Probiotics - we should all be taking these all the time and double the dose following antibiotics and gastroenteritis
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 program 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. Please see Reprogramming the Immune System – where conventional and complementary medicine can come together
Bacteroides - 90% of total gut flora - feed them
The problem is that there is no probiotic on the market that supplies bacteroides for the above reasons - these only survive outside the human gut for a few minutes. However it is very difficult to get rid of bacteroides completely and if they were entirely absent then serious bowel pathology would result - such as ulcerative colitis or pseudomembranous colitis. One can greatly increase numbers of bacteroides by feeding them pre-biotics - these are fructo-oligosaccharides found in pulses, vegetables, nuts and seed.
The only way that bacteroides can be inoculated into the gut is by faecal bacteriotherapy. Indeed, this 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.
E coli, lactobacilli and bifidobacteria 10% of gut flora - grow them
The three most important aerobic bacteria in the gut are E coli, lactobacilli and bifidobacteria. If we eat these 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 seem to taper off and they may disappear. The best way for bacteria to be accepted into the normal gut and remain, is to be programmed first through somebody else's gut (in this case mother's).
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 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 probiotic bacteria is to use live ferments. These can be 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.
Growing your own probiotics
The idea here is to take a substrate on which to grow the microbes 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 (and so are much better able to colonise the gut). In addition, they can be eaten regularly throughout the day very cheaply and are a delicious snack! It also means that on what ever substrate 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 the risks 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. Please see Leaky gut syndrome - a problem when things go wrong and the test Short chain polypeptides - another measure of protein digestion and absorption
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.
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.
I have been growing Kefir and this works well at room temperature. I am dairy allergic and 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 it 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. I can supply individual sachets of kefir if you have problems finding a source. You can purchase this through the on-line shop:- Sales at Dr Myhill In addition you can buy ready-made coconut kefir from Rhythm Health and you may wish to look at their recipes tab too!
Growing lactobacillus rhamnosus
The same principles as above apply. This microbe likes to ferment glucose and this is greatly enhanced by citrate. Take 10 capsules of the dried microbe, pull the capsules apart and empty the contents into 500ml of coconut or soya milk. Add a teaspoon of glucose (also known as dextrose) together with one teaspoon of magnesium citrate (I can supply). It does like to be warm - it normally ferments in the gut at body heat ie 37 degrees C or 98 degrees F. It thickens nicely in 12 hours to make a palatable yoghurt. After one preparation continue to add soya milk or coconut milk to it when it nears the bottom. This seems very successful and so long as it thickens i.e. ferments, it has worked fine. If it does not thicken or starts to smell then you probably need to make up a new culture. My office stocks L rhamnosus with a starter pack of glucose and magnesium citrate. Please see here: A-probiotic-package-starter-kit
This microbe seems to be an important part of immune programming to switch off allergy. It seems to induce oral tolerance to foods and possibly other microbes. A good combination would be to use lactobacillus rhamnosus with the food drops. See Oral immunotherapy: switching off food allergies using food
Growing E Coli - Mutaflor
See: Growing Mutaflor
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 is that different bacteria do different jobs. There is still a great deal of work to do in this field, but the following points are relevant:
- In acute gastroenteritis one should always use probiotics as a routine.
- When antibiotics are prescribed then probiotics again should be given as a routine.
- Irritable bowel syndrome seems to respond best to Bifido bacteria and also saccharomyces boulardii.
- 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.
- VSL3 (a patented probiotic preparation of live freeze-dried lactic acid bacteria) is a good combination probiotic for all round use. VSL3 is avalable on NHS prescription. In inflammatory bowel disease the best bacteria are bifidus longum, combined with 6 grams of prebiotics
VSL3 can be ordered direct at  where much more information can be found.
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 email@example.com
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. Please see Nutramigen website
- Comprehensive Digestive Stool Analysis with parasitology
- Microbial ecology profile
- Short chain polypeptides - another measure of protein digestion and absorption
- Fermentation in the gut and CFS
- Reprogramming the Immune System – where conventional and complementary medicine can come together
- Faecal bacteriotherapy
- Leaky gut syndrome - a problem when things go wrong
- Oral immunotherapy: switching off food allergies using food
- Growing Mutaflor
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