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Bacterial, Fungal & Parasitic Overgrowth

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Bacteria and the Immune System
Detrimental Medical and Dietary Factors
Imbalanced Flora
Effects of Pathogenic Organisms in the GI Tract
     Hydrogen Sulphide

Bad Bacteria, Mycoplasma & Lyme Disease
     Lyme Disease
     Enterobacter cloacae
     Chlamydia pneumoniae
     Biochemical markers for Clostridia and Pseudomonas
           Lactobacillus acidophilus and Bifidobacterium
           Enterococcus faecalis and Enterococcus faecium
           Mutaflor - Escherichia coli strain Nissle 1917
           Propionibacterium freudenreichii
           Soil Based Organisms
                 Bacillus subtilis
                 Bacillus coagulans
                 Bacillus laterosporus
                 Rhodopseudomonas palustris
                 Rhodopseudomonas sphaeroides
                 Saccharomyces boulardii
                 EM Technology
                 AGM Grainfields
                 ThreeLac and FiveLac
                 Bio-Kult Advanced Probiotic Formula
                 Dr Ben Kim's Greens and Natural Soil Organisms; and Dr Ohhira
                 Peter Smith Strains of SBOs
                 Nature's Biotics
                 Body Biotics
                 Primal Defense
                 Use of Humate
                 Source of Probiotic Cultures
                 Jordan Rubin's own use of SBOs and Humate
           Kombucha, Kefir, Sauerkraut Juice - Live, Home-Fermented Drinks
           Commercial Probiotic Drinks
     Antimicrobial Supplements

Yeasts, Fungus and Moulds
     Candida albicans
     Biochemical markers for Candida
     Fungal Infections, Biofilms and Sinusitis
     Yeast - Saccharomyces cerevisiae
     Eliminating Candida
           Fungicidal Herbs
           Cellulases & Proteases
           Antimicrobial Foods and Condiments
           Mushroom Extracts
           Colonic Irrigation
           Prescriptive Agents
           Dosages and Treatment Management
     Oxygen Ion Releasing or 'Oxygenating' Treatments
     Parallels between Candida, Cancer and Acidosis

Leaky Gut Syndrome (LGS) and Food Allergies

           Giardia lamblia
     Roundworms (Nematodes)
           Crytostrongylus pulmoni
           Toxoplasma and Toxocara
     Anti-Parasitic Treatments
           Examples of Combination Herbal Formulations
           External Application of Oils
           Diatomaceous Earth (D.E.)
           After Note

The Anti-Candida Diet

Bacteria and the Immune System:

The gastro-intestinal tract's healthy function relies on the presence of beneficial bacteria, in a relationship called symbiosis. Beneficial bacteria aid in digestion, correct pH balance, break down of foods and prevent the build up of harmful bacteria. They are an extension of our immune system; and probably make up the majority of our body's immune system. A different cross section of beneficial bacteria types exists in different parts of the small and large intestine. They act to consume much of the simple carbohydrate food sources available in the intestinal tract so that bad bacteria and organisms are deprived of food and cannot reproduce as fast. Dys-symbiosis, or dysbiosis occurs when the balance of flora and organisms in the GI tract becomes upset.

'The bacteria in your bowels outnumber the cells in your body by a factor of 10 to one. This gut flora has incredible power over your immune system, which, of course, is your body's natural defense system that keeps you healthy. In other words, the health of your body is largely tied into the health of your gut, and it's hard to have one be healthy if the other is not. One of the reasons why your gut has so much power has to do with the 100 trillion bacteria--about three pounds worth--that line your intestinal tract. This is an extremely complex living system that aggressively protects your body from outside offenders.'

Whilst we are emptying our bowels of stool once or more a day (hopefully) and expelling this stool together with the bacteria, good and bad therein, we are continually introducing new food from the mouth and stomach into the digestive tract. The digestive tract is slowly moving the food through it via peristalsis. This means that bacteria is continuously breeding and multiplying and spreading itself to the new food or chyme and moving up the digestive chain, and thus staying in the same place in the body, wherever conditions are most suited to the particular strain in question.

Probiotics are good or supportive bacteria which help to consume available food sources in the intestine and thus deprive bad bacteria (and also yeasts and parasites to an extent) of their normal food sources, and hence help to starve the bad bacteria. Approximately 70% of the body's immune system capability derives from the beneficial bacteria in the GI tract. The average adult body contains approximately 2.5 kg of bacteria (100 trillion bacteria), both good and bad types. It is estimated that the large intestine (colon) alone should contain approximately 1.5kg of probiotic (good) bacteria. There are more bacterium cells in the body than the actual body's own cells. There are approximately 400+ varieties of bacteria in the digestive tract and take many years to build up through a healthy diet. Of these 400+ variants that have been identified to be able to survive in the GI tract, the majority of the GI tract's bacteria is comprised of 30-40 of these species, the other species being present in very small numbers. Dr Elie Metchnikoff Ph.D, Nobel, laureate, postulated that the ideal ratio of good to bad bacteria should be 80:20, which is often the reverse way around in many modern Westerners.

Bidfidobacteria (collectively known as Lactobacillus bifidus) outnumber other Lactobacilli species by approximately 1000 to 1, and is in many sense the dominant healthy bacteria, although Lactobacillus is more hardy and resilient. The five most common strains of Bifidobacter include B. infantis, B. adolescentis, B. bifidum, B. longum, and B. breve. The levels of bifidobacteria levels tend to decline with age and reduced levels have been linked to declining health. Bifidobacteria are predominantly found in the large intestine (i.e. the colon) whereas Lactobacillus acidophilus primarily inhabits the small intestine.

Lactobacilli and Bifidobacteria help to inhibit potential pathogenic bacteria, such as E.coli or Clostridium perfringens. They help to prevent diarrhea caused by rota virus or salmonella. They help to reduce the proliferation of candida. They assist in increased defacation and help to reduce constipation. They help in digestion in general, by altering the pH (by producing lactic acid) and improving the uptake of minerals, especially calcium. They also help to digest lactose for the lactose-intolerant persons. They are also involved in the production of vitamins, for example, B1, B2, B3, B5, B6, B7, B12, A, D and K, and also essential fatty acids. They are particularly important in the production of Biotin (B7), which is the body's main source of Biotin (dietary sources containing a minimal amount). Lactobacilli and Bifobacteria also assist in protein digestion. They help to clean the digestive tract. They produce natural antibiotics and antifungals such as hydrogen peroxide (not in the ridiculously high quantities that are available with H2O2 supplementation or other oxygenating products). Lactobacillus acidophilus secretes the antifungal and antimicrobial agents including lactocidin, lactobacillin, acidolin and as mentioned above, hydrogen peroxide. Acidophilus also produces lactic acid, which helps keep down the pH in the intestinal tract. Too alkaline a pH in the colon favours bad bacteria and yeasts, whereas more acidic conditions help to prevent their excessive growth. In 1988, the US surgeon general's report noted that 'Normal microbial flora provide a passive mechanism to prevent infection.' They may increase the number of immune system cells in the body. They may even help to protect the body from environmental toxins and reduce waste at the cellular level. They also help to maintain healthy cholesterol levels and triglyceride levels, and break down and rebuild our body's hormones.

Enterococcus species are prominent facultative anaerobic, beneficial, lactic bacteria. They are fermenting to produce Lactic acid but are not gas producing. They are able to survive in relatively harsh environments. They provide antimicrobial activity against the methicillin-resistant Staphylococcus aureas (MRSA) bacteria and also inhibit the growth of food-borne pathogenic bacteria and other microorganisms.

When intestinal flora is in a healthy and balanced state, the beneficial bacteria (probiotic) make up a significant proportion of the body's total microflora. The probiotic bacteria have many health-protecting functions in the GI tract including the fermentation of soluble fibre into Short Chain Fatty Acids (SCFAs), vitamin production, protein and disaccharide lactose digestion, and stimulating an increase in the number of immune system cells (with associated anti-inflammatory and anti-tumor action). Acidophilus, Bifidus and Enterococcus produce both lactic acid as well as SCFAs (e.g. acetate, propionate, butyrate and valerate). Bacteriodes also produce large amounts of SCFAs. The production of SCFAs in the colon helps to keep the pH of the colon slightly lower (more acidic), to discourage the proliferation of microbial pathogens such as pathogenic bacteria or yeasts etc. Many GI tract pathogens thrive in low oxygen, alkaline environments such as the colon. Enterococcus also produces antibacterial agents against methicillin-resistant S. aureus (MRSA) and food-borne pathogens. Enterococcus sp. are noticeable aerobic beneficial bacteria in the GI tract. They are fermenting but not gas producing, and can survive in harsh environments. MRSA are resistant to multiple antibiotics, and hospital-based infections have dramatically increased. The Pharma industry is concerned that it may not be able to keep up with new strains of MRSA, and so maintaining a healthy level of Enterococcus sp. in the GI tract is a very important part of our immune system defence against such pathogenic microbes. Probiotics play a useful role in prevention and treating antibiotic associated diarrhea, preventing diarrhea and inhibiting the spreading and overgrowth of Candida albicans.

[Source: Doctor's Data]

Dr Sarah Myhill has a useful page regarding fementation in the GI tract and different bacterial strains.

The bacterial strain E.coli Nissle 1917 is one of the probiotic strains of E.coli found in large amounts in the GI tract. It helps to inhibit pathogenic bacterial infection and is non-lactic acid producing. A deficiency in this form of probiotic bacteria can result in reduced production of folic acid, the amino acids Tyrosine, Phenylalanine and Tryptophan, SCFAs and also Co-Enzyme Q10.

The GI tract of a healthy human foetus is sterile. There are no good or bad bacteria. It is during birth and shortly thereafter that bacteria from the mother and the environment start to colonise the infant's GI tract. It is estimated that an infant takes 1 month for their intestinal microflora to become established. Infants born by caesarean section may take 6 months (on account of additional exposure to harmful bacteria). Bifido-growth factors in mother's breast milk (GOS) - prebiotics - may assist in the domination of bifido bacteria in the infant's gut. The bacterial profile of formula fed infants is more diverse with both good and bad bacteria, but after months of solid food, both types of reared babies tend to have a similar gut profile. A mother may of course pass pathogenic bacteria, parasites or fungi onto her foetus in the womb through the umbilical cord, if they are present in the bloodstream.

According to Ardeypharm, manufacturers of beneficial E.coli (NIssle 1917) bacteria, it is left to chance whether an infant is colonised by commensal or pathogenic micro-organisms, depending on hygienic conditions in the hospital and also the systematic microbial colonisation of the mother (i.e. what is passed on through the umbilical cord and what comes out of the breasts). Ardeypharm and other manufacturers have infant formulas or probiotics to assist in early colonisation with probiotic/commensal species.

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Detrimental medical and dietary factors:

Intestinal bloating, gas, fatigue, lack of appetite and poor mood are some of the many symptoms of dysbiosis. Bloating in particular can be a result of severe dysbiosis, inappropriate food choices (particularly excessive quantities of/simple carbohydrates or starches) which the bad bacteria feed on, producing carbon dioxide, which causes pressure inside the intestinal lining, pushing out on the walls of the abdomen and making the abdomen look distended and bloated; it can also be a result of sheer numbers of bad bacteria in the intestines, out of balance with the good bacterial numbers, even if the diet is very conservative. In addition, it can be a result of inflamed gut lining - in this case the walls of the intestine relax and lose their natural shape and structure and tend to fill up with gas produced by bad bacteria more readily, which causes the bloated abdomen look, either in the centre of the belly (lower part of the small intestine) or the sides (colon). Inflammation of the gut lining may be caused by numerous factors including the presence of sufficient numbers of pathogenic microbes such as bacteria, moulds and parasites - or it could be due to improper immunity and excessive cytokine activity against certain protein types, e.g. milk protein or wheat for instance.

Good or probiotic bacteria act as competition for imbalance or pathogenic flora, and help to starve them of their usual food sources, feeding on and absorbing any remaining viable food sources in the stool that the body is not able to utilise, thus keeping the less desirable competitor's numbers down. When numbers of (certain strains of) good bacteria become too low, there is less competition for food sources, and so imbalanced and/or pathogenic flora are able to feed and multiply more, shifting the balance more and more in their favour. Anything that serves to deplete one's good bacteria (e.g. daily exposure to chemicals that are toxic to good bacteria, use of antibiotics, oral contraceptives, other medications, stress, etc.), to excessively feed imbalanced or dysbiotic bacteria with their preferred food sources (e.g. diets high in simple carbohydrates) or introducing new or increased numbers of harmful bacteria into the GI tract (e.g. contaminated food or water, poor domestic/personal hygiene) etc.) can result in harmful micro-organism overgrowth and dysbiosis.

General Practitioners tend to prescribe antibiotics for any suspected bacterial infection, whether local or systematic. This may well kill off a bacterial infection, but will also kill off a large part of the body's immune system (beneficial bacteria), rending the body susceptible to bad bacterial or candida overgrowth. There are alternatives to antibiotics, including Olive Leaf Extract, Grapefruit Seed Extract, Lemon Balm, Garlic and Coconut Oil (or coconut oil extracts, e.g. Caprylic Acid). For local infections, such as an ear infection, depending on the severity, it could for example be treated with the application of garlic oil or olive oil. Garlic oil capsules can be pierced and the contents squeezed into the ear. This is best performed with the head tilted so that gravity can assist.

Our good, supportive bacteria (as well as many bad bacteria) are virtually completely killed off with the use of antibiotics, which many GPs tend to give out like sweets to patients who come with any kind of bacterial or viral illess. Penicillin-based antibiotics are only effective against gram positive bacteria, and so leave many species of gram negative pathogenic bacteria unaffected - but whilst killing off one's probiotic bacteria in the process. Broad-spectrum antibiotics are effective against both types and kill off most good and bad bacterial species (e.g. Amoxycillin). Repeated use of antibiotics can virtually eradicate our good bacteria, which have to build up from scratch again each time a course of antibiotics is taken, allowing bad bacteria and yeast to take a foot hold in our GI tract and multiply at high rates.

This is exaccerbated by poor modern, western diets high in sugar and simple carbohydrates, which help to feed bad bacteria, and consumption of tap water over decades, which contains chlorine, which helps to inhibit good bacteria to some degree. In addition, there is considerable evidence to suggest that eating antibiotics fed animal meat can kill off good bacteria in the GI tract and therefore encourage harmful micro-organism overgrowth. Most non-organic meat derives from antibiotics fed animals. Antibiotics has also other damaging effects on the body, for example, a prolonged influence on folic acid metabolism it the body, making methylation (adding carbon atoms to carbon chains) and DNA synthesis more difficult. Synthetic (sulphur-based) antibiotics may also stick to one's mitochondrial membranes and inhibit proper metabolic functioning (energy production). Antibiotics should only really be taken in very serious conditions, where necessary. Otherwise, a good natural anti-microbial herb can be taken instead, such as Olive Leaf Extract, amongst others. Herbal treatments for infections are discussed elsewhere on this page.

There are three categories of nasty organism that thrive in the low oxygen (anaerobic) environment and neutral pH of the intestines: bad bacteria, candida and parasites. Pictures of these microorganisms can be seen at the link below. They are examined in more detail in subsequent sections on this page.

