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"Alterations in the bowel flora are now believed to be contributing factors to many chronic conditions"


Alterations in the bowel flora and its activities are now believed to be contributing factors to many chronic and degenerative diseases. Irritable bowel syndrome, inflammatory bowel disease, rheumatoid arthritis, and ankylosing spondylitis have all been linked to alterations in the intestinal microflora. The intestinal dysbiosis hypothesis suggests a number of factors associated with modern Western living have a detrimental impact on the microflora of the gastrointestinal tract. Factors such as antibiotics, psychological and physical stress, and certain dietary components have been found to contribute to intestinal dysbiosis. If these causes can be eliminated or at least attenuated then treatments aimed at manipulating the microflora may be more successful.

Introduction: The gastrointestinal tract (GIT) is one of the largest interfaces between the outside world and the human internal environment. From mouth to anus, it forms a nine-meter long tube, constituting the body's second largest surface area. Over a normal lifetime, approximately 60 tons of food will pass through the GIT. Food is obviously extremely important for well-being, but its passage through the GIT can also constitute a threat to health. While the GIT functions to digest and absorb nutrients, food also provides exposure to dietary antigens, viable micro-organisms, and bacterial products. The intestinal mucosa plays a dual role in both excluding these macromolecules and microbes from the systemic circulation and absorbing crucial nutrients.

As mentioned above, the mucosa is exposed to bacteria referred to as endotoxins which can have a detrimental effects on both mucosal and host health. The presence of many of these toxic metabolites is directly dependent on the type of fermentation that occurs in the bowel. In turn, this fermentation is dependent on the type of bacteria present in the bowel, as well as the substrates available for fermentation. Diets high in protein combined with poor digestive enzymes and sulfate (derived primarily from food additives) have been shown to contribute greatly to the production of these potentially toxic products. The production and absorption of toxic metabolites is referred to as bowel toxemia.


The bowel toxemia theory has historical roots extending as far back as Hippocrates. In 400 B.C. he stated that, "... death sits in the bowels ..." and "... bad digestion is the root of all evil...." More modern proponents of the bowel toxemia theory have included naturopath Louis Kuhne in the late nineteenth century, as well as naturopath Henry Lindlahr and Nobel prize laureate Elie Metchnikoff in the early twentieth century. Louis Kuhne proposed that excess food intake, or the intake of the wrong types of food, resulted in the production of intestinal toxins. Fermentation of these toxins resulted in increased growth of bacteria within the bowel and, subsequently, disease. He believed a predominantly vegetarian and mostly raw diet would prevent build-up of intestinal toxins and, hence, would prevent and even cure disease. Despite being a relevant opinion it has now been shown that the consumption of excess levels of processed carbohydrates in the diet will contribute to dysbiosis of the bowel as much if not more as excess protein in the diet.

Only a few years later, Metchnikoff popularized the idea that fermented milk products could beneficially alter the microflora of the GIT. He believed many diseases, and even aging itself, were caused by putrefaction of protein in the bowel by intestinal bacteria. Lactic acid-producing bacteria were thought to inhibit the growth of putrefactive bacteria in the intestines. Thus, yogurt consumption was recommended to correct this "autointoxication" and improve composition of the microflora.

The bowel toxemia theories eventually evolved into the intestinal dysbiosis hypothesis. The term "dysbiosis" was originally coined by Metchnikoff to describe altered pathogenic bacteria in the gut. Dysbiosis has been defined by others as "... qualitative and quantitative changes in the intestinal flora, their metabolic activity and their local distribution." Thus dysbiosis is a state in which the micro biota produces harmful effects via: (1) qualitative and quantitative changes in the intestinal flora itself; (2) changes in their metabolic activities; and (3) changes in their local distribution. The dysbiosis hypothesis states that the modern diet and lifestyle, as well as the use of antibiotics, have led to the disruption of the normal intestinal microflora. These factors result in alterations in bacterial metabolism, as well as the overgrowth of potentially pathogenic microorganisms. It is believed the growth of these bacteria in the intestines results in the release of potentially toxic products that play a role in many chronic and degenerative diseases.

There is a growing body of evidence that substantiates and clarifies the dysbiosis theory. Altered bowel flora is now believed to play a role in myriad disease conditions, including GIT disorders like irritable bowel syndrome (IBS) and inflammatory bowel disease, as well as more systemic conditions such as rheumatoid arthritis (RA) and ankylosing spondylitis. Thus, knowledge of the factors that can cause detrimental changes to the microflora is becoming increasingly important to the clinician.

