Scientists say they have hard evidence foods containing "friendly bacteria" do have a tangible effect on the body.
Bifidobateria is a friendly bacteria found in the gut
The journal Molecular Systems Biology reports that mice fed probiotic drinks had different levels of key chemicals in their blood and urine.
The Imperial College London research - which was part-funded by food giant Nestle - also suggested they could change fat digestion.
But dieticians say they work only for relatively small numbers of people.
The science of probiotics has been controversial, with suggestions that even the billions of bacteria in a pot of yoghurt could not possibly influence the trillions already found in our guts.
However, the mouse research does offer some evidence of an measurable effect, say the researchers.
They fed some mice a normal diet, but added a drink containing "friendly bacteria" to the diet of others.
Screening the blood, urine, faeces and livers of the mice revealed that levels of several key chemicals related to important processes in the body were altered in the probiotic-treated animals.
'Whistling in the wind
One of the differences they spotted was a change in the way the mice with probiotics handled bile acids, released into the gut to help the body break down fat.
They found chemical clues in the mice which suggested that the probiotics might, in some way, be helping break down bile acids more effectively.
In theory, this might mean more fat passing undigested through the body rather than being absorbed - although the study did not prove this.
Professor Jeremy Nicholson, who led the project, said: "Some argue that probiotics cannot change your gut microflora - whilst there are a billion bacteria in a pot of yoghurt, there are a hundred trillion in the gut, so you're just whistling in the wind.
"Our study shows that probiotics can have an effect and they interact with the local ecology and talk to other bacteria.
"We're still trying to understand what the changes they bring about might mean, in terms of overall health, but we have established that introducing 'friendly' bacteria can change the dynamics of the whole population of microbes in the gut."
A spokesman for the British Dietetic Association said that most theories about the way probiotics worked involved the new "friendly bacteria" getting rid of harmful bacteria by competing more strongly for their food.
"It's believed that they can displace them by being dominant, rather than interact with them directly, so this would be something new."
She added that relatively few people had actually been shown to benefit from probiotics, including people with irritable bowel syndrome, those at risk from travellers' diarrhoea, and patients whose own gut bacteria had been wiped out by antibiotics.