About 18 months ago a number of things conspired against me: I was having a very stressful and uncertain time at work/home, and I went on a strong course of antibiotics for an infection which wiped out my gut (a known side effect). For about six months I had serious digestive problems, both bloating, gas, diarrhea, nausea, abdominal pain - real, visible, symptoms...but despite a barrage of tests, nothing at all medically wrong. I had dozens of blood tests, an ultrasound, a gastroscopy, and a colonoscopy with biopsies - nothing. At the same time, I went through a serious depression and malaise that nearly always coincided with my digestive problems.
A year an a half later, I have a lot more respect for how the gut is tied in to general mental health. I'm not totally back to normal, but I'm a lot better than I was, thanks to meditation, watching my diet (my gut is a lot more sensitive to what I put in now - previously, I would eat any old junk), and generally making that connection between my mood and my stomach.
Related: https://news.ycombinator.com/item?id=7790727
* This is key. A therapist who works off their intuition ("why do you think you freaked out?") is a waste of money.
In my case, I can't eat certain foods (I'm still trying to work out which, but it includes chocolate) when I'm stressed. I get severe cramps, bloating, pain and even hot flushes (intense sweating). It happened to me on a train once and people thought I was OD-ing.
And stressed doesn't mean "close to the edge". Just a bit of nerves about something, definitely not enough to keep me up at night, will do the trick.
When the evidence suggested chocolate made me really unwell, but only if I was a bit stressed, it was really hard to accept because it just sounds so weird and implausible.
I get IBS myself, so I find it a little strange that some people don't. My guess is that my nervous system is simply more liable to over-activate than most people's. This is useful in that it gives me copious amounts of mental energy and ability to crank out amazing code very quickly and do stuff that most people (present company excepted) wouldn't be able to do, like design and build a compiler/VM for my own programming language, or build an HTML5 web conferencing system by myself. The downside is that I am prone to IBS and burnout.
While there is ample evidence of the brain influencing the gut, there isn't really much evidence of the gut influencing the brain. It seems unlikely that 'butterflies in the stomach' is caused by the gut influencing the brain, rather than the other way around. The afferent vagus nerves do signal to the brain when there is a gut infection, and that can certainly cause anxiety and depression. However most people with anxiety/depression/IBS don't have any active infection, and there is more evidence that it is the brain influencing the gut rather than the other way around. One possibility is that people with these conditions are genetically programmed to release more serotonin, and that happens both in the brain and the gut.