The Importance of Normal GIT Microflora

The microflora of the gastrointestinal tract represents an ecosystem of the highest complexity. The microflora is believed to be composed of over 50 forms of bacteria accounting for over 500 different species. The adult human GIT is estimated to contain 10 viable microorganisms. Some researchers have called this microbial population the "microbe" organ--an organ similar in size to the liver. Indeed, this microbe organ is now recognized as rivalling the liver in the number of biochemical transformations and reactions in which it participates.

The microflora plays many critical roles in the body; thus, there are many areas of host health that can be compromised when the microflora is drastically altered. The GIT microflora is involved in stimulation of the immune system, synthesis of vitamins (B group and K), enhancement of GIT motility and function, digestion and nutrient absorption, inhibition of pathogens (colonization resistance), metabolism of plant compounds/drugs, and production of short-chain fatty acids (SCFA’s) and polyamines.

Many factors can harm the beneficial members of the GIT flora, including antibiotic use, psychological and physical stress, radiation, altered GIT peristalsis, and dietary changes.

The Impact of Antibiotics on GIT Microflora

Antibiotic use is the most common and significant cause of major alterations in normal GIT microbiota. The potential for an antimicrobial agent to influence gut microflora is related to its spectrum of activity, pharmacokinetics, dosage, and length of administration. Regarding the spectrum of activity, an antimicrobial agent active against both gram-positive and -negative organisms will have a greater impact on the intestinal flora.

In terms of pharmacokinetics, the rate or intestinal absorption plays a fundamental role. Also important is whether the drug is excreted in its active form in bile or saliva. Both of these pharmacokinetic factors determine the drug's ultimate concentration in the intestinal lumen and, hence, the severity of the micro floral alteration. In general, oral antimicrobials well absorbed in the small intestine will have minor impact on the colonic flora, whereas agents that are poorly absorbed can cause significant changes. Parenteral administration of antimicrobial agents is not free from these consequences, as some of these agents can be secreted in their active forms in bile, saliva, or from the intestinal mucosa, and result in considerable alterations in the colonic flora.

The dosage and length of administration of an antibiotic will also determine the magnitude of impact on the intestinal flora. In general, the greater the dosage and length of administration the larger the impact on the microflora in the GIT.

Recent epidemiological research has shown that individuals who had taken only one course of antibiotics had significantly lower serum concentrations of enterolactone (a change caused antibiotic therapy) up to 16 months post-antibiotic use compared to individuals who had remained antibiotic-free during the same time period. As serum concentrations of enterolactone are dependent on colonic conversion of plant lignans to enterolactone by the intestinal microflora (via beta-glycosidation), this study suggests infrequent antibiotic use has much longer-lasting effects on the microflora and its metabolic activities than was previously believed. This negative association between serum enterolactone levels and antibiotic use has clinical importance due to recent studies showing correlations between high serum enterolactone concentrations and protection from cardiovascular mortality and breast cancer.

If an antimicrobial agent severely impacts the microflora, negative repercussions on host health can result, and include:



Overgrowth of already-present microorganisms, such as fungi or Clostridium difficile. Overgrowth of these organisms is a frequent cause of antibiotic-associated diarrhoea, and overgrowth of C. difficile can develop into a severe life-threatening infection.


Decreased production of SCFA’s, which can result in electrolyte imbalances and diarrhoea. Short-chain fatty acids play a vital role in electrolyte and water absorption in the colon. Reduced production of SCFA’s post-antibiotic use may be a causative factor in antibiotic-associated diarrhoea. Short-chain fatty acids also contribute to host health in other ways, such as improving colonic and hepatic blood flow, increasing the solubility and absorption of calcium, increasing the absorptive capacity of the small intestine, and n3aintaining colonic mucosal integrity.


Increased susceptibility to intestinal pathogens due to the decrease in colonization resistance. A decrease in colonization resistance after antibiotic administration has been observed in animal models. Such experiments have shown that disruption of normal microflora decreases the number of pathogens necessary to cause an infection and lengthens the time of infection.