All three classes of organism thrive and grow in number on account of modern, western eating habits, mainly a high sugar intake, a high pasturised dairy intake (many vegetarians), a high wheat (bread) intake and high alcohol intake. All these are simple carbohydrates and are readily digested food for these bad organisms. Diets high in such foods tend to provide an ideal environment for harmful organisms in the intestinal tract, which multiply in alarming numbers. All of the foreign organism problems have a major impact on your digestive system and overall health. They put a constant strain on your immune system, and excrete a variety of toxins straight into your blood and digestive system (including Hydrogen Sulphide), often spread throughout the entire body, and may well contribute to early aging. Poor digestion also leads to poor nutrient uptake and vitamin and mineral deficiencies, that over years can really build up and massively impact the bio-chemical balance of your body and the efficiency of the basic processes therein, such as your neurotransmitters, hormones and energy production. The three above categories of harmful organisms are known to contribute to conditions such as Irritable Bowel Syndrome (IBS) and Irritable Bowel Disease (Ulcerative Colitis or Crohn's Disease). These conditions are likely to be partly the result of inflammation on account of overgrowth of harmful organisms and presence of large amounts of toxins in the GI tract. There are currently (as of June 2008) 2904 studies on IBS listed on PubMed, and it is indeed curious that so few doctors and GPs have any knowledge in this area.

Low protein diets also tend to set one up for organism infection (e.g. vegetarians not replacing meat/fish with enough pulses) as they encourage the body to produce less stomach acid (Hypochlorhydia), as it is the acidic pH that helps to break down proteins, and the body does not produce what it does not need. However, the stomach acid also acts as a barrier to kill off foreign organisms before they can reach the unprotected environment of the intestine. If this protective barrier is impaired, then harmful organisms can reach the intestines and multiply, particularly affecting the small intestine which immediately follows the stomach.

Sporty types who think they can eat whatever they like, including sugary sweets, high fat snacks and foods, and burn off the calories are unfortunately missing the point. The media focusses very much on the calorific impact of such foods, which is secondary to the impact they have on one's intestinal health. A life time of ill health is more of a debility that the final slap in the face of heart disease! The media tends to just focus on the heart disease component only however.

Excessive sugar, honey or artificial sweetner consumption tends to encourage harmful organism overgrowth. If you have a particularly sweet tooth, you can use a powerful, natural sweetner such as 'stevia'. This can be used liberally if desired without feeding harmful organisms in your GI tract. Please see the links page for information about where to buy this from, or better still, perhaps you can locate a supplier closer to you. Another alternative sweetner is xylitol, a sugar alcohol (not a sugar but tastes sweet), which also has anti-fungal properties - this may however cause Food Intolerance and IBS symptoms if consumed in excess. However, even natural plant (e.g. stevia) or sugar alcohol based sweetners may tend to aggravate dampness, qi deficiency and spleen meridian deficiencies, according to Traditional Chinese Medicine. Refined sugar has many other detrimental effects on one's health, including endocrine system disruption, tooth decay and may even contribute to the spread of cancer.

Of course, bacteria can enter the body in other ways besides dietary sources, from water or orally from touching objects and then touching the mouth. We can inhale bacteria and also bacteria can enter the hair folicles (e.g. boils). Keeping the skin clean, frequent washing of one's hands and clean toilet and food preparation areas is a useway way to reduce the chance of unnecessary localised bacterial infections, which can spead into the blood stream if the immune system is weak in certain circumstances. Of course, once in the body, numbers of bad bacteria in the body are hopefully kept in check, but if the immune system is weakened and we are feeding the bacteria and other harmful microbes with the wrong types of foods (high in simple carbohydrates) and toxins or other immune impairing practices (e.g. stress), and encouraging their growth with a low oxygen environment (which is often the case in CFS patients), then bacterial, fungal and parasite overgrowth can occur.

Here is a metaphor for the use of anti-biotics and a diet high in simple carbohydrates. Imagine you are a captain, in charge of a unit defending a village. And that village is under attack by an enemy unit. Now imagine there is a stale mate, with neither side capable of totally defeating the other, but with some casualties on each side. Now you want to help your troops to kill off the enemy. If you decide to call in an air strike to bomb the entire village and surrounding area, killing all the enemy soldiers, but also killing your entire unit and yourself, that wouldn't be very sensible would it? If you kill off most of your troops, you leave yourself wide open to another attack by another unit of enemy troops or enemy troops that can regroup quicker than your own slow reinforcements. And imagine actively giving the enemy troops ammunition and supplies! I doubt a captain who killed his own troops and actually gave ammunition to the enemy troops would be receiving any medals! Perhaps a better approach would be to use whatever means are available to eliminate or neutralise the opposition but without killing your own men or any villagers, and without helping the enemy strengthen their positions and numbers!

Clearly viruses may contribute to CFS or related conditions, or at least be a trigger for these conditions to occur. Viruses are not technically living organisms. Certain rare viral strains may wreak havoc with the body, for example the West Nile virus. Their contribution to immune system overload is described in the Immune System Deficiencies page.

The role of probiotic bacteria was not very well understood in the 19th Century. Germ theory and the application of penicillin and antibiotics was based on the concept that killing bacteria would help to stop the spread of disease, and in the short term it was correct, but as a long term strategy, indiscriminate killing of bacteria if non-selective is highly flawed and not without its downsides as we can see above.

Articles examining the foundation of modern medicine and the theory behind treatment of infectious diseases and antibiotics usage (i.e. the principle that all bacteria are bad), and the historical philosophical battle between Beauchamp and Pasteur, with Pasteur's ideas winning in the end (and not being questioned today), perhaps much to our detriment, can be found below.

'Friendly Bacteria Protect Against Type 1 Diabetes' by Dr Joseph Mercola

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Imbalanced Flora:

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When we talk about dysbiosis, we are often referring to two things. One of imbalanced flora and the other is dysbiotic flora. Indeed, this may also be in absolute terms and in relative terms, i.e. high levels of imbalanced flora overall, and high relative to the amount of good bacteria, which is perhaps another way of saying that there is a relative deficiency of good bacteria (which can vary from very mild to very chronic). As stated above, a lack of probiotic bacteria in the digestive tract can result in a number of problems, one example of these being a biotin (vitamin B7) deficiency.

Not all bacteria present in the GI tract are either 'good' or 'bad'. Imbalanced flora are those bacteria that are not pathogenic in nature, but rather commensal. Commensalism is the ecological relationship where two organisms share a food source or resources, but where there is no victim, and the second organism does not survive at the other organism's expense (which would be parasitism). Imbalanced flora reside in the host organism's GI tract and neither injure nor benefit the host organism (i.e. the human being). Certain types of dysbiotic (i.e. pathogenic or otherwise harmful) bacteria may appear to be imbalanced flora in certain individuals as they are present in low levels, and are not pathogenic at the levels detected. However, when their numbers increase, they will be noticeably pathogenic.

The appearance of imbalanced flora is often associated with inadequate levels of one or more good bacterial strains and/or too high a fecal pH (more towards the alkaline end of the reference range of 6.0 to 7.2 pH units). An alkaline pH (in relative terms) can be the result of too little dietary soluble fibre too few beneficial bacteria to digest the soluble fibre intake or perhaps a dietary absence of true fermented/lactic acid based foods. Doctor's Data has observed benecial E.coli mutate in alkaline conditions, rendering them less 'beneficial'.

A deficiency in beneficial E.coli or too alkaline a stool pH (affecting the health of beneficial E.coli populations through mutation) is often observed to result in a proliferation of Non-Lactose Fermenting (NLF) E.coli (i.e. imbalanced flora) and Haemolytic E.coli (i.e. pathogenic/dysbiotic flora that break open red blood cells to release hemoglobin into the blood plasma).

In general terms, if certain strains or levels of imbalanced flora appear in one's stool, the main treatment recommendation is to simply supplement with more probiotic bacteria (i.e probiotic supplements) and ensure a more appropriate diet and intake of sufficient dietary fibre. Treatment with antimicrobial herbs (or otherwise) is not necessary.

[Source: Doctor's Data Comprehensive Stool Analysis/Parasitology x1 Report]

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Lactic bacteria, including Lactobacillus, Bifidobacteria, Streptococcus and Enterococcus bacteria, ferment carbohydrates in the absence of oxygen to produce lactic acid. The two isomers of Lactic acid produced are L-Lactate and D-Lactate.

Lactic acid is also produced by the body's cells during anaerobic respiration. Accumulation of lactic acid in the muscles causes pain (myalgia). Humans (and mammals in general) only produce L-lactate as part of anaerobic respiration and only possess the enzymes Lactate Dehydrogenase (LDH) for metabolising L-Lactate in any significant quantity. The LDH breaks down the lactic acid relatively quickly in normal circumstances. Mammals do not possess the D-Lactate Dehyrogenase enzyme in any significant quantity, and this is generally only found in plants and bacteria.

In humans, the two LDH enzymes act on L-Lactate to convert it into Pyruvate (and vice versa). One of these enzymes e.g. in Glycolysis in the NAD(P) dependent L-Lactate Dehydrogenase enzyme (EC. The other LDH enzyme is a Cytochrome c-enzyme found in the liver (EC. Mammals including humans however can metabolise D-Lactate using the D-alpha-hydroxy acid dehydrogenase enzyme found in the mitochondria (at 20% of the rate of a proper D-Lactate Dehydrogenase enzyme as found in plants).

Lactate production in the GI tract helps to suppress the growth of yeasts and harmful bacteria. However, if excessive conmensal Streptococcus and Enterococcus fermentation in the GI tract occurs, then D-Lactate levels tend to rise in th body, and acidosis (a drop in blood pH) occurs - known as D-Lactic Acidosis. D-Lactate can accumulate in the mitochondria and inhibit their proper function.

The body then has two main methods available to eliminate D-Lactate are renal excretion (i.e. whatever is in the fluid filtered off by the kidneys into urine) and via faeces (excreting the D-Lactate remaining in the stool) - which is not particularly efficient in clearing the D-Lactate, especially if it is being produced continually in the GI tract. Recent studies however have claimed to show that humans do actually possess the D-Lactate Dehydrogenase enzyme on the inner mitochondrial membrane. Studies from the 1920s showed that D-Lactate was poorly metabolised compared with L-Lactate, whereas studies from the 1980-90s found that D-Lactate was actually readily metabolised, although most academic and medical sources still quote the 1920s results as fact. The area is still hotly debated.

Individuals with CFS and related conditions may already be producing energy anaerobically in their mitochondria excessively and thus producing more lactic acid than normal, and if there is severe dysbiosis, commensal bacteria may also add to this acidity by producing the type of lactate that is harder for the body to break down.

D-Lactic Acidosis is rare in general terms and usually only occurs in the case of short bowel syndrome in humans (malabsorption disorder caused by surgical removal of the small intestine) and children with gastroenteritis. It can of course occur in patients who have markedly poor digestion with a large proportion of undigested carbohydrate in the GI tract. In animals, it can occur through excessive grain consumption by ruminants (e.g. cattle, goat, sheep etc.) or in cases of diarrhea in calves.

Steptococcus and Enterococcus are types of lactic acid bacteria. There are many different species, some are probiotic, some are commensal and some are pathogenic. Probiotic strains include S.thermophilus, S.salivarius and S.faecium; and E.faecium and E.faecalis. The species most likely to be relevant in this instance are the commensal strains (i.e. imbalanced flora) that mke up the bulk of these species in the GI tract.

Other pathogenic bacteria besides Steptococcus and Enterococcus also produce D-lactate, although these are probably not so likely to be the cause in most cases of D-Lactic Acidemia:

'Various pathogenic bacteria produce D-lactate, including Bacteroides fragilis, Escherichia coli, Klebsiella pneumonia, and Staphylococcus aureus. The use of D-lactate as a marker for infection was proposed in 1986.'

It is possible that a disproportionately large amount of probiotic lactic acid producing species such as Strepococcus and Enterococcus can be responsible for D-Lactic acidemia. It is more likely that the imbalanced S. and E. flora species would be responsible (in instances of elevated undigested carbohydrates in the GI tract) and that repopulation with the relevant required numbers of probiotic species, both lactic and non-lactic acid producing species, would help to correct the problem. Some recommendations do include abstaining from taking additional D-lactic acid producing probiotic bacteria (including those found in many yoghurt types and also kombucha and kefir), and only consuming non-d-lactate producing bacteria and also bacteria that consume D-Lactate.

Below is a list of D-Lactate producing Lactobacillus bacteria (Source: Breakspear Medical Group Newsletter Issue 26).

Lactobacillus species producing only D-Lactate:

The following L.delbruecki subspecies are often found in certain types of live/natural yoghurt. All yoghurt contains Streptococcus thermophilus which creates the creamy taste, and usually Lactobacillus acidophilus and Bifidobacteria. A large percentage of yoghurt products also contain Lactobacillus delbrueckii species (specifically bulgaricus), which produce only D-Lactate, which are listed below. Check the ingredients before you buy or simply avoid yoghurt in general.

  • Lactobacillus delbrueckii subsp. bulgaricus (f.k.a. Lactobacillus bulgaricus until 1984 - found in yoghurt)
  • Lactobacillus delbrueckii subsp. delbrueckii
  • Lactobacillus delbrueckii subsp. lactis (not the same as Lactococcus lactis)

Other less common Lactobacillus species that produce only D-Lactate are:

  • Lactobacillus jensenii
  • Lactobacillus vitulinus

Lactobacillus species that produce Racemate Lactate (50% D-Lactate and 50% L-Lactate):

  • Lactobacillus acidophilus
  • Lactobacillus brevis
  • Lactobacillus fermentum
  • Lactobacillus helveticus
  • Lactobacillus plantarum/li>
  • Lactobacillus reuteri

Other less common Lactobacillus species that produce Racemate Lactate are:

  • Lactobacillus amylovorus
  • Lactobacillus aviarius subsp. aviarius
  • Lactobacillus buchneri
  • Lactobacillus crispatus
  • Lactobacillus curvatus
  • Lactobacillus gasseri
  • Lactobacillus graminis
  • Lactobacillus hamsteri
  • Lactobacillus homohiochii
  • Lactobacillus pentosus
  • Lactobacillus sakei

Lactobacillus species producing only L-Lactate:

These are the ideal probiotic Lactobacillus species to supplement for those with Lactobacillus deficiencies and elevated D-Lactate levels.

  • Lactobacillus casei
  • Lactobacillus paracasei subsp. paracasei
  • Lactobacillus salivarius
  • Lactobacillus rhamnosus

Other less common Lactobacillus species that produce only L-Lactate are:

  • Lactobacillus agilis
  • Lactobacillus amylophilus
  • Lactobacillus animalis
  • Lactobacillus bavaricus
  • Lactobacillus mali
  • Lactobacillus maltaromicus
  • Lactobacillus murinus
  • Lactobacillus paracasei subsp. tolerans
  • Lactobacillus ruminis
  • Lactobacillus sharpeae

Breakspear Medical Group's general suggestion from the newsletter is that CFS patients in general should avoid bacteria that produce solely D-Lactate, and if they have myalgia (e.g. M.E., Fibromyalgia, MPS etc.), to avoid the strains that produce Racemate Lactate (i.e. 50% D-Lactate and 50% L-Lactate).

In any case, killing off the bad and excessive commensal bacterial species, and repopulating the GI tract with a variety of good bacterial strains (i.e. addressing dysbiosis in general) should correct the excessive D-Lactate production problem, but it may of course help to avoid those D-Lactate producers in the interim to alleviate symptoms and not slow down recovery.

Please see the Mitochondrial Function page for more information.

D-Lactate levels can be measured in a blood test. Please see the Tests page for more information.

