Colon Notes

I have trimmed the previous notes down and added some more snippets.

I hope you find it helpful:

Detoxification and Retoxification

Certain beneficial bacteria are able to neutralise toxic metabolites. This is called detoxification. The opposite is retoxification. This means the conversion of non harmful products to harmful ones. Probiotics reduce the pH in the intestine which inhibit the activity of the coliform putrefactive bacterias, such as bacteroides and clostridias. The production of their toxins are reduced. Additionally the absorption of these is impaired, resulting in them being excreted in the faeces.

Conjugation and Deconjugation

One of the methods the liver use is to neutralise toxins by conjugating them with glucuronic acid, thereby creating glucuronides. This process is called conjugation. When these are excreted via the gallbladder out into the intestine, the body is given the possibility to get rid of toxins. When there is a dysbiotic condition in the intestine, certain bacterias improve their ability to digest these conjugates. This is called deconjugation. The toxins are reabsorbed into the blood. The result is retoxification. Some of the enzymes that deconjugate and retoxify toxic waste products are betaglucuronidase, azoreductase and nitroreductase. The outcome of their action is an increased accumulation of toxic metabolites. By probiosis this is reduced. Beta-glucuronidase and other hydrolytic bacterial enzymes also deconjugate bile acids.
Deconjugated bile acids are toxic to the colonic epithelium and cause diarrhoea. They or their metabolites appear to be carcinogenic and are thought to contribute to the development of colon cancer(6,9) and to ulcerative colitis(10). Gut bacteria also reduce primary bile acids like cholate and chenodeoxycholate to secondary bile acids like deoxycholate (DCA) and lithocholate. The secondary bile acids are absorbed less efficiently than primary bile acids and are more likely to contribute to colon carcinogenesis. The prevalence of colon cancer is proportional to stool concentration of DCA.

Altered microbial ecology in the gut may produce disease and dys- function because of the intense metabolic activity and antigenicity of the bacterial flora. Bacterial enzymes can degrade pancreatic en- zymes, damage the intestinal brush border, deconjugate and reduce bile acids and alter the intestinal milieu in numerous ways, some of which can be easily measured in a properly collected sample of stool. Bacterial antigens may elicit dysfunctional immune responses which contribute to autoimmune diseases of the bowel and of connective tissue. Effective treatment of dysbiosis with diet, antimicrobial sub- stances and biotherapies must distinguish among patterns of dys- biosis. The failure of common approaches utilizing fibre and Lacto- bacilli is a strong indication of small bowel bacterial overgrowth, a challenging disorder which demands a radically different approach.

When the colon becomes the primary feeding ground of unfriendly flora like e-coli and candida, a condition called toxic colon develops and the pH of the colon becomes alkaline. Ammonia, amines and other toxins produced by unfriendly flora impair liver function and immune function more significantly than any other single factor we have discovered to date.

When the colon is toxic, it is because harmful bacteria that produce scores of toxins have multiplied in great numbers. These toxins are absorbed from the large intestines and go the liver to be broken down. The toxic overload on the liver leads to a depletion of Glutathione levels that then impairs cell-mediated immune function. The toxins also impair the ability of the liver to produce enzymes needed for metabolic functions throughout the body. The immediate result is fatigue and eventually chronic fatigue. The depleted Glutathione levels reduce the ability of the liver to remove heavy metals and more stress is placed on other organs like the adrenal glands and kidneys. In a sequence of events, toxins (poisons) in the large intestines began to adversely affect the entire person.

Just one or more of certain strains of unfriendly flora can produce a variety of toxins including amines, ammonia, skatol, hydrogen sulfide, histamine, indole, phenol and cadaverin (3). The liver has the job of breaking down these toxins and if the liver function is impaired, the toxins circulate and can cause neurological problems. Candidiasis increases Interluken 6 levels, a cytokine that is overproduced in HIV infection, CFIDS and cancer and contributes to the cytokine shift from TH1 to the less effective TH2 immune response.

A toxic colon by contributing to the depletion of Glutathione levels increases the activity of free radicals and oxidative stress that further damages cells and body organs. Unfriendly flora also move the pH of the colon in an alkaline direction creating an environment more favourable to their own survival. No complete or sustained recovery from chronic immune dysfunction is possible without restoring a healthy colon. This is the point of beginning, the foundation for rebuilding health.Some of the specific by products of friendly flora fermentation (bifidobacterium) in the large intestines are butyric acid that help rebuild the mucus membranes of the G.I. tract and heal a 'leaky gut.' B. Longum and other bifidobacterium also produce lactic acid, acetic acid and proprionic acid. Researchers have found that acetic acid and proprionic acid are more effective than lactic acid in killing off bad microbes in the large intestines. Both acidophilus and bifidus fermentation of undigestible carbohydrates in the colon produce short chain fatty acids. These fatty acids cause the stools to float in water. Large diameter floating stools that are golden brown are healthy stools and indicative of a healthy colon whereas the sinkers and small diameters stools are loaded with toxins and harmful bacteria and come from a toxic colon. Little or no odour is emitted from healthy stools and strong or sour odours are emitted from toxic stools. David Webster writes that 'a floating stool is often an indicator of the existence of a predominately acidophilus flora.'

