Michael Wilson, Professor of Microbiology at University College London, said there were some cases when topping up on "good bacteria" could help recovery from illness, but understanding of the supplements is "shaky" and needs a more robust scientific investigation.

"There are certain instances when probiotics are useful but the problem is there's no regulation," Prof Wilson said. "They are regarded as food supplements not medicinal products – anyone can get a suspension of bacteria and market it as a probiotic," said Prof Wilson, speaking at the Cheltenham Science Festival.

"With medicinal treatments, the pharmaceutical industry makes sure the things they produce are safe."

He said that there was some "instinctive sense" that adding to the gut flora will help with adverse events.

In recent years, probiotics have been promoted as a healthy food supplements, in the form of yoghurts, drinks and capsules, and the market is worth an estimated £200 million in Britain.

Clinical trials have shown that eating live bacteria can help sufferers of certain illnesses, such as antibiotic-associated diarrhoea, and there is evidence they can help women who have recently given birth to lose weight.

However, according to Prof Wilson, for people with compromised immune systems, increasing the bacterial load could lead to health problems.

"No bacterium is totally innocuous. If you are healthy there is probably no harm in taking probiotics, but there is also no benefit. But to increase the bacterial burden if you are immuno-compromised is asking for trouble," he said.

A spokesman for Yakult, one of the leading probiotic brands, disputed Prof Wilson's warning.

"We have 75 years of studies, carried out by independent scientific research bodies in the UK, Europe and Japan, including human trials, which have all demonstrated the health benefits of supporting the gut flora with Yakult."

A spokesman for Danone, the company which produces Actimel and Activia probiotic yoghurts, added: "The efficacy of these products has been shown in many studies and the results have been published in highly reputed scientific journals.

"Most recently an independent study, published in the British Medical Journal, showed a significant reduction in the incidence of C difficile-associated diarrhoea in hospitalised patients who drank Actimel twice a day."