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Effects of Pathogenic Organisms in the GI Tract:

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Pathogenic organisms excrete toxins; which poison the body's cells, impair normal biochemical and mitochondrial function, put an additional burden on the liver; and put also put a constant and background strain on the immune system, rendering it slightly less prepared to deal with any other additional infections that might arise, of a microbial or viral origin. In addition, the constant strain on the immune system renders it slightly incapacitated, and it is likely to be further impaired in any case for toxicological and nutritional deficiency reasons. A constant immune system response also uses up a great deal of cellular energy and can result in excessive fatigue. Pathogenic organisms are responsible for a number of different diseases and disorders.

Dysbiotic bacteria, yeasts and parasites can produce a number of toxic substances including:

  • Amines - amines are produced naturally through the breakdown of amino acids. Amines are also produced in the body as neurotransmitters, e.g. Adrenaline, Noradrenaline, Dopamine, Serotonin and Histamine. Amines can result in a fishy odour. Amines are also produced by some probiotic or commensal bacteria. Excessive amine production may result in neurological disruption, i.e. imbalance in neurotransmitters and possibly neurotoxicity.

  • Ammonia - Ammonia is a product of normal protein catabolism, and ammonia is removed from the blood by the liver. Elevated ammonia levels may occur where bad bacteria are also producing significant amounts of additional ammonia. Patients who have liver or kidney disease may often have elevated ammonia levels also. Ammonia is highly caustic. Ammonia interferes with neurological function and the synthesis of both GABA and Glutamine, as well as causing neurotoxicity, resulting in confusion, drowsiness, tremors, vomiting, and in extreme cases can case cerebral adema, coma and death.

  • Hydrogen sulphide - interferes with oxygen transport - synonymous with 'bad eggs' smell. Discussed below.

  • Nitric oxide - a highly reactive oxidant molecule (RNS - Reactive Nitrogen Species) which may elevant Peroxynitrite production and cause further oxidative stress

  • D-Lactate - also produced by commensal bacteria, is examined in the section above.

  • Phenols - has adverse effects on the nervous system and heart, causing cardiac dysrhythmia). Also forms phenoxyl radicals (causing oxidative damage). High levels can damage the liver and kidneys.

  • Secondary bile acids - may cause inflammation or damage to the brush border of the small intestine. The brush border is the name for the microvilli-covered epithelium surface of the small intestine, the site of terminal carbohydrate digestion.

Some larger pathogenic organisms, such as tape worms, also carry with them secondary infections, such as a variety of protozoan parasites, which can leap frog their way into the body via the larger parasite.

Each of the three main categories of pathogenic organism are examined on this page, including a variety of treatment protocols.

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Hydrogen Sulphide:

Hydrogen Sulphide (H2S) is an endogenous toxin produced in the body by the action of bad bacteria (such as Prevotella) and fungi (such as Candida Albicans) fermenting sugar in the gastrointestinal tract. Elevated levels of H2S in the blood and tissues can result in mitochondrial dysfunction. Please see the Mitochondrial and Toxicity pages for more information regarding H2S effects and treatment.

Hypothesis: Is ME/CFS caused by dysregulation of hydrogen sulfide metabolism? (2008) by Marian Dix Lemle

Please see the Effects of Toxicity and the Inefficient Liver Function pages for more information on H2S build up and its effects.

Pathogenic organisms can also produce secondary bile acids that may cause damage or inflammation to the microvilli lining (epithelium) of the small intestine (a.k.a. Brush Border). The microvilli lining is the interface where the absorption from the gut takes place, and absorptive efficiency may be considerably reduced by inflammation or damage to the Brush Border or the presence of mucoid plaque. Long term damage to the intestinal microvilli may potentially result in a variety of problems such as Leaky Gut Syndrome, allergies, IBS, autoimmune diseases (such as rheumatoid arthritis), headaches and food sensitivies etc. Pathogenic bacteria can also produce acute symptoms such as nausea, vomiting, abdominal pains, diarrhea and a fever (in cases of food poisoning).

[Source: Doctor's Data Comprehensive Stool Analysis/Parasitology x1 Report]

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Bad Bacteria:


Because of a reliance on anti-biotics by General Practioners for all manner of ailments, the delicate balance of beneficial bacteria in the GI tract in many people is utterly destroyed on a periodic basis and bad bacteria and yeasts are allowed to flourish unchecked (above is a picture of an E.coli bacterium).

And because the modern diet contains high levels of simple carbohydrates and refined sugar, and does not include many true fermented foods that contain beneficial bacteria (such as natural yoghurt, live kefir (see the recipes page), sauerkraut, kombucha, miso etc. - do not confuse these with their poorer, pasturised relations) then good bacteria have very little chance of repopulating the GI tract. A sign of bad bacteria overgrowth is large volumes of frequent, odourless wind. This is carbon dioxide produced by the imbalanced flora and bad bacteria. The GI tract requires beneficial bacteria to aid in the digestion process.

There are a large number of different species and strains of pathogenic bacteria that can reach dysbiotic levels in the GI tract and indeed spread throughout the body if the gut lining is particularly impaired. Whilst it is not possible to examine each relevant species and strain, a small selection of some of the more noteworthy examples are listed in the following sections.

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Lyme Disease:

Certain strains of bad bacteria are found to cause a variety of extremely harmful diseases and conditions, for example Lyme Disease. Lyme Disease is an infectious disease caused by at least 3 species of Borrelia bacteria (and perhaps up to 12 species of the 36 Borrelia bacterial species). It is the most common tick-borne disease in the Northern Hemipshere.

Borrelia infections via a tick bite are frequently accompanied by other Lyme Disease Co-Infections, including Ehrlichia, Anaplasma, Babesia, Bartonella, Rickettsia, Coxiella, Toxoplasma, Mycoplasma and others. These are all very hard to identify and treat.

Borrelia is an intracellular bacterium and chiefly affects the cells of the nervous system and may result in severe CNS inflammation, vision problems, joint inflammation etc.

Natural antimicrobials that may help to deal with Lyme Disease and its potential Co-Infections include Artemisinin, Samento, Banderol, Cumanda and Quina. As Borrelia is a biolfim loving organism, it will likely be necessary to take a number of biofilm-busting supplements.

American Lyme Disease Foundation:

Sarah Myhill:


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Mycoplasma or Cell Wall Deficient (CWD) bacteria:

Bad bacteria also include mycoplasma (a.k.a. L-form bacteria), a group of simple, single cell bacteria which have no outer membrane or cell wall (and are thus resistant to antibiotics). They are therefore also known as Cwell Wall Deficient (CWD) bacteria. Because of this, it is hard for the body to fight them, and certain strains may penetrate and infect individual cells, contributing to various diseases.

The mycoplasma fermentans genome is found in approximately a third of CFS patients, is a co-factor in immune system deficiency. Mycoplasma fermentans tends to concentrate in the mucosal tissues, although it is shown also to infect other cells, such as white blood cells. It may even contribute to Gulf War Syndrome cases.

Mycoplasma is postulated to contribute to elevated levels of the oxidant Peroxynitrite (resulting in a vicious circle of oxidative damage to the body's cells). The theory goes that mycoplasma infections 'induce excessive production of inflammatory Cytokines that induce, in turn, the inducible nitric oxide synthase (iNOS). This enzyme, in turn, synthesizes excessive amounts of nitric oxide which reacts with another compound (superoxide) to produce the potent oxidant peroxynitrite. Peroxynitrite acts via six known biochemical mechanisms to increase the levels of both nitric oxide and superoxide which react to produce more peroxynitrite. In this way, once peroxynitrite levels are elevated, they may act to continue the elevation, thus producing a self-sustaining vicious cycle.'

Some information on Mycoplasma Fermentans can be found at the ImmunoSciences Lab and Shasta CFS web sites below.

A video of Trevor Marshall PhD's Keynote Presentation at the 2008 World Gene Congress is shown at the link below.

He states that 'In Homo sapiens, the VDR Nuclear Receptor transcribes genes for the Cathelicidin and beta-Defensin anti-microbial peptides, essential to intra-phagocytic innate immune defenses. This microbiota evades the human immune system by blocking DNA transcription by the VDR, which consequently blocks expression of these endogenous anti-microbials.'

Marshall T.G.; 'Bacterial Capnine Blocks Transcription of Human Antimicrobial Peptides'. Nature Precedings : doi:10.1038/npre.2007.164.1 : Posted 21 Jun 2007.

A pdf summary of this report can be found at the link below.

In the Keynote Presentation above, he also states that 'The microbiota changes expression of over 903 genes, including MTSS1 ('Metastasis Suppressor 1'). Homeostasis of other Type 1 Nuclear Receptors is indirectly upset by the pathogens: VDR, PXR, GCR, Thyroid-alpha-1, Thyroid-beta-1. Note especially that the loss of Glucocorticoid and Thyroid homeostasis leads to the diagnoses of 'hypo-thyroidism' and 'adrenal insufficiency.' We have demonstrated both to be reversible.'

Marhsall, T.G: 'Vitamin D Discovery Outpaces FDA Decision Making'. BioEssays May 2008, 30:2.

This paper can be found at the link below.

'Vitamin D not only regulates the expression of genes associated with calcium homeostasis, but also genes associated with cancers, autoimmune disease, and infection. It does this by controlling the activation of the Vitamin D Receptor (VDR), a type 1 nuclear receptor and DNA transcription factor.'

The VDR is the Vitamin D Receptor which plays a role in the immune system as a well as other functions. Low vitamin D levels are not infrequently recorded in CFS and ME cases, and may often coincide with mycoplasma infections and impaired immune systems.

'The hormonally active form of vitamin D mediates its biological effects by binding to the vitamin D receptor (VDR), which is principally located in the nuclei of target cells.'

Vitamin D deficiencies are discussed on the Nutritional Deficiencies page.

Some posts on the Marshall Protocol (which I do not personally endorse) forum on the subject, including from Trevor Marshall himself, can be found at the link below.

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Enterobacter cloacae:

Enterobacter cloacae is a gram negative, facultatively-anaerobic, rod-shaped bacterium. It is a member of the Enterobacteriaceae family. It is classified as a Biohazard Level 1. It is widely distributed in the environment. Enterobacter cloacae are opportunistic pathogens, often associated with diarrhea in children and can be involved in extraintestinal infections, especially the urinary tract. It is also one of the main causative organisms in infections such as nosocomial septicemia (blood poisoning that can lead to sepsis or whole body swelling and inflammation) and surgical wound infections. They are also common causes of intraabdominal, respiratory tract infections, and also bloodstream infections in organ transplant patients.

Environmental strains of Enterobacter cloacae are capable of growth in foods stored at refrigeration temperatures. It is commonly found in both human and animal faeces. It produces a heat-stable toxin similar to that produced by pathogenic E.coli. Whilst low levels are commonly found in fresh stool in healthy persons, elevated levels of these pathogenic bacteria can be extremely detrimental to one's health.

Gram negative bacterial species, such as Enterobacter cloacae, are unaffected by Penicillin-based antibiotics, which only suppress gram positive bacteria.

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Chlamydophila pneumoniae:

Chlamydophila pneumoniae (formerly known as Chlamydia pneumoniae) is a species of Chlamydophila bacteria. C.pneumoniae (or Cpn for short) must infect another cell in order to reproduce and is therefore classified as an obligate intracellular pathogen. It exists as an Elementary Body (EB) in between hosts. EBs of Cpn can be observed attached to red blood cells in afflicted persons. The EB is not biologically active but is environmentally resistant. The EB can be spread by droplets of moisture from the lungs of one person to another. Upon arrival in the lungs of another victim, the EB is taken up into the endosome (membrane bound compartment) of Eukaryotic cells by phagocytosis. It is not destroyed in this process like most phagocytosed material but instead is transformed into a Reticulate Body (RB) and starts to replicate within the endosome. This process steals energy (ATP) from the cells of your body. The RBs then convert back into EBs and are released back into the lung, often resulting in the death of the host cell. If an RB is under sufficient attack then it may transform into a Cryptic Body (CB), a third form - and not a usual part of the life cycle. This is a particularly resistant form, of 'hibernation', where it exists in an anaerobic state of starvation. It will later change back into an RB and carry on with its normal life cycle, as it can only exist in this state for so long or else it dies.

It infects humans and is one of the major causes of atypical Pneumonia, along with Mycoplasma pneumoniae. Pneumonia normally being caused by the gram positive bacterium Streptococcus pneumoniae. Chlamydophila pneumoniae is also associated with atherosclerosis, Alzheimer's disease, Multiple Sclerosis, Interstitial Cystitis, Prostatitis, IBS, Arthritis, Asthma, Fibromyalgia, Chronic Refractory Sinusitis, Macular Degeneration and Chronic Fatigue Syndrome. It is also implicated in causing pharyngitis (sore throat), laryngitis (sore throat/hoarse voice) and sinusitis (nasal congestion) more than any other form of bacteria; as well as bronchitis (inflammation of the mucus membranes in the lungs). It may also worsen Porphyria (genetic Heme production enzymes deficiency) - known as Secondary Porphyria.

Cpn contains two endotoxins that (when released after killing the bacteria) can result in tissue damage, inflammation, chronic immune system activation and an increase in toxicity in the body.

Chlamydia pneumoniae is not to be confused with the sexually transmitted disease 'Chlamydia' which is caused by the bacterium Chlamydia trachomatis, that is generally symptomless and can damage a woman's reproductive organs if left untreated.

Symptoms of infection with C.pneumoniae are indistinguishable from other causes of pneumonia (bacterial, fungal, viral etc.) They include a cough, fever, breathing difficulties. Nasal congestion, chest pressure and depression are also common. Cpn may start off as a respiratory infection, but on account of its replication mechanism, can be carried to many other parts of the body and infect their tissues, including nerve tissue, the brain, muscles, the lining of blood vessels (c/f atherosclerotic plaque) and even Macrophages of the immune system. CFS cases are not uncommonly implicated with Cpn infections, and these may not be noticeable as pneumonia symptoms but may be simply mild lung irritation and a dry cough.

Chlamydia pneuomoniae Elementary Bodies (EBs) can be identified using dark field microscopy on Red Blood Cells (see above picture), amongst other methodologies. PCR blood tests are not always reliable but can be implemented. The 'NAC Test' may be taken, which involves taking a high dosage of NAC (building up to 4 x 600mg of NAC per day over a number of days) and observing if any significantly adverse toxicity symptoms are experienced. This is touched upon below.

Standard treatments including single courses of antibiotics (of a 2 week duration), can only kill Cpn in one of its three life cycle phases, leaving live forms of Cpn bacteria in the body which can continue the infection thereafter in other phases of their life cycle. Therefore a more sophisticated antibiotics regime is required.

According to the CPN Help web site, a combination of approaches can be employed, to attack all 3 forms of the bacterium.

  • D-Penicillamine (a chelating agent) and N-Acetyl Cysteine (NAC) break the disulphide bonds in the cysteine-rich proteins of the outer coating of the Elementary Bodies (EMs). This forces them to prematurely burst open and perish. This can result in a rather severe die off reaction from the endotoxins.

  • Protein synthesis inhibitors/antibiotic drugs - namely Doxycycline (INN), Azithromycin, Rifampicin - perform two functions:

    • Prevent the Reticulate Bodies (RBs) resisting fusion with the deadly host lysosomes,thus killing them

    • Force the RB to enter the anaerobic starvation Cryptic Body (CB) state

  • Metronidazole (brand name Flagyl) actively kills the Cryptic Bodies (CBs).