Decreased therapeutic effect of some medicinal herbs and phytoestrogens-rich foods. The activity of many medicinal herbs depends on bacterial enzymatic metabolism in the colon. Of the many enzymes produced by intestinal flora, bacterial beta-glycosidases probably play the most significant role, as many active herbal constituents are glycosides and are inert until the active aglycone is released via enzymatic hydrolysis. Herbs such as willow bark (Salix spp.), senna (Cassio senna), rhubarb (Rheum palmatum), devil's claw (Harpagophytum procumbens), soy (Glycine max), and red clover (Trifolium pratense) would be essentially inactive without this colonic metabolism. Based on the results of the above-described epidemiological study, it can be inferred that antibiotic use interferes with microbial beta-glycosidation in the GIT for a considerable period post-antibiotic administration, which could significantly impact the efficacy of many phototherapeutic agents prescribed post-antibiotic use.

Hence, antimicrobial agents such as antibiotics should be used sparingly and selected carefully in order to minimize the impact on GIT microflora.

The Effect of Stress on GIT Microflora

To determine whether psychological stress results in an altered gastrointestinal environment, changes in indigenous GIT microflora was measured in primates after maternal separation. GIT microflora was evaluated in 20 infant rhesus macaques ages 6-9 months who were separated from their mothers for the first time. All infant monkeys were found to have typical focal bacterial concentrations at baseline. A brief increase in Lactobacilli shedding on the first day post-separation was followed by a significant decrease in the concentration of Lactobacilli in the faeces . An inverse relationship was also found between the faecal concentration of shed pathogens and shed Lactobacilli. The study demonstrates that psychological stress can alter the integrity of indigenous microflora for several days.

Other authors have also theorized the Lactobacilli population responds to stress-induced changes in GIT physiology, such as inhibition of gastric acid release, alterations in GIT motility, or increased duodenal bicarbonate production. These changes may result in an intestinal environment less conducive to Lactobacilli survival, adherence, and replication. Alterations in GIT milieu may lead to detachment of Lactobacilli from the intestinal epithelium and subsequent passage through the GIT, thus resulting in decreased numbers of replicating Lactobacilli. This would explain the increased shedding of Lactobacilli found on the first day of stress, followed by a dramatic decrease in numbers of Lactobacilli over the next six days.

The effects of psychological stress on the intestinal environment have been studied in Soviet cosmonauts. In general, it was found that on return from space flight there was a decrease in faecal Bifidobacteria and Lactobacillus organisms. These changes were attributed primarily to stress, although a diet low in fiber may also have contributed.

The change in microflora observed by Lizko led to a subsequent decline in colonization resistance, which in turn resulted in increased numbers of potentially pathogenic organisms. It has been found that exposure to psychological stress results in a significant reduction in the production of mucin and a decreased presence of acidic mucopolysaccharides on the mucosal surface. Since both mucin and acidic mucopolysaccharides are important for inhibiting adherence of pathogenic organisms to the gut mucosa, a decrease in either contributes significantly to successful colonization by pathogenic organisms.

Lizko states that exposure to stress results in decreased production of immunoglobulin A (IgA). As IgA plays a vital role in the defence against pathogenic organisms by inhibiting bacterial adherence and promoting their elimination from the GIT, Lizko postulates that any decrease in IgA secretion would most likely increase intestinal colonization by potentially pathogenic microorganisms.

A 1997 study assessed the effects of psychosocial stress on mucosal immunity, specifically the effect of emotional stress on secretory IgA levels. The study was conducted on children ages 8-12 years. Ninety children were included in the trial, half of whom had a history of recurrent colds and flu, while the other half were healthy controls. The results demonstrated that stressful life events correlated with a decreased salivary ratio of IgA to albumin. The ratio of IgA to albumin controls for serum leakage of IgA and is thought to give a clearer indication of mucosal immunity than total IgA concentration. This result provides additional evidence of the likelihood of stress effectively decreasing mucosal immunity and, thus, diminishing intestinal colonization resistance.

Other studies on college students have found IgA concentrations decrease during or shortly after examinations. Salivary concentrations of IgA are inversely associated with norepinephrine concentrations, suggesting sympathetic nervous system activation suppresses the production and/or release of IgA. (60) Thus, frequent suppression of mucosal immunity by the sympathetic nervous system during stressful experiences could increase colonization of the intestinal mucosa by potentially pathogenic microorganisms.

Holdeman et al studied factors that affect human faecal flora. They noted a 20-30 percent rise in the proportion of potentially pathogenic microorganisms in the faeces of individuals in response to anger or fearful situations. When these situations were resolved, the concentration of these organisms in the faeces decreased to normal levels.

To summarize, stress can induce significant alterations in GIT microflora, including a significant decrease in beneficial bacteria such as Lactobacilli and Bifidobacteria and an increase in potentially pathogenic microorganisms such as E. coli. These changes may be caused by the growth-enhancing effects of norepinephrine on gram-negative microorganisms or by stress-induced changes to GIT motility and secretions.

