Probiotics are microbes that protect their host, and in some cases they can prevent disease. They are immunomodulating bacteria that have very low virulence compared with the more pathogenic gut flora such as Escherichia coli and clostridia. Lactobacilli and bifidobacteria are examples of probiotics found in the large intestine.

Lactobacillus GG can prevent diarrhoea and atopy in children. 1 2 In the gut, probiotic bacteria are thought to occupy binding sites on the gut mucosa, preventing pathogenic bacteria from adhering to the mucosa. Lactobacilli also produce proteinaceous compounds—bacteriocins—that act as local antibiotics against more pathogenic organisms. But what is known about what happens in vitro cannot necessarily be extrapolated to the complexity of the ecosystem of the human gut.

Diarrhoea associated with antibiotics is presumed to result from the antibiotics disrupting the normal flora in the gut of a healthy person. Such disruptions cause dysfunction of the gut's ecosystem, and they may allow pathogenic bacteria to colonise the gut and gain access to the mucosa. Whether probiotic supplements stop this process by reducing the disruption or by acting as substitutes for the healthy flora is unclear. Probiotics may compete with pathogens for the nutrients the pathogens need to grow, or they may modify toxins produced by pathogens or toxin receptors found in the gut wall, or they may stimulate immune responses to pathogens.

The exact mechanisms by which probiotics prevent atopy are also under debate.3 One suggestion is that the establishment and maintenance of innate immune tolerance is mediated by T helper 1 cells and linked in some way to the faecal flora. If the Th1 response is particularly robust, the allergic response mediated by T helper 2 cells tends not to be so strong. Probiotics may prevent atopy by supporting the faecal flora, strengthening the Th1 response, and reducing the allergic response.

In the countries of continental Europe, probiotics are regarded as medicines, and they are prescribed alongside antibiotics. In other countries, probiotics are marketed as supplements and are sold over the counter—although preparations such as “bioyoghurts” do not always contain probiotic strains proved to be clinically useful.