Not sure how, if at all, it's related, but another interesting caveat here is that the gut is surrounded by neurons and produces large amounts of serotonin. One can imagine that if the microbes are altering the GI chemistry to a great degree that this system will also be effected. Here is an article on the topic.
I'm by no means an expert on the topic. I have a colleague who used to work on brain-gut interaction. His studies were all in mice, so I know that it's not unique to humans, but how different humans are from other animals isn't something I know anything about, sadly. I've been reading a lot recently about how the immune system affects the brain, which is also a complicated, but fascinating topic. All these things just go to show how much of a whole we are. I know I preach this all the time, and it might be getting stale, but don't ever believe the hype when anyone says that your brain thinks X, Y or Z. A person is so much more than circuits.
The idea what we are a deeply integrated whole is absolutely interesting. I'd imagine that this kind of thing is something that makes creating artificial organs such a difficult task. I'm not sure I've ever really believed that the brain was all there is to thought, or even that thoughts are the only things guiding human behaviors. There certainly seems to be a lot more to understand about the human body and I'd bet, how it can best operate.