Given that there are organisms that can literally effect human and animal behavior, in a way the system itself is partly controlled by the organisms inside it.

The big ones are toxoplasma, rabies, etc but there's a theory that many viruses and bacteria seek to control the behaviour of the host to enable successful spread. Perhaps flu makes people more social before they get too ill? Perhaps some sexually transmitted diseases change behaviour to make the host more promiscuous? Almost impossible to perform any studies on humans, but for fish...