Whilst the above drugs are varying in their levels of toxicity, NAC of course is a good source of Cysteine and a Glutathione precursor, and can help to support liver function, detoxification and the immune system in general (if taken to supplement a deficiency in Cysteine or Glutathione). It may however result in some Mercury mobilisation. The above regime is a short term treatment plan, to kill off the entirety of a Cpn infection and is not intended to become a long term and harmful antibiotics programme. This is a specialist protocol and does not fit in with the more generic anti-bacterial treatments described elsewhere on this page. It is reproduced here for information purposes only. It is possible that some of the antibiotic drugs cited above can be substituted with certain herbs.

Natural antimicrobials that may help to deal with Cpn include Nutramedix Samento, Banderol and Quina. As Cpn is a biolfim loving organism, it will likely be necessary to take a number of biofilm-busting supplements.

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Biochemical markers for Clostridia and Pseudomonas:

2,3 Dihydroxyphenylpropionic acid (DHPPA) is an organic acid byproduct of the bacterial metabolism of phenylalanine, tyrosine and/or tryptophan.

Various species of Clostridia (gram positive) bacteria have been shown in vitro to produce DHPPA.

'A variety of foul smelling compounds are formed during the fermentation of amino acids and fatty acids. The clostridia also produce a wide variety of extracellular enzymes to degrade large biological molecules (e.g. proteins, lipids, collagen, cellulose, etc.) in the environment into fermentable components...Clostridium tetani and Clostridium botulinum produce the most potent biological toxins known to affect humans.'

Pseudomonas are gram-negative rod bacteria, and are responsible for most hospital based infections. Quinoline research has demonstrated the production of DHPPA by Pseudomonas species.

Presence of elevated levels of DHPPA in the urine may suggest overgrowth of either Clostridia and/or Pseudomonas in the gut, as well as a degree of malabsorption of aromatic amino acids. However, by examining the amino acid levels, for example, Threonine, a very hard amino acid to absorb in relative terms, one could rule out the latter explanation.

Both DHPPA and citramalate levels can be identified in a urine test such as the Optimal Nutrition Evaluation (ONE) by Genova Diagnostics.

In addition, the organic acid citramalic acid or citramalate can also be formed by anaerobic bacteria as well as yeast/fungal organisms.

Other bacterial dysbiosis markers include Ammonia, Benzoic/Hippuric Acids Ratio, Beta-Alanine, Ethanolamine, Gamma-aminobutyric Acid, Indoleacetic Acid, Phenylacetic Acid, Phosphoethanolamine and Succinic acid.

Beta-alanine is often elevated when the dietary peptides anserine and carnosine are elevated because they contain beta-alanine. Beta-alanine is also a metabolite of the pyrimidine bases cytosine and uracil. Catabolism (breakdown) of damaged or diseased bodily tissue, tumors and malignancy feature increased production and urinary disposal of beta-alanine. Besides elevated anserine or carnosine and accelerated catabolism of unwanted bodily tissue, the next most likely source of beta-alanine in urine is imbalanced gut flora. The normal gut flora produce some beta-alanine, which they make pantothenic acid (vitamin B5) from. However, elevated levels of staphylococcus or streptococcus, use of antibiotics, and the breakdown of yeast or fungi in the body can cause an increase in urinary beta-alanine levels. Continuously elevated beta-alanine can be detrimental by impairing renal conservation of taurine.

Please see the Identification page for more information about the ONE test. There are of course more direct methods of identifying bad bacteria, for example, stool analysis or live blood microscopy, but if one is evaluating amino acids and organic acids, then the results can provide some useful markers for bad bacteria and Candida.

So what is the solution for an overgrowth of bad bacteria?

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Probiotics Supplements:

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There are approximately 400+ varieties of bacteria in the digestive tract and take many years to build up through a healthy diet. Dr Elie Metchnikoff Ph.D, Nobel, laureate, postulated that the ideal ratio of good to bad bacteria should be 80:20, which is often the reverse way around in many modern Westerners. This is why eradicating all of one's probiotic bacteria by taking anti-biotics (or to a lesser extent colonic hydrotherapy) and simply taking a probiotic supplement afterwards (containing perhaps 2 or 3 strains of probiotic bacteria) is not really going to build up that same level of diversity of good bacteria as would occur naturally with a good diet rich in vegetables (especially those containing prebiotic sugars which are the optimal food for probiotic bacteria).

A healthy GI tract's composition of beneficial flora is not just a case of quantity but also diversity or quality. Most probiotic supplements focus on Lactobacillus acidophilus as it is probably one of the toughest probiotic strains and is relatively acid resistant. As discussed above, a deficiency in any one particular species may render the GI tract suspectible to certain strains of pathogenic species more than others. To maintain optimum flora balance and digestive health, it is recommended to ascertain what probiotic species are represented in one's stool and which are deficient. It is sensible to then take this data and target those probiotic species and strains that are deficient. For more information on stool testing, please see the Identification page. Certain probiotic strains may not seed properly, or so effectively, in the presence of large concentrations of dysbiotic or pathogenic species, and so probiotic supplementation may require the taking of antimicrobial herbs to fight off such pathogenic microorganisms.

Sources of probiotics include true fermented products, for example, fermented cabbage juice, live kefir or (bio-)live natural yoghurt and also probiotics supplements. As a general rule, good fermented foods and drinks are those that are fermented (i.e. acidified with lactic acid) using probiotic bacteria.

Good probiotics supplements may come in enterically coated format also to ensure deeper penetration into the GI tract, as under normal circumstances most bacteria entering the GI tract are destroyed by the stomach acid in the stomach. I have not seen any actual test results yet to confirm the effectiveness of enterically coated probiotics. However the theory is sound. There is some debate as to how many viable cells of bacteria are necessary to be effective - some supplement boast about the number of viable cells they contain at the time of manufacture. Others contain less than a billion but emphasise that they are more viable.

The vast majority of active probiotic bacterial cells are destroyed by the stomach before they reach the small and large intestine. Therefore the exact number taken could in some ways be considered irrelevant or not so critical. Many people consider at least 1 billion active cells as a minimum, and 4-5 billion being fairly good. More is of course a bonus! There is no upper limit as such to probiotic supplements and the frequency of their consumption during the day, per se. One should however exercise one's common sense. The main purpose of taking probiotics is to provide viable cells of good bacteria which can seed or multiply in the small and large intestine. It is not really to physically populate the colon with good bacteria from literally just the probiotic bacteria (from supplements) that survive and reach the colon. This would be a mammoth task given the small number that actually reach the colon and the several kilos of good bacteria actually required there. Providing a regular supply of seeding bacteria to the colon, and also ensuring optimal conditions (and food) for the good bacteria and adverse conditions (and a lack of food) for the bad bacteria, is the main goal to achieving and maintaining a healthy floral gut balance.

Certain strains prefer certain parts of the GI tract. Many probiotic bacteria are killed off by the stomach acid and never reach the GI tract. Probiotics supplements are normally stored in the fridge unless stated otherwise on the label. Probiotics should be taken at least 2 hours away from any anti-microbial supplements (see below regarding candida and parasites treatment). If you are taking anti-microbial supplements, then it is doubly important to be taking probiotics as well during the course of each day.

In my experience, probiotics work very well, unless there is a significant state of dysbiosis or commensal bacterial overgrowth, in which case many types of probiotics may work well up to a certain point, then achieve very little until the unwanted bacteria are killed off with antimicrobial treatments, afterwhich point the prebiotics can work more effectively again to boost probiotic bacterial numbers. Probiotics in general seem to struggle to suppress excessive commensal bacterial numbers if already present without antimicrobial intervention. It is in my experience, species dependent of course (E.coli numbers seem to be easier to increase with probiotic supplementation than Lactobacillus or Bifidobacteria in the presence of dysbiosis).Each probiotic species is targetted often at suppressing growth of or actively reducing numbers of certain types of commensal or pathogenic species.

There is much to say about inserting/squirting probiotics actually directly into the anus. You perhaps could moisten your finger, moisten the capsule, and push it as far up your anus as comfortably possible. :-) Clearly, this bypasses the stomach completely, and avoids the mass destruction of the majority of probiotic bacteria in probiotic supplements in the strongly acidic environment of the stomach. However, some may regard this as an extreme measure, or as highly unpleasant. There are various methods available. One could create a solution using room temperature water or probiotic drink (e.g. kefir or fermented cabbage juice) and squirt this directly up the bottom using a rectal syringe (available from a dispensing chemist); or use an enema kit including a tube and funnel. These methods probably require a (lucky!) second person. Alternatively one could take a piece of cotton wool, soak it in organic bio-live yoghurt, empty a capsule or two of a probiotic supplement onto it, and insert it into the anus, leaving it in overnight and removing it in the morning. I haven't tried either of these methods, but wanted to present all possible options!

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Lactobacillus and Bifidobacterium

The most common genus found in probiotics supplements tend to be Lactobacillus and Bifidobacterium species. These are technically speaking the 'probiotic' bacteria geni. Of these, the most common species found in probiotic supplements are Lactobacillus acidophilus and Bifidobacterium longum.

Bifidobacterium contain several species including:

  • Bifidobacterium infantis
  • Bifidobacterium breve
  • Bifidobacterium longum
  • Bifidobacterium breve
  • Bifidobacterium animalis subsp lactis (f.k.a. B.lactis)

Bifidobacterium infantis is found in mother's breast milk and is one of the first few colonisers of a newly born infant's GI tract (hence the name deriving from 'infant').

A few strains of note however are:

  • Bifidobacterium infantis 35624

  • Bifidobacterium infantis 35624 is marketed under the trademark 'Bifantis' by Procter and Gamble. It is found exclusively in the Procter and Gamble supplement 'Align'. It has undergone extensive trails and has the most evidence for effectiveness against IBS and other bowel conditions. This is not currently for sale in Europe although it can be purchased from US vendors, e.g. on Amazon or on 'fleabay'.

  • Lactobacillus reuteri

  • Lactobacillus reuteri is not found in all GI tracts but is a highly effective probiotic bacterial strain, also found in mother's breast milk in small quantities.

    L.reuteri is only currently found in one probiotic supplement, Nature's Way's Primadophilus Reuteri, which also contain Lactobacillus acidophilus, Lactobacillus rhamnosus and Bifidobacterium longum. This is currently available in 3 different formats. The Primadophilus Reuteri Pearls do not require refrigeration.

  • Lactobacillus rhamnosus GG (ATCC 53013)

  • Lactobacillus rhamnosus GG, a.k.a. Lactobacillus GG, is a trademarked form of Lactobacillus rhamnosus. It is found in a small number of supplements including most notaby/famously Allergy Research's Culturelle Lactobacillus GG (10 billion cells + 245mg Inulin).

Examples of good generic Lactobacillus acidophilus and Bifidobacterium probiotics supplements are listd below (number of cells quoted per capsule or sachet).

  • Garden of Life's Primal Defense (5 billion cells) - contains Bacillus subtilis, Humate and Fermented Greens
  • RenewLife's Ultimate Flora range, particularly Critical Care (50 billion) and Super Critical (200 billion) - refrigeration recommended - enteric-coated, v.high in bifidobacteria)
  • O'Donnell Formulas' The Ultimate Acidophilus plus Bacillus Coagulans (250 million CFU B.Coagulans plus 2 billion CFU L.Acidophilus DDS-1 (Nebraska Cultures strain))
  • Dr Ohhira's Probiotics 12 Plus (Original or Professional)
  • Safe Remedies' Organic Prime Directive (a.k.a. FermPlus in Australia) - contains fermented greens
  • VSL#3 (450 billion cells)
  • Bio-K+ CL1285 (30 billion)
  • Jarrow Formula's Ultra Dolphilus (40 billion) - in gel matrix to protect from stomach acid
  • BioCare's Bio-Acidophilus Forte (24 billion / refrigeration required)
  • Klaire Labs' Ther-biotic Complete (25 billion)
  • Archturus' Pro-Bifidus powder (containing 1 billion cells per gram - using Nebraska 3 Bifido strains - B. breve, B. longum, B. infantis)
  • Source Naturals' Bifidyn (1 billion CFU Nebraska Cultures' B.longum and B.bifidum per gram)

A number of soil-based bacteria formulas are available, and which are not listed above, with the exception of Primal Defense. These are examined in more detail in the SBOs section.

One of my practitioners has found that only three commercial probiotic products that he's tried seem to work best with his patients - Garden of Life's Primal Defense (Standard or Ultra), Securil and Allergy Research's Culturelle Lactobacillus GG.

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Enterococcus faecalis TH10

The two probiotic bacterial strains of Enterococcus sp. including faecalis and faecium, can be found in Kefir or a small number of specialist probiotic supplements. Kefir contains 7 strains of Enterococcus faecalis and 2 strains of Enterococcus faecium, and is arguably a superior source of Enterococcus sp. probiotics than any of the supplements listed below. These probiotic supplements include:

  • Global Health Trax ThreeLac and FiveLac - contain 500 million cells of Entercoccus faecalis per sachet
  • Dr Ohhira's Probiotics 12 Plus (Original or Professional) - contain a smaller number of Enterococcus faecalis TH10 per capsule.
  • Discovery Health's Probiotic Plus
  • Symprove liquid - contains both E.faecalis and E.faecium per serving.
  • Quantum Nutrition Labs (PR Labs) HM Nano Detox, Melatonin Nano-Plex, Nano-DHLA and others (stated on ingredients) - these are not primarily probiotic supplements although they do contain probiotics. They contain both Enterococcus faecalis TH10 and Enterococcus faecium.

Dr Ohhira's product is fermented over 5 years using fruits, vegetables, mushrooms and seaweeds, containing 12 probiotic species (no SBOs) and various organic acids (including citric, lactic, formic and acetic acids). It is reputed to be one of the best probiotics products on the market. Ben Kim has a very good reputation and he is probably right! There are two versions of Dr Ohhira's Probiotics 12 Plus, Original Formula and Professional Line. Ben Kim recommends the latter. The difference is in the amount of organic acids (Professional containing more) and lactic bacteria blend (Professional containing slightly less). Probiotics 12 Plus Professional Line is also marketed in some countries as OM-X 100 or OM-X 12.

The strains contained in Dr Ohhira's formula include:

- Bifidobacterium breve
- Bifidobacterium infantis
- Bifidobacterium longum
- Enterococcus faecalis TH10 (proprietary strain isolated from Malaysian Tempeh ferment)
- Lactobacillus acidophilus
- Lactobacillus brevis
- Lactobacillus bulgaricus
- Lacrobacillus casei
- Lactobacillus fermentum
- Lactobacillus helveticus ssp. jugurti
- Lactobacillus plantarum
- Streptococcus thermophilus

My practitioner muscle tested this product on me and it tested negatively (allergic reaction).

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Mutaflor - Escherichia coli strain Nissle 1917:

Mutaflor is the brand name for the probiotic species of Escherichia coli (E.coli), known as strain Nissle 1917 or Mutaflor for short, which is manufactured by German firm Ardeypharm. It is a beneficial species of E.coli. Most E.coli strains are harmless, although a few are pathogenic and highly virulent. E.coli tends to reside in the Ileum, the final part of the small intestine, just before the bowel. E.coli is a facultative anaerobe and a gram-negative rod-shaped bacterium. E.coli does not produce lactic acid.

Beneficial E.coli produce folic acid, Co-Enzyme Q10, vitamin K2 and the amino acids Tyrosine, Phenylalanine and Tryptophan. It also helps to ferment soluble fibre into Short Chain Fatty Acids (SCFAs) and inhibit pathogenic bacterial growth.

