Over the past two decades, it seemed that our guts had never had it so good. Probiotic products claiming to rid the body of the bad bacteria that causes illness burst on to the market and two million of us now swallow their promise of improved digestive health, provided by so-called “friendly bacteria”. We spend almost £350 million a year on drinks, yoghurts, powders and capsules, in the hope of improving our gut health. But is it money well spent? A growing number of experts think not. While they do not dispute that a balance of gut flora is beneficial, many believe that probiotics are not as helpful as was once thought.

Studies supporting the use of probiotics for general wellbeing, and as an additional support for people with specific illnesses, have been plentiful in recent years. This month, for instance, Swedish researchers revealed that a course of probiotics can offer protection for those with pneumonia. But critics are now doubting their usefulness. “In some areas, there is evidence that taking a probiotic supplement can be helpful,” says Anna Denny, a nutrition scientist at the British Nutrition Foundation. “But it is not clear-cut and not all probiotics are helpful to all people.”

The Russian Nobel prize winner, Élie Metchnikoff, is credited with having discovered probiotics at the beginning of the 20th century when he discovered that Bulgarian peasants who consumed milk containing fermenting bacteria appeared to enjoy extraordinarily good health.

It is now accepted among nutrition scientists that so-called friendly bacteria account for 10-15 per cent of bacteria in a healthy adult gut and that levels become depleted through a poor, low-fibre diet, or other factors such as stress, courses of antibiotics or illness. Proponents claim that probiotic supplements, which provide a regular shot of live, beneficial bacteria, help to top-up a body's natural supplies. But even those who were once self-confessed fanatics are questioning their place and proposing alternatives.

“Only highly resistant forms of bacteria, such as lactobacillus and bifidobacteria, have been shown to survive transit to the gut - others are likely to be destroyed by the highly acidic environment in the stomach,” says Professor Glenn Gibson, a food microbiologist at the University of Reading's school of life biosciences who is widely regarded as the UK's leading expert. “Unless capsules have a special enteric coating, they won't survive the transit. Heat also destroys probiotic bacteria, so if someone drinks a cup of coffee just before or after consuming them, the bacteria will be killed off.” In some tests, even if certain probiotics did survive, Professor Gibson found that they did not necessarily enhance gut flora, rendering them useless.

Lax labelling laws also mean that it is difficult for people to know which products are effective. Two years ago, Professor Gibson and Professor Christine Edwards, the head of human nutrition at Glasgow University, cautioned that 50 per cent of probiotic products do not have the healthy bacteria claimed on the label. Shoppers should be suspicious unless manufacturers stipulate that a capsule or drink provides a minimum of ten million bacteria per dose. Although the leading brands such as Yakult, Activia, Danone and Multibionta contain these amounts, many others “either have the wrong bacteria or the wrong numbers”, Professor Gibson says. One powder was withdrawn a couple of years ago as it contained clostridium, a bacteria that causes diarrhoea and colitis.

Probiotics have also been widely used for childhood allergies. Eczema is believed to be a disorder of the immune system and, since probiotics can enhance immunity, they have been considered effective. Yet two new studies question their use. Last month Dr Robert Boyle, a senior lecturer in paediatric allergy at Imperial College, London, found that use of probiotics in the treatment of childhood eczema was ineffective, even risky. In a review of 12 studies involving 781 children for the Cochrane Database of Systematic Reviews, Boyle found no evidence that probiotics reduced symptoms or altered the severity. He does not recommend that even healthy children take probiotics and he would not advise them for anyone with eczema.

Another recent trial, conducted at the University of Western Australia, showed that giving children a type of “good bacteria” early in life did nothing to reduce allergies as they grew up. Indeed, in one of their trials, Dr Susan Prescott and her colleagues gave 178 children either a probiotic or a placebo for the first six months of their life, those given the good bacteria were more, not less, likely to develop a sensitivity to allergens.

There are concerns, too, that in people with compromised immune systems friendly bacteria could be treated as hostile invaders by the body. Indeed, in their recent trial, the Cochrane researchers found probiotics to carry a risk of bowel damage and infection in children who were given them to treat their eczema. “A wide trawl of literature showed that, although probiotics are recognised as a safe treatment in otherwise healthy people, in those who are severely unwell, there is a significant risk in using them,” Dr Boyle says. Earlier this year, a controversial study at the University Medical Centre in Utrecht, Netherlands, reported that 24 out of 296 patients died during a study to find out whether probiotics affected inflammation of the pancreas. The Dutch food and consumer product safety authority ruled that the supplements should not be given to patients in intensive care.

Some NHS hospitals employ wide use of probiotics, often considered beneficial in the fight against MRSA, but others are becoming more cautious. At St George's Hospital in London, the chief dietitian, Catherine Collins, says that the risks for some patients are high. “A growing number of hospitals don't embrace probiotics as they used to, simply because we now know they can cause infections in vulnerable people,” Collins says. “They can lead to a potentially fatal illness called lactobacillus septicaemia and we have treated a few cases at St George's.”

According to some experts, the new bugs on the block - prebiotics, naturally present in food and easily obtained in the diet - are what we should have been taking all along. “Whereas probiotics provide new doses of bacteria, prebiotics nourish and feed the friendly bacteria already present,” Denny explains. Found naturally in breast milk, prebiotics are also present in foods that contain non-digestive carbohydrate (see box). “Substances such as inulin, a non-digestible part of carbohydrate, and oligosaccharides sail through the digestive system and are fermented to boost the immune system.”

Emerging trials on prebiotics, which are also available in supplement form and added to foods as diverse as breakfast cereals and desserts, show promise. This month, Professor Gibson has published a trial in the American Journal of Clinical Nutrition showing how the prebiotic powder Bimuno helped to prevent the natural decline in immunity for people aged 65 and older. “Typically, there is a natural decline in gut bacteria with age,” Professor Gibson says. “But in the study on volunteers aged 64 to 79, the prebiotic had a direct effect on immune defence cells and boosted immune function compared with a placebo.”

Another small study conducted by Dr Gemma Walton, a colleague of Professor Gibson's, compared the effects of prebiotics and probiotics in eight subjects. “We examined the faeces of the subjects daily to see whether the good bacteria had multiplied in number,” she says. “In the prebiotic group, there was an increase in good bacteria by 133 million, small in bacteria terms but an encouraging effect.” However, the probiotic group showed little change. “It seems that the best thing you can do is to treat your good bacteria to a prebiotic meal,” Dr Walton says.

Professor Gibson says: “Research on prebiotics is in its infancy, but is very encouraging. Not all probiotics are unhelpful. Some people can benefit. But if I was asked to choose, then I'd take prebiotic every time.”

Prebiotics: the new bugs on the block

Research at the Institute of Food Research in Norwich identified that finely ground almonds increased beneficial gut bacteria, although the effect was not seen when the fat content of the nuts was removed, suggesting that the gut bacteria used the almond lipids to grow.

A prebiotic-rich diet should contain 7g a day of inulin, found in oats, chicory, bananas, garlic and onions.

Commercially produced prebiotics, including cheese and dairy products, as well as supplements such as Bimuno, sprinkled on to cereals, can be helpful.

Breakfast cereals and cereal bars have a naturally occurring prebiotic. Eating cereals, including Shredded Wheat, Shreddies and Cheerios, was shown to increase two types of friendly bacteria in a test and in trials of 38 people who ate cereal daily for three weeks.

Some honey has prebiotic properties, says the University of Reading and the Instituto de Fermentaciones Industriales in Madrid. Manuka honey from New Zealand has been shown in trials to encourage the growth of healthy bacteria.