating systems.
I simply see the same pattern happening in biology. In fact I feel that we are just seeing the normal processes of evolution occurring in digital fields as we have seen in the biological ecosystems.