Mutaflor was first isolated by the German Microbiologist, Prof. Alfred Nissle, in 1917 during WWI from the faeces of an NCO in Dobrudsha in the Balkans, an area highly contaminated with enteropathogens at the time. All of his fellow soldiers had become very ill. Since then it has been marketed in capsule form.

Mutaflor can now be purchased both in capsule or suspension form (as of 2009). The capsules are enterically coated and are designed to open up in the terminal ileum. Each capsule contains 2.5-25 billion viable cells. The product is available in 'mite' capsule form, where the strength is only 20% of the regular capsules, for use in severe cases where the patient cannot tolerate the stronger capsules at first. Dosage is 1-2 capsules per day, taken with food and sufficient liquid.

Mutaflor is also available in suspension form, in 1ml or 5ml vials, presumably at the same strength as the capsules described above. They have been designed primarily for use with infants and toddlers in mind, who cannot easy swallow capsules. Of course, one could break open a capsule and sprinkle the contents into food etc., but this may not be so easy and of course would negate the benefit of the enteric coating. The suspension of Mutaflor bacteria is presumably not enterically coated in any way. The suspension form is much more expensive than the capsule form and has a shorter shelf life of 2-3 months vs 9 months for the capsules. A recipe for making Mutaflor yoghurt can be found on the Recipes page.

Mutaflor capsules can be purchased in the US and Canada directly from the respective Mutaflor web sites. The capsules should be refrigerated at all times, but are ok to be kept out of a refrigerator during shipping for up to 72 hours (but no more) according to Ardeypharm.

A German reseller of Mutaflor is Berlinda Versand Apotheke, who sell both capsules and suspension. Myhill has full instructions for ordering from this site in English (at the Growing Mutaflor link above) for those who cannot read German or use Babelfish. Their standard delivery is via DHL but 5-10 working days. Specify that you want it delivered with DHL's Weltpacket Premium which is a 2-3 working day delivery, and that it must be posted on a Monday only to avoid being stuck over the weekend (as happened with my delivery). According to Ardeypharm the Mutaflor should be still completely in tact after 4 days out of refrigeration (the cold pack and insulated box should keep it cool for 2-3 days).

Another alternative suggested by Ardeypharm is Metropolitan Pharmacy, who are based at an airport and who guarantee 2 day deliveries for all international shipping (if I am not mistaken). Their prices are however significantly higher. Visit their e-shop for pricing.

If you search on, you can find a number of other resellers of Mutaflor. Please note that some may not ship outside of Germany, so it is best to enquire before placing an order.

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Securil - Propionibacterium freudenreichii:

Propionibacteria freudenreichii is a type of gram-positive, non-motile (not free swimming) bacterium that is used in the production of certain types of cheeses, for example, Emmental and to a lesser extent Leerdammer. Other bacterial species present in Emmental include Streptococcus thermophilus and Lactobacillus. Emmental is quite rich in P. freudenreichii. Other non-Swiss cheese types do contain it, but not in such large quantities. It is also found in small quantities in soil.

During cheese production, Propionibacterium freudenreichii ferments lactate to form acetate, propionate and carbon dioxide. The Propionate is a salt of propionic acid. Propionic acid is an organic, carboxylic acid, and is strongly anti-fungal, and supplementation with P. freudenreichii can boost the localised Propionate levels in the GI tract and help to eliminate Candida albicans and other yeasts and moulds. The Propionic acid molecule is shown below.

According to Michal Culp, whilst the P. freudenreichii bacteria are not native to the GI tract, the Propionic Acid they produce is one of the favourite foods of the GI Tract's Bifidobacteria, so supplementation with P. freudenreichii can produce an anti-fungal agent as well as a prebiotic.

'To be healthy you need a balance of bacteria in your gut. The average person has about 100 trillion bacteria (more than the number of cells in your entire body) and more than 400 different species of bacteria have been identified able to live in your gut, although only 30-40 species are common. These bacteria constitute an ecosystem all on their own. There are two very important types of bacteria to help your ecosystem stay in balance: Bifidobacteria and Lactobacillus acidophilus (the latter is found in fermented foods like yogurt or sauerkraut). However, the Bifidobacteria appear to be the dominant healthy bacteria, outnumbering Lactobacillus strains by about 1000:1. Five strains of Bifidobacteria are common in humans, but each person will have their own unique ratio of the five, and this will change with age and in response to environmental factors. The five common strains of Bifidobacter include B. infantis, B. adolescentis, B. bifidum, B. longum, and B. breve. [P. freudenreichii]...provides the food that allows growth of all Bifidobacteria, so your body can maintain its own unique, health-promoting combination of the different stains. The Bifidobacteria levels remain high in your gut only while they have adequate food and stimulation to grow. '

Sources of Propionibacterium freudenreichii include Emmental cheese, and a supplement such as Securil which contains 'Propio-Fidus' a brand name for Proprionibacterium freudenreichii. Each capsules contains 5 billion active cells, in a base of the prebiotic FOS. Two capsules of Securil daily is said to be equivalent to eating 100g of Emmental cheese, which is not THAT much, but for those that cannot easily tolerate dairy products or are concerned with weight gain, then a more expensive probiotic like Securil may be more convenient. Securil is made by the French firm 'Compagnie Generale de Dietetique Laboratoire Yalacta'.

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Soil Based Organisms:

Certain probiotic products claim to contain Soil Based Organisms or SBOs. Whilst not native to the GI tract, they have many beneficial properties for the GI tract and the immune system as a whole. There seems to be a great deal of hype around them, certain manufacturers claiming to have have a unique product. But rarely is any explanation offered of what SBOs actually are. I will attempt to briefly describe what SBOs are, what products they are found in, and what their benefits are.

SBOs are naturally occurring bacterial strains (i.e. microorganisms) found present in soil that release powerful enzymes that help to kill off yeasts, mould, fungi and parasites. Modern farming methods, including the use of herbicides and pesticides are reputed to kill them off to a large extent. It is believed by some that even organic produce is grown from depleted soil and so are not very rich in SBOs.

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Bacillus subtilis:

One strain of SBO is Bacillus subtilis, has been used by Africans for many centuries. Alternative names include Bacillus globigii, grass bacillus or hay bacillus. It is a predominantly soil-based form of bacterium, commonly found in soil and decomposing organic matter. Some strains are known to produce antibiotics. It was inadvertently discovered by German soldiers during WW2. A large number of German soldiers were dying of dysentery in the African campaign with little or no medicine readily available. A team of German scientists eventually found out that when the local 'Arabs' were suffering from dysentery, they would eat a small amount of fresh camel dung. This dung was later found to be extremely high in a form of bacteria later named Bacillus subtilis. Bacillus subtilis was later grown commercially and used by the German army to cure dysentery.

B.subtilis was marketed throughout America and Europe in 1946 as an aid to stimulating the immune system in treatment of gut and urinary tract diseases, but declined in popularity because of the introduction of cheap antibiotics, despite causing fewer allergic reactions and having lower toxicity to beneficial gut flora. Cultures of B.subtilis were used throughout the 1950s as an alternative medicine.

According to Bio-Kult blog:

'...Bacillus subtilis remains one of the most potent and beneficial of all health-promoting and immune-stimulating bacteria. According to clinical studies documented in the medical research report, IMMUNOSTIMULATION BY BACILLUS SUBTILIS PREPARATIONS, by micro-biologist J. Harmann, the cell wall components of ingested Bacillus Subtilis are able to activate nearly all systems of the human immune defense, including the activation of at least three specific antibodies (IgM, IgG and IgA secretion) which are highly effective against many of the harmful viruses, fungi and bacterial pathogens which regularly attempt to invade and infect the human system.'

So which products today contain Bacillus subtilis?

- Kiki Health's Nature's Biotics

- Life Science Products' Body Biotics (also contains Fulvic & Humic Acid)

- Garden of Life's Primal Defense (12 species in total - 5 billion CFU) - (also contains Humate)

- Garden of Life's Perfect Food Original (also contains Humate)

- Garden of Life's RAW Protein

- Global Health Trax' ThreeLac or FiveLac (500 million CFU of B.subtilis, 3 or 5 species in total)

- Protexin Health Care's Bio-Kult Advanced Probiotic Formula (14 species in total - 2 billion CFU)

- Dr Ben Kim's Greens (also marketed by HealthForce Nutritionals as 'Vitamineral Green')

- Efficient Microorganisms (EM) Technology (a 'mother culture' containing Bacillus subtilis as well as other beneficial bacterial and yeast strains, marketed by various manufacturers)

- Natto, the Japanese fermented food. Natto is prepared by adding Bacillus natto (a strain of the species Bacillus subtilis) to cooked soy beans. Bacillus natto is often found in various supplements as an ingredient, named 'Bacillus subtilis Natto Extract'. However, this is a dead form of the bacteria, as the bacterial cells are boiled to extract the beneficial Nattokinase enzyme or Vitamin K2. Examples of such supplements include Source Naturals Vitamin K2 and Doctor's Best Best Vein Support with DiosVein. Not all products with 'Natto Extract' contain the dead Bacillus natto however.

An unofficial Bio-Kult blog site equates Bacillus subtilis to being interchangeable with Bacillus licheniformis. This is probably an error in communication.

However Wikipedia defines it as a separate Bacillus species, and not a probiotic one, but a pathogenic species.

'Bacillus licheniformis is a bacterium commonly found in the soil. Recently, studies have also shown that it is found on bird feathers, especially chest and back plumage, and most often in ground dwelling birds (like sparrows) and aquatic species (like ducks). Bacillus licheniformis, Bacillus subtilis, and Bacillus pumilus comprise the subtilis group, which has been associated with a range of clinical conditions, food spoilage such as ropy bread, and incidents of food-borne gastro-enteritis.'

Others define it as one bacterium strain within the Bacillus subtilis group. It is however a facultative anaerobe whereas Bacillus subtilis tends to be aerobic.

The protease enzyme from Bacillus licheniformis is used widely in the food processing industry, namely for its ability to hydrolyse (break down) proteins. For example, Bacillus licheniformis Protease is used in the hydrolysis of Hydrolysed Whey Protein.

Bacillus licheniformis is used in the production of Garden of Life's Primal Defense, presumably to predigest the cereal grasses, but Garden of Life claims that only its enzymes are found in the final product and not the bacterium itself (in line with most hydrolysis practices). Kiki Health actually state that Bacillus licheniformis is one of the ingredients of Nature's Biotics, however, as their product uses the same basic preparation method as Primal Defense, and that much of their marketing material is slightly amateurish, that one might assume that they mean the same thing as Garden of Life.

Is this a typo on the unofficial Bio-Kult blog site? Not a very clear picture. So is Bacillus licheniformis actually a probiotic SBO or not?

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Bacillus coagulans:

Another type of highly resistant Soil Based Organism of the Bacillus species include Bacillus coagulans, a.k.a. GanedenBC30 or Lactobacillus sporogenes. Bacillus coagulans is a spore forming and lactic acid producing bacterium, which has been used in animal feeds and in assisting human vaginal flora. Bacillus bacteria are spore forming and their spores highly resistant to chemical and physical agents. As Bacillus coagulans is also lactic acid forming, it could be said to fall somewhere between the classifications of Lactobacillus and Bacillus, however the Lactobacillus name for it, Lactobacillus sporogenes (i.e. spore forming Lacto bacterium) is somewhat incorrect on account of its spore forming abilities and has been superceded since 1939.

Which products include Bacillus coagulans?

- Global Health Trax' ThreeLac and FiveLac (reviewed further below - 500 million CFU)

- Source Naturals DuraFlora (125mg or 5 billion CFU)

- TwinLab Super Probiotic (150mg or 2.1 billion CFU)

- O'Donnell Formulas' The Ultimate Acidophilus plus Bacillus Coagulans (250 million CFU B.Coagulans plus 2 billion CFU L.Acidophilus DDS-1 (Nebraska Cultures strain))

- Life Extension Enhanced Super Digestive Enzymes with Probiotics (166,500 CFU)

- Nature's Plus Ultra Juice Green (50 million CFU)

- Rainbow Light Candida Cleanse (20 million CFU plus a variety of anti-candida herbs)

- Prime Directive (aka FermPlus)

Garden of Life Raw Meal

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Bacillus laterosporus:

There is another SBO supplement on the market, by O'Donnell Formulas called Flora-Blalance. This utilises the patented Bacillus strain Bacillus laterosporus (a.k.a. Bacillus laterosporus BOD). It contains 35mcg per capsule which is equivalent to 1 million cells (a very low number in relative terms) - but it is a unique product/species in probiotic supplement terms. It is also available in powder form. I did not notice anything different when taking it but that is not to say it isn't a useful species to take.

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Rhodopseudomonas palustris:

Rhodopseudomonas palustris is a purple, phototropic bacterium, most commonly found in soil and water.

The only product to my knowledge that definitely contains this bacterium species are those based on Efficient Microorganisms (EM) Technology, e.g. SCD EM, and EM Earth's EM-1 and ProEM-1, etc.

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Rhodopseudomonas sphaeroides:

Rhodopseudomonas sphaeroides is a purple, phototropic bacterium (i.e. one that can produce energy through photosynthesis) and is found in deep lakes - not strictly speaking an SBO, but still a useful probiotic species.

The only product to my knowledge that definitely contains this bacterium species are a subset of those based on Efficient Microorganisms (EM) Technology, e.g. SCD EM Plus.

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Saccharomyces boulardii:

Saccharomyces boulardii is a probiotic yeast strain, as opposed to a probiotic bacterial strain.

'Saccharomyces boulardii is a tropical strain of yeast first isolated from lychee and mangosteen fruit in 1923 by French scientist Henri Boulard. It is related to, but distinct from, Saccharomyces cerevisiae in several taxonomic, metabolic, and genetic properties. S. boulardii has been shown to maintain and restore the natural flora in the large and small intestine; it is classified as a probiotic. Boulard first isolated the yeast after he observed natives of Southeast Asia chewing on the skin of lychee and mangosteen in an attempt to control the symptoms of cholera. S. boulardii has been shown to be non-pathogenic, non-systemic (it remains in the gastrointestinal tract rather than spreading elsewhere in the body), and grows at the unusually high temperature of 37¡C.'

Saccharomyces boulardii is found in the following products.

- AGM Grainfields

- NuFerm's FermPlus (aka Prime Directive)

- Garden of Life's Primal Defense ULTRA

- Garden of Life's Primal Defense (enzymes of S.boulardii only)

- Garden of Life's Perfect Food Raw

- Some Kombucha mother cultures

Are SBO/HSO-based probiotic supplements any better than Lactobacillus and Bifidobacteria based probiotic formulations? Some experts seem to think so. They are reputed to be more hardy and resilient. Try them out and find out! You should probably experiment a little with different probiotics in any case.

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EM Technology:

'Effective Microorganisms, also called EM Technology, is a brand name for a series of products utilizing a base culture called EM¥1 Microbial Inoculant. "EM Technology" is an as yet scientifically unconfirmed method of improving soil quality and plant growth using a mixture of microorganisms consisting mainly of lactic acid bacteria, purple bacteria, and yeast which co-exist for the benefit of whichever environment they are introduced.'

'Efficient Microbes', another name for Efficient Microorganisms or EM Technology, are described at the link below.

