The study, the first to use human stool samples, detected microplastic particles in the gut and linked them to altered microbial activity.
Researchers from the University of Graz examined stool tissue from five healthy volunteers and found that the particles changed bacterial behaviour in ways previously associated with bowel cancer and depression.
Experts described the findings as significant but said more research was needed to confirm how microplastics cause such damage.
Microplastics are fragments as small as two micrometres that enter food, water and air as plastic products degrade.
Past studies have found them in human lungs, blood, breast milk and placental tissue.
Earlier research has also connected microplastic exposure to cancer, heart disease, dementia and reduced sperm quality.
Christian Pacher-Deutsch, lead author and microplastics researcher at the University of Graz, said the findings were important given widespread exposure.
“Microplastics have been found in fish, salt, bottled water and even tap water,” he said.
“The key takeaway is that microplastics do have an impact on our microbiome.
While it's too early to make definitive health claims, reducing microplastic exposure where possible is a wise and important precaution.”
In the study, scientists grew gut microbiome cultures from stool samples and exposed them to five types of microplastics — polystyrene, polypropylene, low-density polyethylene, poly(methyl methacrylate) and polyethylene terephthalate.
Samples treated with microplastics became more acidic, showing signs of altered microbial activity.
Changes mainly occurred among Bacillota, a bacterial group essential for digestion and gut health.
The researchers said some of the observed bacterial shifts mirrored those seen in depression and bowel cancer.
They suggested biofilm formation and chemical contamination on plastic surfaces could be driving the changes.
The findings will be presented on October 7 at the United European Gastroenterology Congress in Berlin.
Bowel cancer is the fourth most common cancer in the UK and US, with 44,000 and 142,000 annual cases respectively.
Symptoms include persistent changes in bowel habits, blood in stool, abdominal pain, bloating and unexplained weight loss.
Rates have risen by 50% among younger adults in the past three decades.
Cancer Research UK estimates that more than half of bowel cancer cases are preventable.