Taking the healthful bacteria called probiotics can be great for gut health, but new research has uncovered a serious potential side effect—trouble thinking straight, aka brain fogginess.

Why would researchers even look for such a connection? It all started when Satish S.C. Rao, MD, director of neurogastroenterology at the Medical College of Georgia at Augusta University, noticed that a number of his patients with gastrointestinal symptoms had also been experiencing mental symptoms—confusion, impaired judgment, short-term memory problems and difficulty concentrating. The brain fogginess happened intermittently but usually after the patients ate—for four of them, the fogginess was so severe that it was interfering with their careers.

So he conducted a study of 38 patients who had GI complaints of bloating, stomach distention, pain and gas without any obvious cause. Thirty of these patients had not only the GI symptoms but also had complained of brain fogginess.

A variety of tests revealed that the patients with brain fogginess had up to three times the normal level of D-lactic acid, which is made in the gut. Under normal circumstances, D-lactic acid is produced in very small amounts, easily cleared by the kidneys. But when the body produces large amounts of D-lactic acid, the kidneys can’t clear it all and it accumulates. The D-lactic acid is then able to enter the brain and cause brain fogginess. (Note: This is different from L-lactic acid, which can accumulate in muscle and cause muscle cramps during exercise.)

How did the patients get those high levels of D-lactic acid? The researchers were able to trace it back to their intake of probiotics. They found that in 68% of the patients on probiotics, the probiotics and other bacteria had colonized in the small bowel and produced a condition called SIBO, small intestinal bacterial overgrowth. Every time these bacteria came into contact with sugar—from the carbs in the patients’ diets—D-lactic acid production went into overdrive. The result was the brain fogginess along with the GI symptoms. Once they stopped taking probiotics and were treated for bacterial overgrowth with antibiotics, both types of symptoms went away.


The problem isn’t with probiotics themselves—Dr. Rao does prescribe them to some patients with GI issues. The problem is when people self-prescribe them (only four people in the group of 30 patients with brain fogginess were taking them after consulting with a health-care provider) and have other aggravating factors that can help set the stage for SIBO and high D-lactic acid levels.

Two known culprits are the heartburn drugs proton pump inhibitors, or PPIs, and opioid pain relievers, says Andrew Rubman, ND, medical director of Southbury Clinic for Traditional Medicines in Southbury, Connecticut.

PPIs make your stomach less acidic, but in doing so they change your gut microbiome and expose the small bowel to bacteria overgrowth. (To ease the occasional acid stomach, Dr. Rubman recommends skipping PPIs in favor of drinking a half-teaspoon of baking soda mixed into a half-cup of water between meals.)

Opioids slow your gut motility and can paralyze the small bowel, making it easier for bacteria to colonize there.

If you’d like to get only the benefits of probiotics, follow these guidelines…

Eat probiotic foods. These include yogurt and kefir, pickled vegetables such as kimchi and sauerkraut, and tempeh and miso.

Eat prebiotic foods. The fiber in these foods basically goes unchanged through the stomach and small bowel and acts as fuel for healthful bacteria in the colon. Prebiotic foods include onions, leeks, garlic, asparagus, Jerusalem artichoke, bananas, whole wheat, yams and sweet potatoes.

Get healthful guidance. Have a medical evaluation to help you determine the right type and amount of supplemental probiotics for you. This is especially important if you have any health conditions, GI or otherwise, in order to avoid an adverse reaction. Don’t take a probiotic supplement on your own.

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