'EM is a natural, probiotic technology developed for over 25 years around the world. It is based on beneficial and effective microorganisms ("EM"). The microbes in EM are non-harmful, non-pathogenic, not-genetically-engineered or modified (non-GMO), and not-chemically-synthesized. The basic groups of microorganisms in EM are lactic acid bacteria (commonly found in yogurt, cheeses), yeast (bread, beer), and phototrophic bacteria ("cousins" of blue-green algae). All Efficient Microbes [SCD (EM)] are produced through natural fermentation processes; and are not chemically synthesized or genetically engineered. EM is sold as a concentrate and can be added to water and applied as is, or activated and extended up to 2000 times its volume. The microorganisms in EM are known to produce bioactive substances, vitamins, hormones, enzymes, amino acids, and antibiotics, which enrich and detoxify the soil. EM directly enhances plant growth and produces high yielding crops, which are drought, frost, pest and disease resistant without the need of any agricultural chemicals. Activated EM can also be used to create an environment where grease, mould, rust do not thrive due to the ant oxidative properties of EM. SCD Efficient Microbes (EM) consists of a wide variety of effective, beneficial, non-pathogenic aerobic and anaerobic micro organisms cultured in diluted molasses that are mutually compatible with one another.'

EM liquid is also an excellent probiotic suitable for human consumption. Examples of two manufacturers of EM liquid include SCD and EMEarth.

SCD and Emerald Earth market a number of EM products, for industrial, agricultural, domestic and health applications. Both SCD Food Grade and EM-1 are available in a 1 gallon bottle at roughly the same price as 180 capsules of Primal Defense. My contact believes that the form of freeze (?) dried/processed EM present in Primal Defense is not as effective as its natural form in EM liquid.

The bacterial strains (mother culture) present in SCD EM Food Grade are listed below, including 1 Bacillus species, 3 Bifidobacterium species, 6 Lactobacillus species, 2 Lactococcus species, 1 Steptococcus species, 1 Rhodopseudomonas species and 1 Saccharomyces species.

- Bacillus subtilis
- Bifidobacterium animalis
- Bifidobacterium bifidum
- Bifidobacterium longum.
- Lactobacillus acidophilus
- Lactobacillus bulgaricus
- Lactobacillus casei
- Lactobacillus delbrueckii
- Lactobacillus fermentum
- Lactobacillus plantarum
- Lactococcus diacetylactis
- Lactococcus lactis
- Streptococcus thermophilus
- Rhodopseudomonas palustris
- Saccharomyces cerevisiae (brewer's yeast)

SCD EM Plus additionally contains (i.e. a 2nd Rhodopseudomonas species):

- Rhodopseudomonas sphaeroides

MSDSes can be found for both products below.

An associate of mine, referenced below, believes this to be the cheapest and most effective probiotic supplement available, partly because it can be extended with fermentation (i.e. used to produced more at no cost).

One reputed expert on EM Technology is Vinny Pinto. He is affiliated with the Weston A. Price Foundation. He runs a yahoo group on EM.

The following web site provides instructions for making one's own 'Efficient Microbe' or E.M. Tea.

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AGM Grainfields:

According to my contact, when Rubin first created Primal Defense, he decided to combine dried humate, a dried form of EM and also fermented barley grass and oat grass from a company called AGM in Australia.

AGM Grainfields products use a proprietary fermentation process called FermFlora, which my contact claims makes the bacteria very hardy and powerful. The 'food' that the bacteria use to ferment is organic molasses. This FermFlora process yields the following bacterial strains:

- Bifidobacterium bifidum
- Lactobacillus acidophilus
- Lactobacillus casei
- Lactobacillus helveticus
- Lactobacillus bulgaricus
- Lactobacillus leichmannii
- Lactobacillus caucasicus
- Lactobacillus lactis
- Lactobacillus fermenti
- Lactobacillus brevis
- Lactobacillus plantarum
- Lactobacillus delbreukii

And the following Yeast Strains:

- Saccharomyces boulardii (probiotic yeast strain)
- Saccharomyces cerevisiae (brewer's yeast)

The AGM Grainfields products include liquid products and powder products. They do not contain humate or 'SBOs/HSOs'. My contact has found the powder products to be excellent.

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ThreeLac and FiveLac:

FiveLac is a Japanese supplement based on lacto-bacteria. Formerly known as ThreeLac (with 3 strains of bacteria but now with 5 strains). It is distributed in the USA by Global Health Trax. Although there are no documented clinical trials, it appears to help in fighting off Candida, as does taking other probiotics. It probably just acts to assist rather than the sole source for killing candida. It comes in boxes of 60 sachets, and in general, one sachet is taken per day (on an empty stomach), before a meal.

As cam be seem in the picture below, it contains two resilient Bacillus bacterium species:

- Bacillus coagulans (aka Lactobacillus sporogenes)
- Bacillus subtilis (found in the Primal Defense and Nature's Biotics etc.)

As well as:

- Enterococcus faecalis (also found in Kefir)

And (FiveLac additionally contains) the more common probiotic bacteria:

- Lactobacillus acidophilus
- Bifidobacterium longum

And the prebiotic fibres FOS, Fenugreek Fibre (Galactomannan) and Beta-Cyclodextrin. It also contains refined yeast (Saccharomyces cerevisiae). The yeast is in its inactive form (dead) and is there as a prebiotic food for the live probiotic bacterial strains included in the product to assist them to multiply and pass through the acidic environment of the stomach into the intestines.

Whilst FiveLac appears to be the only one of the above three SBO products to contain Bacillus coagulans/Lactobacillus sporogenes, there are other dedicated Bacillus coagulans supplements on the market, for example, Source Naturals DuraFlora (125mg or 5 billion cells of Bacillus coagulans per capsule - 10 times more than FiveLac), O'Donnell Formulas' The Ultimate Acidophilus (250 million cells of Bacillus coagulans), Twinlab Super Probiotic (2.1 billion cells of Bacillus coagulans per capsule) and Rainbow Light Candida Cleanse (20 million cells per capsule plus a variety of anti-candida herbs), etc.

The latter two strains (Lactobacillus acidophilus and Bifidobacterium longum) in the above ingredients list are the only difference between ThreeLac and FiveLac, and if you've already taken a probiotic supplement or natural yoghurt, then there isn't a significant difference between ThreeLac (if you can still buy it) and FiveLac. The retail price should however be the same.

The actual amounts of probiotic bacteria and SBOs in FiveLac are not that great in relative terms (500 million active cells of each type of bacterium, giving a total of 2.5 billion active cells, which is 'average' for a probiotic), but quite 'poor' in terms of each species if one considers the cost. However the first three species make it more effective than most probiotics supplements.

Many web sites sell FiveLac, which is not particularly cheap, and recommend taking a high dosage to kill the candida off more quickly. The nature of probiotics supplements means that the exact number of cells of bacteria consumed is not important, but the type and quality. Thus increasing the dosage beyond one sachet a day is unlikely to make much difference. I would recommend including it or another Probiotic supplement in your diet in any case. FiveLac is extremely popular in Japan, where it is not marketed as a cure for Candida, but as a general aid to health and digestion. Global Health Trax are careful to market it as a digestion aid and as a 'food' and make no claims about candida, for legal reasons, although many resellers do make claims about it (making confident/wild claims about products is nothing new in the alternative health industry.)

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Bio-Kult Advanced Probiotic Formula:

Bio-Kult is a reputedly practitioner strength probiotic supplement that contains 14 different strains of probiotic bacteria, including Bacillus subtilis and also Streptococcus thermophilus.

1. Lactobacillus acidophilus
2. Lactobacillus delbrueckii ssp. bulgaricus
3. Lactococcus lactis ssp. lactis
4. Lactobacillus casei
5. Lactobacillus helveticus
6. Lactobacillus plantarum
7. Lactobacillus rhamnosus
8. Lactobacillus salivarius ssp. salivarius
9. Bifidobacterium breve
10. Bifidobacterium bifidum
11 Bifidobacterium infantis
12. Bifidobacterium longum
13. Bacillus subtilis
14. Streptococcus thermophilus

Information about the probiotic strain Streptococcus thermophilus can be found at the links below. Contrary to Wikipedia's statement, it is known as a beneficial probiotic species.

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Dr Ben Kim's Greens and Natural Soil Organisms (NSOs):

A green superfood and probiotic blend by Dr Ben Kim called Greens Version 2.0 contains cereal grasses, vegetable extracts, spirulina and chlorella, kelp and dulse, digestive enzymes and also a probiotic mixture trademarked as Natural Soil Organisms. It is stated to include 'Exclusive NSO and Implantable Species'.

Quoting from Dr Ben Kim's web site, the probiotic species are said to include:

- A. agilis
- A. brasilienese
- A. citreus
- A. globiformis
- A. luteus
- A. lipoferum
- A. lwolfii
- A. simplex
- A. terreus
- B. brenis
- B. lipolyticum
- B. laterosporous
- B. macerans
- B. pumilus
- B. polymyxa
- B. stationis
- B. subtilus
- B. succinogenes
- L. acidophilus
- DDS-1 L. acidophilus
- L. bifidus (a.k.a. bifidobacterium)
- L. bulgaricus
- L. casei
- L. plantarum
- L. salivarius
- M. verrucaria
- K. zopfit
- P. chrysosporium
- P. calcis
- P. denitrificans
- P. flourescens
- P. gelatic
- P. marinoglutinosa
- P. nigraclens
- P. putida
- R. arrhizus
- S. cellulasae
- S. faecium
- S. fradiae
- S. griseoflavus
- S. thermopolis
- T. viride

= by Nebraska Cultures.

I have not heard of many of these species before, and it would be more helpful with full genus rather than abbreviated names. They are also listed by species and not genus, and use capital letters in the species, which is additionally confusing. Has a marketing person been let loose with the word processor? We do know that the NSOs contain Bacillus subtilis, which is known to be an SBO. Unfortunately no more information is available at this time on NSOs. Ben Kim's Greens is reputed to be one of the best green superfood supplements on the market. On paper it is a technically superior product, rich in greens with no bean shoots etc to 'dilute' down the greens content - however it does not taste very good and feels like it has a very 'cold' energy component compared with the others - to the extent that it does not feel so good after taking it. I got on really well with it at first, but after a week couldn't take it any more. Others may well have a different experience.

Dr Ben Kim's Greens are also marketed by HealthForce Nutritionals as 'Vitamineral Green', who claim to be the originators of the (their) formula.

Strangely however, Dr Kim also sells Dr Ohhira's Probiotics 12 Plus and describes the latter as the best probiotic product on the market! This is probably because his Greens product is primarily a Greens nutritional product than a probiotic.

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Peter Smith Strains of SBOs - Primal Defense, Body Biotics & Nature's Biotics:

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As has been seen above, Bacillus subtilis is not unique to the two most famous probiotics that claim to use Soil Based Organisms, i.e. Nature's Biotics or Primal Defense. There are other Bacillus strains and other probiotics belonging to other geni that are found in other products, as described above also. So let us examine the claims of these two probiotic supplements and try to ascertain what is actually unique about them.

It is claimed that scientist and researcher Peter Smith discovered 'other strains' of SBOs (besides Bacillus subtilis) inadvertently whilst hiking in the form of mould growths on the ground - which he collected and took back to the laboratory to study further. These SBOs when tested on mice and indeed himself produced health benefits.

Miscellaneous links examining the history and facts about SBOs can be found below.

The strains of SBOs discovered by Smith have not been patented but their composition has been kept a closely guarded secret. Were they actually some of the species above? Or were they actually 'new' species? Smith himself has never shared this information in the public domain, however the Smith strain/preparation method for SBO cultivation has been made known to both Kiki Health and Garden of Life, presumably through some commercial or licensing arrangement. Both Garden of Life's Primal Defense and Kiki Health's Nature's Biotics are reputed to use the same 'Smith's' fermentation method, with perhaps different fermentation substrates.

Presumably this is for anti-competitive and anti-educational reasons so that the associated SBO-based products can remain unique for more than the 17-20 years that patent provides exclusivity for, after which time the patent expires and the exact preparation method is available in the public domain for anyone to use in an unrestricted manner.

Clearly the vast majority of the mass is just fermented Barley Grass and Oat Grass, so these values only mean anything if one is comparing exactly the same fermented grass mixture. However, an examination of the labels of Primal Defense (PD) and Primal Defense ULTRA (PDU) in 2009 reveals that the actual stated amounts of this HSO Probiotic Blend is 800mg per caplet in Primal Defense (1 Billion CFU); and 410mg per capsule in Primal Defense ULTRA (5 Billion CFU). Both products are based on different types of HSO Probiotic Blend, PD contains Dunaliella Salina, Barley Grass Juice, Oat Grass Juice and Yucca Juice (hence the increased mass), and PDU contains just Barley Grass and Oat Grass, as bacterial culture 'food'. The values of CFU quoted are combined figures, and the actual blends are different, so it is very difficult to compare products or to know just how many actual viable cells of Bacillus subtilis there are (or indeed any other HSOs/SBOs if present). It is reputed that the ingredients of both products have changed in recent years. Whilst Garden of Life now state the CFU content, Nature's Biotics do not, stating that 'NB's priorities lie with the quality of the CFU and not the quantity'. Perhaps both manufacturers are trying to make it difficult to make direct comparisons!

However exact amount of the 'mother culture' in each respective capsule may not be relevant if one is taking Primal Defense in its powder form. Exact amounts are argued by some to be irrelevant if taken regularly and in at least sufficient quantities. Both products contain a base of green superfoods, Nature's Biotics using phytoplankton and Primal Defense using Barley Grass and Oat Grass.

It is however pretty much industry standard to declare the number of viable cells of bacteria present in a probiotic supplement (preferably how many of each species), as well as all the species actually present. So it is rather dubious that these facts are not declared fully on these two respective products, or at all in the case of Nature's Biotics. Garden of Life in their older formulation of Primal Defense did not declare the CFU value, but in the new formulation they appear to have done so. If all this information was available, then the actual unique attributes of the products would then become more clear, aside the marketing spin, and the products would stand up on their ingredients and also their merit and reputation, as is the case for everyone else.

In fact the vagueness in the marketing material of both companies and the insistence of use of obscure terms like Soil Based Organism and Homeostatic Soil Organism have created a great deal of unease and fear in the marketplace with many more sensitive consumers, who are not sure what is in it, and what these 'organisms' are. The word organism is often associated with creepie crawlies or harmful parasites found in some soil or mud samples and has a rather negative connotation! This confusion could be avoided with clearer and more forthcoming marketing materials.

Patents protect a product's unique preparation method and others knowing of one's methods (e.g. ingredients or fermentation processes) is therefore not an issue as competitors cannot legally copy them. However, part of the reason for this is probably that, according to Garden of Life, Bacillus subtilis is the only Soil Based Organism present in Primal Defense. This would imply that Smith's claims about his preparation method are extremely exaggerated and somewhat dubioush, and that although the method may be unique in certain respects, and that they may include specific enzymatic processes to enhance the blend in some way (from known bacteria and yeasts), it is not actually introducing any additional of new species above what has been discussed above. This is not something either manufacturer probably wants to broadcast and so they are rather vague about their ingredients and methods, with obtuse and inconsistent references to Soil Based Organisms and Homeostatic Soil Organisms. This is why it has taken me so long to get to the bottom of it. The ingredients of both products are examined in more detail below.

