More interesting would be if this goes the other way.. do our belief systems and rationality have a profound impact on our body chemistry?

Some of the articles describe the symbiosis as a two-way communication. For example, the article I mention at the end goes on to say:

There are several mechanisms by which stress can alter the bacterial composition of the GI tract, including changes in epithelial cell function and mucus secretion as well as changes in GI motility. 41,43,44 As described, release of norepinephrine into the GI tract during stress might preferentially stimulate the growth of specific strains of bacteria as well as their ability to adhere to the mucosa. 32–34