Bacteria used to have a bad rap. Then along came probiotics.

Suddenly it became impossible to avoid food products spruiking 'good' bacteria, but while there's evidence to suggest probiotics can be beneficial to your health, new research shows they may also have serious side effects.

In a new study led by a team from Augusta University, researchers found what they say is the first known link between probiotic use, bacterial overgrowth in the small intestine, and symptoms of disorienting brain fogginess.

In the study, patients who reported confusion and difficulty concentrating – in addition to experiencing gas and bloating feelings – were found to be harbouring large colonies of bacteria breeding in their small intestines, with high levels of D-lactic acid being produced by bacterial fermentation of sugars in their food.

"What we now know is that probiotic bacteria have the unique capacity to break down sugar and produce D-lactic acid," explains lead researcher and gastroenterologist Satish S.C. Rao.

"So if you inadvertently colonise your small bowel with probiotic bacteria, then you have set the stage for potentially developing lactic acidosis and brain fogginess."

Inadvertent would be the key term there, because probiotics are supposed to work in the colon – not in the small intestine or stomach.

But if they end up there and start breeding in the organ – abetted by probiotics boosting their numbers – the consequences can be serious.

D-lactic acid is temporarily toxic to brain cells, and can interfere with people's cognition, ability to think, and sense of time.

In the study, the researchers found some patients had two to three times the normal amount of D-lactic acid in their blood, leading to bouts of brain fogginess that could last for hours after eating, and in some cases were so severe that patients had to quit their jobs.

Sometimes, the effects could be rapid, with the researchers finding one patient who experienced brain fogginess and bloating within a minute of eating.

"It happened right in front of our eyes," Rao says.

Of course, not all people would experience the same symptoms from taking probiotics, and not all probiotics are the same either.

But Rao says the experience of the patients he and his team clinically observed over three years shows nobody should casually or indiscriminately be taking probiotics without taking medical advice.

"Probiotics should be treated as a drug," he says, "not as a food supplement."

Researchers had previously found probiotics could lead to health problems in people with a short bowel – where the small intestine doesn't function properly – but the new findings indicate otherwise healthy people can succumb to brain fogginess and bloating if bacterial colonies start to thrive in the small intestine.

The good news is the symptoms, for the most part, weren't permanent.

When patients experiencing brain fogginess and bloating took treatment –taking antibiotics, giving up probiotics, and staying away from foods that naturally contain them, like yoghurt – most symptoms were alleviated.

About 70 percent of patients reported significant improvement, with 85 percent saying their brain fogginess disappeared, and those who experienced bloating also reported improvements.

If you're experiencing any of the same cognitive or bloating problems, you should really see a doctor – but if you regularly take probiotics or eat a lot of yoghurt, it looks like there's a decent chance that could be contributing.

The findings are reported in Clinical and Translational Gastroenterology.