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Nature's Biotics

Nature's Biotics are a marketed in the UK by KIKI Limited. Nature's Biotics are manufactured by Life Science Products, Inc. in the USA. Kiki Health states that the active ingredients of Nature's Biotics (NB) are (incorrect grammar corrected):

- Lactobacillus acidophilus
- Lactobacillus lactis
- Bifidobacterium bifidum
- Bacillus licheniformis
- Bacillus subtilis
'...symbiotized in a SBO (soil based organisms) host medium of mineral trace elements...Nature's Biotics contains at least 61 nutrients:-including naturally occurring phytoplanktons, amino acids, a wide range of vitamins and minerals, an important variety of anti-oxidants, proteolytic enzymes, and an array of nucleic acids. These are vitally important keepers of the code of life which appears to be in charge of growth and continuous cell repair. Natures Biotics also contains SOD (Superoxide Dismutases), highly digestible proteins which include a collection of pigments and enzymes. The product also contains mineral, trace elements, vital starches and essential fatty acids.'

This is a rather vague, and confusing 'marketing' description, but we can safely assume that the SBO Bacillus subtilis is at least definitely included. The implication is that the 'SBO host medium essentially just consists of nutritional metal salts. It is ambiguous but it could be implied that the host medium contains SBOs not listed above. This is unlikely. We know that Garden of Life's Primal Defense only contains one type of SBO, Bacillus subtilis, and that both PD and NB use the same core Smith's preparation method. The actual product description does not make any definite reference to the various other strains of SBO that Smith alludes to, which if they existed, would presumably be a good selling point. There appears to be slightly less exaggeration in their marketing claims that in Garden of Life's.

Kiki Health's product contains 400mg of bacterial ferment. As stated above it also contains phytoplankton. KIKI have confirmed to me that it does not contain humic or fulvic acid. The composition is a dark, black powder, that does not dissolve readily in water, which is unlike Garden of Life's Primal Defense which is a lighter shade and does dissolve readily in water. Nature's Biotics only come in capsule form.

I was muscle tested on Nature's Biotics by his practitioner and were 'neutral'.

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Body Biotics

Life Science Products, Inc. in the USA manufacture a number of products including Body Biotics. This appears to be a similar ferment used in Nature's Biotics, but with a few minor differences. Both products contain Lactobacillis acidophilus, Bifobacterium bifidum, Bacillus licheniformis, Bacillus subtilis and Lactobacillis lactis. However instead of Lactobacillus bulgaricus, Body Biotics uses three strains, Lactobacillus casei, Lactobacillus fermentum and Lactobacillus plantarum.

To summarise, Body Biotics contains the following bacterial strains.

- Lactobacillis acidophilus
- Bifobacterium bifidum
- Bacillus licheniformis
- Bacillus subtilis
- Lactobacillis lactis,
- Lactobacillus casei
- Lactobacillus fermentum
- Lactobacillus plantarum

'Proprietary formula of SBO (Soil Based Organisms) symbiotically blended in a proprietary nutrient-rich host medium of Humic Acids, Fulvic Acids, minerals, and micro-nutrients.'

The Body Biotics web site states that it contains 500mg of ferment per capsule, and uses Humic and Fulvic acids in the ferment. Nature's Biotics uses 400g per capsule and does not contain Humic or Fulvic acids. Body Biotics does not no mention of phytoplankton as an ingredient. Perhaps one could more closely compare Body Biotics to Primal Defense than Nature's Biotics, in terms of exact ingredients - being a chelating/moblising agent as well as a probiotic - although PD only contains Humate.

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Primal Defense

Garden of Life Primal Defense Product Description

Garden of Life describes the Primal Defense product as follows.

'Primal Defense is a natural blend of 12 species of probiotics and Homeostatic Soil Organisms (HSOs), utilizing the Poten-Zyme process and delivered within a whole food matrix.'

Each tablet contains 610mg of the ferment matrix.

It is available in powder form or caplet (tablet) form. Besides the whole food matrix of Barley Grass and Oat Grass, the 'Proprietary HSO Probiotic Blend' is said to contain 7 species of Lactobacillus bacteria, 4 species of Bifidobacteria and 1 species of Bacillus bacteria:

- Lactobacillus plantarum
- Lactobacillus rhamnosus
- Lactobacillus casei
- Lactobacillus brevis
- Lactobacillus salivarius
- Lactobacillus acidophilus
- Lactobacillus paracasei
- Bifidobacterium longum
- Bifidobacterium breve
- Bifidobacterium bifidum
- Bifidobacterium lactis
- Bacillus subtilis

Garden of Life describe the first 11 species as 'unique blend of Lactobacillus and BifidobacteriumÊprobiotics which support regular bowel function and immune health.'

Garden of Life have informed me that there is only one 'Soil-Based Organism' (or HSO) in the final assay in Primal Defense, Bacillus subtilis - the final strain in the above list. Homeostatic Soil Organisms (HSOs) is a trademarked term used by Garden of Life to describe Soil-Based Organisms (SBOs) and the terms can effectively be used interchanegeably.

According to iHerb's web site, Primal Defense is created by 14 probiotic species or their enzymes. In addition to the 12 species listed above, this includes:

- one probiotic yeast strain, Saccharomyces boulardii
- one soil-based bacterial species Bacillus licheniformis

It should be noted that Bacillus licheniformis is NOT a probiotic bacterium by many scientists, but a pathogenic bacterium, as described above!

According to Garden of Life, all 14 probiotic species or their enzymes are used as part of the fermentation process during manufacturing, but only the 12 strains listed in the ingredients are present in the final Primal Defense assay (i.e. the product you buy). Saccharomyces boulardii and Bacillus licheniformis (also classed as HSOs) are therefore not present in the final assay, but directly or indirectly (through their enzymes) contribute to the fermentation process; the enzymes of these species being probably found in the final assay.

One can assume that Nature's Biotics uses the same fermentation process and thus these two strains (Saccharomyces boulardii and Bacillus licheniformis) and their enzymes as part of the manufacturing process, as they are said to use the same Smith's method. What does the fermentation process with Saccharomyces boulardii and Bacillus licheniformis actually achieve if they are not present in the final assay? What benefits do their enzymes actually have on gut flora or otherwise? Presumably these will remain closely guarded secrets.

Garden of Life have described the HSOs in Primal Defense (i.e. Bacillus subtilis) in the follow manner.

- HSOs work from inside the intestines dislodging accumulated decay from the walls and flushing out waste.

- HSOs break down hydrocarbons, a unique ability to split food into its most basic elements allowing almost total absorption through the digestive system. This increases overall nutrition and enhances cellular development.

- HSOs produce specific proteins that act as antigens, encouraging the immune system to manufacture huge pools of uncoded antibodies. This increased production of antibodies may significantly boost the body's ability to ward off disease.

- HSOs are very aggressive against pathological molds, yeasts, fungi, bacteria, parasites and viruses.

- HSOs work in symbiosis with somatic (tissue or organ) cells to metabolize proteins and eliminate toxic waste.

- HSOs stimulate the body to produce natural alpha-interferon, a potent immune system enhancer and powerful virus inhibitor.

- HSOs provide critical Lactoferrin supplementation as a by-product of their metabolism. Lactoferrin is an iron binding protein essential for retrieving iron from foods.

Garden of Life's Primal Defense ULTRA product (PDU) in addition to the bacterial strains found in Primal Defense (but using a different juice matrix), also contains the probiotic yeast strain Saccharomyces boulardii (discussed above) as an actual ingredient in the final assay (i.e. the finished fermented product). The CFU count in PDU is probably lower than in PD, the amount of ferment matrix is less, at 410mg, but it does contain the probiotic yeast strain.

Garden of Life describe Saccharomyces boulardii as 'a hardy probiotic microorganism which nourishes and supports healthy intestinal epithelium lining integrity, the front line in the body's defense system in the gut.' Garden of Life has classed Saccharomyces boulardii as an HSO (Homeostatic Soil Organism), along with the 11 species of Lactobacillus and BifidobacteriumÊprobiotic bacteria.'

The latter statement however contradicts what Garden of Life directly informed me, as stated previously, that Bacillus subtilis is the only HSO present in the final assay. Lactobacillus and Bifidobacterium cannot be classed as HSOs or SBOs as they are of predominantly of milk and human gut origin. This is somewhat misleading and it is likely a marketing person got carried away.

Strictly speaking there is only one HSO/SBO present in PDU, but one could view Saccharomyces boulardii as equivalent in some capacity, even though it is technically of fruit origin.

Saccharomyces boulardii, a yeast strain present in PDU and used in the manufacture of but not actually present in PD, has however not been mentioned by Kiki Health or Life Science Products as a final ingredient in Nature's Biotics. This is not to say that it doesn't contain it. However it is unlikely. However as both Primal Defense and Nature's Biotics are described by some as being equivalent in terms of (SBO?) bacterial strains then one can presume not. One could postulate that the basic Smith's method only involves some of the species present in the ingredients list of Nature's Biotics, and that Poten-Zyme, Garden of Life's fermentation process, includes the Smith's method as well as using other sources of more common probiotic bacteria. This is examined more below.

PDU is available in capsule form only, unlike PD which is available in both powder and caplet forms.

I was muscle tested on PD and PDU during the late summer of 2010. PD tested positively, along with a probiotic Securil, and PDU tested negatively (i.e. the body did not want it).

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Use of Humate

A contact of mine, who has been a candida sufferer of 20 years, asserts that Primal Defense was initially based on three products already available on the market, these being humate, Efficient Microorganisms (EM) Technology and fermented cereal grasses (as stated above).

GOL's Primal Defense contains 285mg of 'Ionic Plant Based Minerals' per capsule, and Primal Defense Ultra contains 290mg of 'Ionic Plant Based Minerals' per capsule. Kiki's Health's NB contains 'SBO (soil based organisms) host medium of mineral trace elements'. These are all actually just Humate.

Humate, specifically Humic Acid and Fulvic Acid, is examined in detail and reviewed on the Detox page. Fulvic and Humic acid both contain a wide variety of DNA/RNA, enzymes and amino acids. Both acids are very powerful mobilising agents of Mercury, as well as being antioxidants, electrolytes, anti-viral and anti-fungal. PD and PDU are therefore probiotics as well as detoxification products. Depending on the method of preparation of the Fulvic acid, they may also be rich in trace mineral elements. It is likely that at least part of Rubin's recovery from illness was not just on account of taking a 'new probiotic' but the fact that that probiotic supplement actually contained Humate, but that diet was another big factor.

Garden of Life have previously chosen not to state that Humate is used in PD and PDU, instead using a marketing spin term to describe this constituent of Primal Defense. Life Science Products are (now) open about the use of Humic and Fulvic acid in their Body Biotics product in comparison. As of 2010, GOL now finally state how many active cells there are in Primal Defense Ultra - 5 billion CFU. Rubin also chose not to educate the public on what rival probiotic product that he actually took (having probably licensed it to market a similar product himself), and what the benefits of Humate, Humic and Fulvic acid are, but market a product capitalising on this lack of knowledge.

If we compare Primal Defense Ultra with Enzymatic Therapy's Complete Metal Cleanse, the former product therefore has 290mg of 'Humate' per capsule whereas the latter product has only 75mg of Humifulvate per capsule. Whilst Complete Metal Cleanse is an excellent product, it is extremely expensive, and Primal Defense Ultra represents better value for money in terms of weight of Humate, as well as being a probiotic. The other way of looking at it is that the chelating capability of PD or PDU is potentially very high, which is not really made clear on the packaging. However, I cannot comment on the source of the Humate in Primal Defense, but it is unlikely to be of a high quality a source as the Humifulvate. Fulvic and Humic acid liquids are of course hugely cheaper than actual Humate or Humifulvate as sold above. Primal Defense therefore does not represent value for money in terms of being a source of Fulvic or Humic acid.

Humate (i.e. PD or PDU) or Humifulvate should however not be used if one has significant amounts of circulating heavy metals in the body, either from Mercury Amalgam filling removal, too heavy use of mobilising agents in the recent past or other reasons, as it will carry that Mercury across the blood-brain barrier into the brain, and perhaps draw more Mercury out of the tissues into the bloodstream, compounding toxicity problems even further. It is slightly irresponsible to market a product with Humate in it without declaring it. Some users of PD have reported 'horrific die off reactions', but in some cases, this is likely not to derive from the probiotic bacterial action but from ingesting too much humate at once. Humate, humic acid or fulvic acid in general should not be used until one has removed/chelated a significant amount of one's Mercury burden from one's system first. Both myself and my contact have experienced this type of Mercury mobilisation headache from using Primal Defense, even at low dosages, at various points in time, and had to resort to taking another type of probiotic supplement until the Mercury issue was dealt with. Mercury Mobilisers are discussed in detail on the Detox Protocols page.

My contact has personally found that Humate is a very powerful detoxifying and chelating agent, and personally believes that it should not be taken unless one's bowels and liver and clear first. Presumably it depends on the quantities taken and of course the amount of heavy metals present in the body at the time of taking it. With a combined product, it is clearly not so easy to 'split up' the constituent ingredients, and to say enjoy the benefits of EM Technology mother cultures and Bacillus subtilis, without having to take the Fulvate in a fixed quantity/ratio. Of course, if one's levels of toxins in the body or liver/bowel function is too poor, and taking 285-290mg of Fulvate in one go (i.e. one caplet/capsule) is too much, one can take small doses of Primal Defense by either using the powder form or breaking a Primal Defense caplet (i.e. tablet) into small chunks. However, this would mean taking less probiotic as well, and in some cases one might want to take no fulate and a very high dosage of EM mother culture and Bacillus subtilis. Then perhaps later on one might want to focus in on a high humate intake for heavy metal detoxification, without necessarily needing so many probiotics as the dysbiosis issues would probably be resolved by then.

This is what happened to my contact, who was not able to tolerate Primal Defense when she first started taking it, presumably on account of very high levels of heavy metals and poor bowel and liver function. However, 6 years later, when she independently discovered the actual ingredients of Primal Defense, starting taking EM mother cultures to target her candida most effectively, and introducing Fulvic acid in the quantities she wanted/required, and targeting her candida/M.E. issues much more effectively. My contact believes that Fulvic and Humic acid solutions are generally better tolerated by Humate, which she considers to be a more powerful detoxifying and chelating agent (in general, clearly source dependent).

I took Primal Defense (and ThreeLac) during the early part of my candida and protozoa eradication programme, and found I could tolerate it quite well; unlike later in my health regime when I had unfortunately mobilised too many heavy metals at once, when I was unable to take PD for a number of months. However, I could not comment on its effectiveness, and noticed no significant change. This is in contrast to when I first started taking a run of the mill Lactobacillus and Bifidobacterium probiotic for the first time, and also when I first took Kombucha and Kefir, all of which had a profound effect on the digestive tract. This is not to say Primal Defense was 'no good' but that it wasn't contributing significantly more than another other regular probiotic at the time of taking it (and this is indeed something very hard to measure). Clearly if I had taken a large enough amount of Primal Defense, I would have experienced a chelation headache, but as it was so expensive (when purchased in the UK at any rate) he only took one caplet a day, and this limit of chelation was never achieved. I have recently (February 2009) taken the new formation of Primal Defense ULTRA, and even inserted some capsules anally, but noticed nothing in particular. However, at this stage, I had no significant dysbiosis issues and had nearly completed my detoxification programme, so any dramatic results would have been unlikely in any case. From the summer of 2010 onwards, I has been using PD once or twice a day, on recommendation from my practitioner.

An associate of mine, who has taken the new formulation of Primal Defense Ultra, has reported good results to date. This person however had relatively severe dysbiosis. I believe that it is probably sensible to try as wide a cross section of probiotic species as possible.