Diet and Intestinal Microflora

The composition of the diet has been shown to have a significant impact on the content and metabolic activities of the human faecal flora. Some diets promote the growth of beneficial microorganisms, while others promote microfloral activity that can be harmful to the host.


Sulfur compounds, including sulfate and sulfite, have been shown to increase the growth of potentially pathogenic microorganisms or increase production of potentially harmful bacterial products in the GIT. In the colon is a specialized class of gram-negative anaerobes known as sulfate-reducing bacteria (SRB). SRB include species belonging to the genera Desulfotomaculum, Desulfovibrio, Desulfobulbus, Desulfobacter, and Desulfomonas. (76) The principal genus, however, is Desulfovibrio, which accounts for 64-81 percent of all human colonic SRB.

Sulfate-reducing bacteria utilize a process termed "dissimilatory sulfate reduction" to reduce sulfite and sulfate to sulfide. The consequence of this process is the production of potentially toxic hydrogen sulfide, which can contribute to abdominal gas-distension. Hydrogen sulfide can also damage colonic mucosa by inhibiting the oxidation of butyric acid, the primary fuel for enterocytes. Butyrate oxidation is essential for absorption of ions, mucus synthesis, and lipid synthesis for colonocyte membranes. This inhibition of butyrate oxidation is characteristic of the defect observed in ulcerative colitis and leads to intracellular energy deficiency, as well as disruption of essential activities. Sulfide has also been shown to cause a substantial increase in mucosal permeability, presumably due to the breakdown of the polymeric gel structure of mucin through the cleavage of disulfide bonds.

Sulfate-reducing bacteria are not present in all individuals and there appears to be considerable variation in SRB concentrations depending on geographical location, a variation hypothesized to be connected to dietary differences. Sulfate-reducing bacteria directly compete with methanogenic bacteria (MB) for vital substrates, such as hydrogen and acetate. In fact, methanogenesis and sulfate reduction appear to be mutually exclusive in the colon. In the presence of sufficient amounts of sulfate, SRB have been shown to out compete MB for both hydrogen and acetate: whereas, under conditions of sulfate limitation the reverse occurs. The amount of dietary sulfate that reaches the colon appears to be the primary lector in determining the growth of SRB. On the other hand, endogenous sources of sulfate (e.g., sulfated glyco-proteins, chondroitin sulfate) appear to have little impact on SRB levels.

Sources of dietary sulfate include preservatives, dried fruits (if treated with sulfur dioxide), dehydrated vegetables, shellfish (flesh or frozen), packaged fruit juices, baked goods, white bread, and the majority of alcoholic beverages. It also appears probable that ingestion of foods rich in sulfur-containing amino acids encourages both the growth of SRB and the production of sulfide in the large bowel. Major amounts of sulfur-containing amino acids are found in cow's milk, cheese, eggs, meat, and cruciferous vegetables. Consumption of large amounts of these foods may significantly increase sulfide production in the colon. Research conducted in the 1960s found elimination of milk, cheese, and eggs from the diet of ulcerative colitis sufferers resulted in substantial therapeutic benefit, suggesting that reducing the intake of sulfur-containing amino acids decreases colonic production of sulfide.

High Protein Diet

Consumption of a high-protein diet can also increase the production of potentially harmful bacterial metabolites. It has been estimated that in individuals consuming a typical Western diet (containing ~ 100 g protein/day) as much as 12 g of dietary protein per day can escape digestion in the upper GIT and reach the colon. This is in addition to host-derived proteins, such its pancreatic and intestinal enzymes, mucins, glycoproteins, and sloughed epithelial cells. Undigested protein is fermented by the colonic microflora with the resultant end-products of short chain fatty acids, branched-chain fatty acids (e.g., isovalerate, isobutyrate, and 2-methylbutyrate), and potentially harmful metabolites-ammonia, amines, phenols, sulfide, and indoles.

Ammonia has been shown to alter the morphology and intermediate metabolism, increase DNA synthesis, and reduce the lifespan of mucosal cells. It is also considered to be more toxic to healthy mucosal cells than transformed cells and, thus, may potentially select for neoplastic growth.5 Ammonia production and accumulation is also revolved in the pathogenesis of portal-systemic encephalopathy. Indoles, phenols, and amines have been implicated in schizophrenia and migraines. Indoles and phenols are also thought to act as co-carcinogens (5) and may play a role in the aetiology of bladder and bowel cancer.

