What encouraged doctors at the Royal Sussex County Hospital in Brighton to put patients on probiotics was a randomised controlled trial, published in 2007, which found that a yoghurt containing three probiotics cut down the amount of diarrhoea patients suffered as a result of being put on antibiotics to treat the bug C.difficile, which they had picked up in hospital. 
The general public, however, aren’t so cautious. They clearly believe that probiotics are beneficial – around two million Britons now spend an estimated £135 million on buying drinks, yoghurts and capsules containing probiotics. Meanwhile, the medical mainstream continues to regard the gut largely as a form of plumbing to unblock or solidify, to be treated with drugs to damp down inflammation or acid if either seem to too high – and finally to be chopped out if none of that works. What this fails to take into account is the extraordinary complexity of the gut, not least of the ecosystem of the bacteria inhabiting it.
There are more than a thousand species living in our guts, most of which can not be grown in cultures in the lab, and these are intimately involved in the workings of our immune system, as well as helping us extract nutrients and metabolise waste.
A Hidden Sense?
This hidden world was vividly described at a conference three years ago in Dublin by Professor Fergus Shanahan of the Alimentary Pharmabiotic Centre at the University of Cork. He described the constant cross-talk between the bacteria and the “mucosal layer”’ that lines the gut walls, creating a system “which has more cells than the spinal chord and forms the largest metabolic and immune organ in the body with direct connections to the brain.” In fact, Shanahan went on, it behaves like one of the senses. “It has receptors and information flowing in and out that has to be integrated and organised, so it also has memory and learning.”
As with other senses, if it’s not set up properly at the beginning of life and doesn’t get the necessary stimulation, it won’t function so well. “At birth, beneficial bacteria from the mother have to colonise the gut, a process which can be delayed in the case of caesareans,” he said. “Then without the stimulation of some sort of infection, development of the immune response is poor and the chronic inflammation we see in IBS [Irritable Bowel Syndrome] can be the result.” In fact, the result of unbalancing our gut flora could be even more disastrous. Research just published suggests there could be a biological equivalent of global warming going on down there.
Just as our energy consumption is warming up the planet, so the changes in our foods, changes in birth practices, the increasing sterility of our houses and the widespread use of antibiotics all have combined to dramatically alter the make up of our gut bacteria – quite possibly contributing to the recent steep rise in allergies and auto-immune diseases.  But the impact of the activities of our microbial flora isn’t limited to the immune system. The remarkable fact that if you were to add up all the DNA in our bodies, 90% of it would come from the bacteria that inhabits us has huge implications for applying the human genome to health. Take the attempts to predict who will respond well or badly to a drug, based on their DNA. “Drug companies have spent millions trying to tell who’s most likely to have side effects from particular drugs based on variations in their genes,” says Dr Jeremy Nicholson of Imperial College, London. “But just focusing on the human genome is almost certainly doomed to failure unless you take into account the actions of the genes in the gut. The gut is where most drugs are broken down and if you don’t have enough of the right strains of bacteria to do the job, you are likely to have problems.”
What you have here is the paradox of probiotics. On the one hand, mounting evidence of a complex gut ecology with huge implications for health. On the other, no more than a handful of properly conducted trials showing that this bacterial strain given for that condition is better than a placebo. The issues this raises – the trials have not been done because bacteria can’t be patented, so who should pay for them – are best left for another time. Nicholson’s response to this impasse has been to establish a biochemical evidence base so that probiotics, rather than being regarded as some sort of slightly wacky non-drug treatment for conditions that aren’t responding well to pharmaceuticals, will be able to move into the mainstream. In a new study in January 2008, he showed that just giving standard probiotics could in fact produce a whole range of biochemical effects in the liver, blood and urine.  . This will certainly make it much harder for critics to claim that adding just a few bacteria to the diet can’t really make any difference. “We’ve established that friendly bacteria can change the dynamics of the whole population of microbes in the gut,” he says. Not only that, but the study found that different strains could produce quite different responses.
This begins to deal with another of the criticisms of taking probiotics – which is that there is no proper evidence to show which strain is having what effect. Nicholson’s study was done on mice which had had human gut microbes implanted in their own guts, so the set up was highly artificial but it allowed for much more detailed analysis of what was going on. It turned out that ......
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