There was a very interesting study in mice on probiotics and depression just a few months ago:
Next, the researchers severed the vagus nerve, which helps alert the central nervous system to changes in the gastrointestinal tract. They found the bacteria-induced effects on behavior and GABA receptors were diminished, suggesting this nerve is the pathway by which changes in the gut can influence the brain.
http://www.livescience.com/15822-embargoed-probiotic-bacteria-treat-depression.html
I know that studies in humans on depression and probiotics also have shown benefits.
I also had a bad reaction to probiotics in the past, but this past Fall, when my stomach went crazy (possibly an infection, it was horrible cramping that went on for weeks), probiotics saved me. I started taking them 3x a day and if I missed a dose, it was bad. I was loathe to try them at all because in the past they had given me intestinal cramps, but instead, they were great.
Most recently, though, I do have a lot of brain fog, but I've also been sick and am starting on methyl folate with a lot of disrupted sleeping, so, it's not clear if they have a role.