The production of these potentially toxic compounds has been found to be directly related to dietary protein intake, a reduction of which can decrease production of harmful by-products. The production of these potentially harmful by-products can also be attenuated by the consumption of diets high in fiber and/or indigestible starch (both of which reduce intestinal pH).

Diets High In Animal Protein

In comparison to diets high in overall protein. diets especially high in animal protein have specific effects on intestinal microflora. While not appearing to dramatically alter the bacterial composition of the flora compared to control diets, ingestion of huge amounts of animal protein does increase the activity of certain bacterial enzymes, such as beta-glucuronidase, azoreductase, nitroreductase, and 7-alpha-hydroxysteroid dehydroxylase, in animals and humans. This can have important ramifications, as any increase in activity of these enzymes will result in increased release of potentially toxic metabolites in the bowel.

High Simple Sugar / Refined Carbohydrate Diet

Kruis et al observed that diets high in simple sugars slow bowel transit time and increase fermentative bacterial activity and faecal concentrations of total and secondary bile acids in the colony A consequence of slower bowel transit time may be an increased exposure to potentially toxic bowel contents. The mechanism by which high-sugar diets increase bowel transit time is not yet known.

The increase in colonic fermentative activity noted in the Kruis study may not be directly associated with changes in microflora composition, but rather be caused by direct exposure of the colon to simple sugars. Refined sugars are metabolized quickly in the ascending colon whereas, high-fiber foods, containing substantial amounts of insoluble fiber, are metabolized more slowly, releasing fermentation end-products (e.g., hydrogen gas and short chain fatty acids) more gradually.

It is possible, however, that high sugar intake does cause alterations in the microflora. It has been observed that high sugar intakes increase bile output. Some species of intestinal bacteria utilize bile acids as food and. hence, any increase in their production will result in a competitive advantage for this group of bacteria. (63) The changes observed in bacterial fermentation in this study may or may not be related to changes in the species composition of the microflora. Since this was not adequately assessed in this study, the significance of these results requires further investigation.

Other researchers have postulated that when intake of dietary carbohydrates is insufficient, increased fermentation of the protective layer of mucin may occur due to the limited quantity of carbon sources reaching the colon. This may compromise mucosal defense and lead to direct contact between colonic cells and bacterial products and antigens. This, in turn, may lead to inflammation and increased mucosal permeability. Such a situation may encourage the growth of potentially pathogenic bacteria and perpetuate the inflammatory response. (98,99) This theory, however, is yet to be supported by direct evidence.

General Dietary Factors

The effect of the overall diet on the composition and metabolic activities of GIT microflora has been the subject of research since the late 1960s. It was initially believed that changing the content of the diet (in terms of meat, fat, carbohydrate, and fiber content) would dramatically alter the bacterial species composition of the colonic flora. However, when the diets of various population groups consuming different diets were analyzed, the changes noted were not dramatic. (93) Only minor changes were noted among the croups, although these changes were considered to be caused by differences in diet. (100) Table 3 outlines results of several studies comparing the faecal flora of individuals consuming the typical Western diet (high in fat and meat) to that of individuals eating vegetarian and/or high complex-carbohydrate diets.

In general, it appears populations consuming the typical Western diet have more faecal anaerobic bacteria, less Enterococci, and fewer yeasts than populations consuming a vegetarian or high complex-carbohydrate diet. Although one study found a significant difference between a mixed Western diet and a vegetarian diet, overall there appear to be relatively few trends.

In summary, research has shown that consumption of foods rich in sulfur compounds, high in protein, high in sugar and/or high in meat may produce detrimental effects on the host. These changes may be mediated through alterations in composition of the microflora or through increased production of bacterial metabolites.


Alterations in bowel flora and its activities are now believed to be contributing factors to many chronic degenerative diseases. Ample evidence exists to confirm dysbiosis as an important clinical entity. It is therefore imperative to know what factors play a causative role in this increasingly common condition. Antibiotics, psychological and physical stress, and dietary factors contribute to intestinal dysbiosis.

Armed with knowledge of the factors that contribute to dysbiosis, we are better equipped to deal with the causes of this condition. Diets can be altered, the effects of stress attenuated, and antibiotics used sparingly, in order to minimize the effects of these factors on intestinal microflora. If the causes of dysbiosis can be eliminated or at least attenuated, then treatments aimed at manipulating the microflora may become more successful and longer-lasting in effect.

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