In a published study of 30 patients, the 22 who reported problems like confusion and difficulty concentrating, in addition to their gas and bloating, were all taking probiotics, some several varieties.

When investigators looked further, they found large colonies of bacteria breeding in the patients’ small intestines, and high levels of D-lactic acid being produced by the bacteria lactobacillus’ fermentation of sugars in their food.

D-lactic acid is known to be temporarily toxic to brain cells, interfering with cognition, thinking and sense of time. They found some patients had two to three times the normal amount of D-lactic acid in their blood.

“Probiotics should be treated as a drug, not as a food supplement,” Rao says, noting that many individuals self-prescribe the live bacteria.

When brain-foggy patients stopped taking probiotics and took a course of antibiotics, their brain fogginess resolved

Most of our intestinal bacteria is in the colon, the large intestine, not the small intestine:

Normally there is not much D-lactic acid made in the small intestines, but probiotic use appears to change that. SIBO [small intestinal bacterial overgrowth], which was present in most with brain fogginess, can cause bacteria to go into a feeding frenzy that ferments sugars resulting in production of uncomfortable things like hydrogen gas and methane that explain the bloating.

It’s not that the bacteria in the pills are themselves harmful; it’s that they’re ending up in a place they shouldn’t, the small intestine. That’s especially true for people who have slow motility. What can cause slow movement in the bowels? Lack of The Three Fs: fluid, fitness, and fiber. Drugs will also slow motility: pain killers, especially opioids, antidepressants, and simple things like iron or calcium supplements. Having diabetes slows motility. And proton pump inhibitors like Nexium and Prilosec reduce stomach acid which would normally destroy excess bacteria.