The gastrointestinal tract harbours about 100 trillion bacteria, more than 90% in the colon. The intake of merely a few billion probiotic 'friendly bacteria' a day is unlikely to make much of a difference in most instances.

The density of the intestinal flora increases along the digestive tractus: the density of bacterial and yeast populations, low at the exit of the stomach, increase dramatically in the ileum and the colon. Their density peaks in the transverse and left colon (109 to 1011 bacteria/ml). Butyric acid helps L.acidophilus and B.bifidum adhere to gut epithelial tissue. Butyric acid also provides an essential primary source of energy for rapidly growing intestinal cells.
Probiotic retention enemas performed once a week or month, to replace 'friendly' intestinal bacteria is also beneficial. Candida reside mainly in the colon and especially in the lowest part of the colon. This is due to a progressive increase in bacterial numbers and diversity towards more distal regions of the colon, where many gastro-intestinal disorders can develop (see fig. 5 bellow and table 1 in the section 'About Probiotics'). Also, the usage of anti-Candida medications may accumulate part of the 'dead' Candida in the descending and sigmoid colon and hence their removal is beneficial.

Since the majority of 'friendly' bacteria in the colon are bifidobacteria and some lactobacilli, a mixture of pure probiotic powder, dissolved in water and injected as an enema can be helpful to replenish the flora in the lowest part of the colon.

The pH balance of the colon is controlled solely by lactic acid. In other words, there is an actual creation of highly favorable natural chemicals in the colon through the fermentation process of the lactic acid. Lactic acid lowers the pH of the contents in the intestinal tract and prevents the growth of harmful bacteria in the intestines. The presence of lactic acid at low but constant levels on the inner surface of the intestinal tract helps restore the normal balance of the intestinal flora.

The bacteria in a healthy colon ideally should be 85% friendly bacteria, namely lactobacteria and no more than 15% of the putrefactive variety.

All 'coliform' bacteria produce an alkaline environment in the gut by removing the nitrogen from the amino acids and creating 'amines'. These toxic substances, including indole, skatole and cadaverine (present in dead bodies), are foul smelling and give faeces their characteristic odour.

An acid bowel environment is the best defence against unfriendly bacteria.

Lactobacteria live on carbohydrates, whereas putrefactive bacteria live on protein. Putrefactive bacteria do not grow well in the acidic medium produced by the lactobacteria. However, even if we have a reasonable intake of carbohydrates we must still maintain a low protein diet as the ammonia produced by the metabolisation of protein, (deamination), neutralises the acidity produced by the lactobacteria. It therefore takes a vigorous growth of lactobacteria in the intestinal tract to finally predominate over the putrefactive bacteria.

The sheer quantity of bacterial organisms in our intestines far outnumber the number of cells in our whole body. It is estimated that these bacteria, mostly found in our colon, make up about 3lbs in weight.

If the bowel is healthy it will be slightly acidic, the tissues of the body will be slightly alkaline and the skin slightly acidic. With an unhealthy alkaline colon, it creates acidity in the body tissues, which impedes correct cell function as required in the healing process.

Candida cannot thrive in an acidic medium.



Your posts are very interesting, after reading the retoxification post below i ordered some L Salivarius from the gut Doctor, they will get it in next week. I am hoping it will help with small bowel yeast so get rid of some of the metals. Also have some B Bifidum left that i will try in suppositories, get to the war zone as you put it!

Do you not think metals are a problem for you anymore?

I am introducing things slowly to see how i react, i will let you know how probiotics go.


In 1998 I was told mercury was probably my problem. This carrried on until 2003 when I went for the Klinghardt body testing and this said it was not a problem. I had more bloods and they came back negative. Last month I went on a bio-feedback machine which also said it was not mercury.

I think it was a red herring for me but between 1998 and 2003 it made sense with my symptoms. Chelating was agony and made no difference.


Good Post Simon. All this seems to point more and more towards colonic irregation. Surely it would be impossible for good bacteria to repopulate and thrive in a toxic colon. Until its cleansed maybe we would be fighting a loosing battle. Thats how I interpret it anyhow but not sure.


I think from what I read that if you introduce probiotics into the colon the acid they produce makes the bad boys unhook from the gut wall and then be excreted in your stool.

I suppose you need constant and high CFU's to gradually change to an 85/15 symbiosis.

The notes also say Butyric Acid helps the good guy's adhere to the gut wall and heal leaky gut.