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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.

In the interim, the best you can do is grow your own probiotics since this is a cheap and effective way of sorting the situation out as follows:

Growing your own probiotics

The idea here is to take a substrate on which to grow the bugs and to which one is not allergic and make your own culture. This means one can swallow high dose probiotics, which are alive and kicking (so much better able to colonise the gut) and they can be eaten regularly throughout the day very cheaply and deliciously. It also means that on what ever you grow the culture, the sugar is fermented out of it and so this provides a good low glycaemic index food. This inhibits fermentation by yeasts. Furthermore, probiotics convert sugars and starches in the gut into short chain fatty acids, which are the preferred fuel for mitochondria. Therefore, anyone with a tendency to hypoglycaemia will find their symptoms greatly reduced. Even for normally healthy people probiotics will stabilise blood sugar levels and reduce risk of obesity, diabetes, Syndrome X, heart disease, PCOS, cancer and all those problems arising from a hypoglycaemic tendency. Indeed, this idea of using fermented foods is very popular in many human societies and is associated with long and good health!

The sort of problems I expect to see in people with abnormal gut flora result clinically from the fermentation of sugars and starches by yeasts, which form alcohol and gas. They are:

  • Gut symptoms - irritable bowel syndrome (alternating constipation or diarrhoea, wind gas, pain), stools like pellets, foul smelling offensive wind, indigestion, poor digestion, constipation;
  • Tendency to low blood sugar with carbohydrate craving;
  • Tendency to "candida" problems such as thrush, skin yeast infections. Kefir is useful because it creates a toxin that kills yeast cells directly.
  • Tendency to develop allergies to foods;
  • Leaky gut (positive PEG test).

In theory any probiotics on the market can be used to start the culture going but in practice many of the dried preparations are inactive. You could try starting with plain live yoghurt, but the bacteria in yoghurt may be chosen for its ability to make tasty yoghurt rather than what is good for your gut! I recommend Kefir. I can supply individual sachets of kefir if you have problems finding a source. Please, email your request to my dispensing team on or phone the office on 01547 550 331.

Make sauerkraut

Sauerkraut is typically made from cabbage but other vegetables can be used. These fermented vegetables are excellent because any carbohydrate in them is fermented out and one is left with a delicious vegetable teeming with friendly probiotics.

Using Kefir

I have been growing Kefir and it goes well at room temperature. I am dairy allergic so I use soya milk but it also grows on coconut milk and who knows what else! Start off with one litre of soya milk in a jug, add the Kefir sachet and within about 12-24 hours it has gone semi solid. Then keep in the fridge, where it ferments further. This slower fermentation seems to improve the texture and flavour. However, it can be used at once as a substitute in any situation where you would otherwise use cream or custard. Once the kefir is down to nearly the bottom, add another litre of soya milk, stir it in and away you go again. I don't even bother to wash up the jug - the slightly hard yellow bits on the edge I just stir in to restart the brew. This way a sachet of Kefir lasts for life! One idea I am playing with is the possibility of adding vitamins and minerals to the culture. The idea here is that they may be incorporated into the bacteria and thereby enhance the absorption of micronutrients. You could try this if you do not tolerate supplements well.

The use of probiotics is already established practice in animal welfare and probiotics are actively marketed to the horse industry for this very reason. Furthermore, probiotics are routinely used in the pig industry to prevent post-weaning diarrhoea. Anyone who has to take antibiotics for any reason should take these cultures as a routine to prevent "super-infection" with undesirable bugs. These cultures are also an essential part of re-colonising the gut following gut eradication therapy.

Another theme of the meeting was that different bacteria do different jobs. There is still a great deal of work to do in this field, but the following points came up:

  1. In acute gastroenteritis one should always use probiotics as a routine.
  2. When antibiotics are prescribed then probiotics again should be given as a routine.
  3. Irritable bowel syndrome seems to respond best to Bifido bacteria and also saccharomyces boulardii.
  4. The effect of probiotics may be enhanced by giving pre-biotics such as fructo-oligosaccharides 5 grams. In eczema the best bacteria are lactobacillus rhamnosus and lactobacillus reuteri and lactobacillus GG.
  5. VSL3 (a patented probiotic preparation of live freeze-dried lactic acid bacteria) is a good combination probiotic for all round use. In inflammatory bowel disease the best bacteria are bifidus longum, combined with 6 grams of probiotics

Professor Stig Bengmark recommends a combination of lactobacillus plantarum and lactobacillus paracasei, combined with pectin, fructo-oligosaccharides, inulin and resistant starch. You can contact Professor Bengmark directly at

Many of my patients who are allergic to dairy products and soya cannot make their own ferments. However, Nutramigen now produce a baby milk which has probiotics already added. Currently this is only available in France and Spain.

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