In a normal situation free from antiseptics, antibiotics, high-carbohydrate diets, bottle feeding, hormones and other such accoutrements of modern western life, the gut flora is safe. Babies start life in mother’s womb with a sterile gut (although interestingly there is some evidence that their gut becomes innoculated before birth through transfer of microbes across the placenta!). During the process of birth, they become inoculated with bacteria from the birth canal and perineum. These bacteria are largely bacteroides which cannot survive for more than a few minutes outside the human gut. This inoculation is enhanced through breast-feeding because the first milk, namely colostrum, is highly desirable substrate for these bacteria to flourish. We now know that this is an essential part of immune programming. Indeed 90% of the immune system is gut associated. These essential probiotics programme the immune system so that they accept them and learn what is beneficial. A healthy gut flora therefore is highly protective against invasion of the gut by other strains of bacteria or viruses.
The problem is there is no probiotic on the market that supplies bacteroides for the above reasons. If we eat probiotics which have been artificially cultured, for a short while the levels of these probiotics in the gut do increase. However, as soon as we stop eating them, levels taper off and disappear. For bacteria to be accepted into the normal gut and remain, they have to be programmed first through somebody else’s gut (in this case mother’s).
So, when it comes to repleting gut flora, there are two ways that we can go about this either we can take probiotics very regularly (and the cheapest way to do this is to grow your own probiotics, see below) or to take bacteroides directly. Indeed, this latter technique is well established in the treatment of Clostridium Difficile (a normally fatal gastroenteritis in humans) and interestingly in Idiopathic Diarrhoea in horses. In the latter case horses are inoculated with the bacteria from the gut of another horse. These ideas have been developed further by Dr Thomas Borody with his ideas on Faecal bacteriotherapy which can provide a permanent cure in cases of ulcerative colitis, severe constipation, clostridium difficile infections and pseudomembranous colitis. The reason this technique works so well is because the most abundant bacteria in the large bowel, bacteroides, cannot survive outside the human gut and cannot be given by any other route.
The gut flora is extremely stable and difficult to change. Therefore if one is going to take probiotics, they have to be taken long term. Many preparations on the market are ineffective. Those found to be most effective are those milk ferments and live yoghurts where the product is freshly made. It is not really surprising. Keeping bacteria alive is difficult and it is not surprising that they do not survive dehydration and storage at room temperature. So your best chance of eating live viable bacteria is to buy live yoghurts or drinks. These can be easily grown at home, just as one would make home made yoghurt. If you cannot grow easily from a culture, then it suggests that the culture is not active, so this is a good test of what is and is not viable. I have tried to culture on milk and soya from dried extracts with very poor success rates suggesting that the dried extracts are not terribly viable.