This is for Geege's Microbiome Stash.

Your title is more confident than this one:

http://pandawhale.com/post/64467/can-the-bacteria-in-your-gut-explain-your-mood

It has long been known that much of our supply of neurochemicals — an estimated 50 percent of the dopamine, for example, and a vast majority of the serotonin — originate in the intestine, where these chemical signals regulate appetite, feelings of fullness and digestion. But only in recent years has mainstream psychiatric research given serious consideration to the role microbes might play in creating those chemicals. 

...The central theory, quite controversial at the time, suggested that stress worsened disease by suppressing our immune system.

...

The study added to a working hypothesis in the field that microbes don’t just affect the permeability of the barrier around the brain but also influence the intestinal lining, which normally prevents certain bacteria from leaking out and others from getting in. When the intestinal barrier was compromised in his model, normally ‘‘beneficial’’ bacteria and the toxins they produce seeped into the bloodstream and raised the possibility they could slip past the blood-brain barrier.

So who controls whom?

Or is neither in control and they're just a feedback loop?