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Source of Probiotic Cultures

My contact asserts that the Homeostatic Soil Organisms (HSOs/SBOs) are not native to the Humate, which is normally mined from ancient geological strata and contains a limited bacterial content. My contact states that the actual source of the HSOs/SBOs in Primal Defense was a commercially available 'mother culture' known as Effective Microorganisms, a.k.a. EM Technology, described above, which is largely derived from dairy sources. EM usually contains a variety of lactic bacteria and beneficial yeasts, but most importantly two photosynthetic bacteria species, Rhodopseudomonas palustris (and Rhodobacter sphaeroides).

My contact asserts that the Garden of Life processed the EM liquid, which can be purchased very cheaply, to produce an equivalent substrate as part of a wider fermentation process, that is thus patentable (i.e. Poten-Zyme), but not as potent or effective. They could not patent the bacteria used in it. Garden of Life describe it as a proprietary fermentation process. However, as stated further above, both Kiki Health and Garden of Life are reputed to use the same basic fermentation method, the Smith method, Garden of Life presumably doing so under licence in some capacity (or perhaps both doing so under licence from Smith), so there must be some minor modifications to make it 'unique' to Garden of Life. I am unable to comment on whether EM is the source of Bacillus subtilis for Kiki Health's NB or not.

The EM photosynthetic bacteria Rhodopseudomonas palustris has never been listed on the ingredients of either product of Garden of Life, so presumably so that the source of the mother culture, i.e. EM, could/can be kept from the public and competitors, who would otherwise spend 5 minutes on google and buy an EM product at a much cheaper price.

My contact states (in 2008) that Primal Defense changed their formulation, still calling the process Poten-Zyme, but using different ingredients, as the ingredients on the jar has changed in the last few years. This probably includes a move away from using EM liquids as a primary raw material according to my contact. I can attest to this change of composition also, as I purchased some Primal Defense caplets in the second half of 2005, and Molasses were included on the ingredients list. They are no longer on the ingredients list. EM liquids use molasses as part of the fermentation process, so this might also imply that EM liquid is no longer used. Garden of Life appear to have changed the formulation slightly in PD and PDU in 2009/2010, most obviously a larger amount of bacterial ferment. It is not clear if any of the sources of ingredients have changed also or not.

Both SCD Food Grade and EM-1 are available in a 1 gallon bottle at roughly the same price as 180 capsules of Primal Defense. My contact believes that the form of freeze dried/processed EM that was present in the old Primal Defense was not as effective as its natural form in EM liquid. Whilst we are not sure what mother culture is now used in PD and PDU, it is unlikely to be as effective, given reports of a decrease in effectiveness of PD since the reformulation. My contact believes that EM-1 liquid is the most effective and also cost effective probiotic on the market.

According to my contact, when Rubin first created Primal Defense, he decided to combine dried humate, a dried form of EM and also fermented barley grass and oat grass from a company called AGM in Australia. This, my contact believes, gave Primal Defense it's good reputation. It was highly regarded at the time as an excellent product.

AGM Grainfields is an Australian manufacturer of fermented cereal grass products, which include liquid products and powder products. They do not contain humate or 'SBOs/HSOs'. My contact has found the powder products to be excellent, their effectiveness really being felt when mixed with a little water and drunk on an empty stomach (for a candida sufferer). And indeed they helped to make Primal Defense a good product too initially.

Garden of Life previously stated about Poten-Zyme, strongly hinting that it was in fact based on AGM products and EM fermentation, in this rather misleading statement: 'Our fermentation, done in the U.S. Southwest and Australia, is not available anywhere else in the world.'

Garden of Life (GOL) no longer use AGM fermented cereal grass cultures and presumably now manufacture their own for commercial reasons, which contains less Lactobacillus species but a few more Bifidobacterium species. Presumably GOL currently prepares its own fermented grass blend as part of the 'Poten-Zyme' fermentation process. As stated above, the ingredients of Primal Defense have changed (for cost cutting reasons?), and organic molasses are no longer listed as an ingredient. One of the ingredients of AGM Grainfields' fermented probiotic blends are organic molasses. Some people have commented according to my contact that they no longer get the same results with Primal Defense as they once did. Is this why? What was once a very good but expensive product is now merely good?

GOL state that Primal Defense is Gluten Free, which is only technically possible if the Barley Grass and Oat Grass used is classed as Gluten Free, which although it technically should be, invariably some gluten from Barley or Wheat grain processing or from stray grains does tend to cause some minor contamination, unless expensive sources of such grasses are used (which is unlikely as it would probably be boasted about on the packaging). It is tempting to think that such bacterial cultures are fermented and grown on cereal grasses and green mixtures, but this is not strictly the case. The cultures are of dairy origin and the dairy component is usually consumed during the fermentation process. Cereal grasses are added. So it is possible that traces of dairy may exist in Primal Defense and other such products.

I believe that Primal Defense is an excellent product, but that it must be used with respect and the knowledge that it does contain Humate. There are other excellent (and often cheaper) probiotic formulations on the market also, so it pays to be educated and informed. A number of manufacturers use third parties to supply components or constituent ingredients for their products, as they cannot produce all of them themselves. This is true for a variety of industries. The question is whether those components are of a high grade, whether it is appropriate not to reveal the components or constituents of one's end product (a highly annoying, anti-competitive and paranoid practice), and whether the end product is providing good value for money or not.

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Jordan Rubin's own use of SBOs and Humate

Let us examine the background of Garden of Life the company. Jordan Rubin is the author of The Maker's Diet and co-owner of Garden of Life.

On his web site, he states that he recovered from critical illness partially through diet and partially by taking a soil-based probiotic:

'Soon after he left the hospital Jordan's father stumbled onto an eccentric nutritionist living in California.ÊHis diet program consisted of foods that were consumed by our ancestors. Raw, organically grown whole grains, fruits and vegetables. Fermented foods, especially fermented dairy (life kefir).ÊGrass fed beef and poultry. Jordan even moved out to California to be closer to his new diet mentor. As JordanÕs health slowly improved he also began taking a probiotic that contained soil based organisms that used to be plentiful in our diets. While Jordan had tried probiotics previously, with little success, he was intrigued by the new probiotic.'

The implication is that this 'new probiotic' ('a probiotic that contained soil based organisms') is the same as Primal Defense, the product that his company Garden of Life actually markets and sells, and offers to you the consumer. Of course, at the time of his recovery, he had not yet devised and marketed the product. So of course it was not actually Primal Defense. But the implication is that Primal Defense is of the same potency if not more potent that the 'new probiotic' that Rubin actually used himself all those years ago, presumably adding other ingredients added, and with further proprietary enhancements. So what actually was the source of this product that Rubin actually tried himself? Was it Body Biotics that he actually used? According to rumour, it most likely was.

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Kombucha, Kefir, Mutaflor (E.coli) Yoghurt, Sauerkraut Juice - Live, Home-Fermented Drinks:

Those of you experienced with fermentation will know that it is possible to ferment a number of types of vegetables and also dairy (i.e. yoghurt and cheese), to product pre-digested probiotic foods and drinks. These tend to be fermented with Lactobacillus acidophilus.

The easiest vegetable to ferment is probably white cabbage, which, like most fresh vegetables, contains natural acidophilus bacteria, so it essentially ferments itself and there is no need to add a bacterial culture to it. White cabbage juice or fermented cabbage (sauerkraut) is also soothing on the intestinal lining. The number of active lactobacterium cells in live natural yoghurt is quite low, for example, compared with live kefir or fermented cabbage juice, although plain natural live yoghurt can be a beneficial part of one's diet.

There are other types of fermented drinks that are of particular note. These use special types of bacterial cultures. Four are mentioned here, Kefir, Kombucha, Mutaflor (E.coli) Yoghurt and Matsoni, but there are others.

Kefir can be made with cow's milk, goat's milk, soy milk, almond milk. It can also be made with water with added sugar. Kefir is a different kind of beneficial bacteria culture to those used in natural yoghurt. In many ways it is more beneficial for your health. Kefir contains acidophilus but also a number of other useful probiotic bacteria; 40 strains in total! It is also rich in folic acid.

Mutaflor is the brand name for the species of E.coli strain Nissle 1917 manufactured by German firm Ardeypharm. It is a beneficial species of E.coli that can be purchased both in capsule or suspension form. The suspension form can be used to create a yoghurt from soy milk or dairy milk. E.coli produce folic acid, Co-Enzyme Q10, vitamin K2 and the amino acids Tyrosine, Phenylalanine and Tryptophan.

Kombucha is a type of bacterial and yeast culture that is used to ferment tea, feeding on added sugar, which produces a number of useful B-vitamins, as well as beneficial organic acids including Glucuronic acid, which is helpful for healthy liver function. One can also purchase Kombucha extract/concentrate or capsules. These contain the bacterial culture and a concentrate of the nutrients from the Kombucha tea. Extracts vary in strength from 5:1 to 25:1. It is best to use an extract that does not contain alcohol. Kombucha is probably better to assist in detoxifying the body (on account of its organic acid content), whereas Kefir is probably the better probiotic.

Please see the RECIPES page for more information on the composition of these three above probiotic fermented drinks, and how to make them at home yourself.

Matsoni, a.k.a. Caspian Sea Yoghurt, is a type of yoghurt culture used with cow's milk, which originate from Eastern Europe/The Balkans. It contains the bacterial strains:

- Lactococcus lactis subsp. cremoris
- Acetobacter orientalis
- Gluconobacter sp.

Viili, a.k.a. Finnish curd milk, is a type of cultured dairy milk product from Finland. It contains the bacterial strains:

- Lactococcus lactis subspecies cremoris
- Lactococcus lactis subspecies lactis biovar. diacetylactis
- Leuconostoc mesenteroides subspecies cremoris
- Geotrichum candidum

Ginger Beer is a fermented drink made from ginger beer plant, brown sugar, citric acid and water.

Please note that fermented foods and drinks as above do not contain Bifidobacterium, and are mainly Lacto bacteria-based. As such, although fermented products offer many digestive and health benefits, if you are specifically deficient in Bifidobacterium, one of the major bacterial types of the small intestine, then ways to boost these numbers would include prebiotics and also direct supplementation with Bifidobacteria (enterically coated may be optimal).

There may be issues with kefir and kombucha regarding their live yeast content, for those with elevated free glutamate levels and for those with existing yeast (Saccharomyces cerevisiae) overgrowth, as discussed in the Yeast section below.

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Commercial Probiotics Drinks:

Lax laws mean that even though a probiotic supplement states its bacterial content, there is no legal requirement to actually meet that content in each serving, and some batches of certain brands of probiotics have been found to contain no bacteria whatsoever! Clearly, purchasing from a reputable brand is essential. Please see the recipes page for details about fermented cabbage juice, which is clearly a cheaper way to take probiotic bacteria. Fermented cabbage juice may also soothe and heal the GI lining and may also help to reduce inflammation caused by conditions such as IBS/IBD. Probiotics are probably best taken before a meal (e.g. 15-30 mins prior), ideally together with a prebiotic.

Supermarkets sell small probiotic drinks such as Yakult or Danone Actimel. Yakult contains 6.5 billion cells of lactobacteria, which is the average for reasonable probiotic supplements. However, compare this with a probiotic such as Custom Probiotics CP-1 which contains 50 billion cells per capsule, where the dosage cost is around the same for a bottle or capsule. Yakult hardly therefore offers value for money. In addition, Yakult contains sugar, glucose-fructose syrup. Yakult Light also contains dextrin and aspartame, which is hardly very good for you (see toxicity page for more information on aspartame). Yakult ingredients, including number of active bacterial cells, can be seen at the link below. The number of cells is not stated on the product packaging however. Danone Actimel contains sugar and dextrose. Danone Actimel does not state the number of active bacterial cells either on their web site or their product labels.

Live yoghurt uses the milk's natural sugars to feed the lactobacteria. Non-milk based probiotic drinks (i.e. water-based kefir) can be made with just the bacteria, water and sugar, but in the case of using milk, no sugar should be necessary. Milk-based kefir for example is much preferable over water-based kefir. I do not personally recommend probiotic drinks that contain sugar/sucrose or any artificial sweetners. This is because if you have dybiosis, drinking or eating anything with refined sugar in it is the last thing you want to do, as it will feed the bad bacteria.

The reason drinks like Yakult sell is because of heavy television advertising and also the fact that the general public isn't familiar with probiotic supplements and can easily find a product like Yakult in the supermarket. Most probiotic drinks, including Yakult and Danone Actimel, have ignored recommendations by the UN's Food and Agriculture Organisation and World Health Organisation to print the number of live bacteria each bottle contains. Advertising is as usual grossly exaggerating any beneficial qualities the products might have, and in 2006, the UK's Advertising Standards Agency upheld a complaint about an advertisement for Danone's Actimel probiotic yoghurt that featured a child licking a bus window, on the grounds that it implied the product could help prevent children from catching bacterial infections.

Danone also has a live yoghurt product called Activia. The regular Activia contains sugar, and the Fat Free version contains aspartame.

If one is going to consume a bio-live yoghurt, it is cheaper and healthier to just eat plain bio-live natural yoghurt (with no fruit, flavourings, sugar or additives in it). If you rely on a yoghurt for your fruit intake, you are clearly not eating enough fruit! The fruit in the yoghurt is hardly fresh in any case. Natural yoghurt is very versitile and can be consumed as a 'dessert' or with one's meal as a condiment or side dish (e.g. with meat or fish, or with a spicy food like curried vegetables or Mexican chilli - Raitha is sometimes consumed with Indian food, it is a natural yoghurt with cucumber and is very refreshing - you could try making your own.)

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Although manufacturers often state a maximum recommended dosage for probiotics, in reality, there isn't really one.

There are not many conclusive scientific studies regarding the health benefits of probiotic supplements. It is clear that noticeable benefits are more likely in those with impaired digestive systems, for example irritable bowel syndrome etc. or those that have recently taken antibiotics, or those that are taking them for the first time, than those with already good digestive health and a healthy bacterial balance. The studies that there are do not take into account the diet of participants, which is a major factor in the success of the probiotics. For example, even though you are consuming additional cells of beneficial bacteria, if you are eating large amounts of simple carbohydrates, sugar, alcohol, wheat etc. then you are providing so much food to the bad bacteria in your colon, that the addition of a small number of good bacteria makes very little difference. Probiotics are marketed in a way that implies that you do not need to have a healthy diet, but as long as you keep buying probiotics, then you will have health benefits and improved health. Such a notion is clearly short sighted. It is debatable whether any conclusive scientific study can be carried out, putting sufficient numbers of people (who have the same digestive starting point) on the same diet and given the same brand of probiotics in the same dosage. In reality there are too many variables.

It could be argued that the bacterial balance in one's gut takes a lifetime to build up properly, and that one should not meddle with it with probiotic supplements. However, this logic is flawed, as by eating refined sugar, processed simple carbohydrates and having antibiotics, one has already radically meddled (negatively) with this bacterial balance. If one had had a perfect diet from birth and never had any antibiotics, then perhaps this might be a valid argument.

As stated above, the most noticeable benefits with probiotics are observed at the start of one's programme, or perhaps after a case of food poisoning, and use of antibiotics or colonic irrigation. However, just because it is not noticeable does not mean that it is not good practice of course. However, the financial focus on probiotics should clearly be aimed more towards the beginning of one's programme. Whilst there is no harm in taking hugh amounts of probiotics later on in one's treatment programme, if the floral balance in the gut is relatively good, taking more probiotics is not going to address one's other root causes to CFS which may include toxicity, hormonal imbalance/deficiency, poor mitochondrial function etc. Other types of treatment are required to address these of course, so one should not solely focus on probiotics.

The first time I took formal probiotic supplements, I had a moderate case of parasite (protozoa) overgrowth, candida overgrowth and bad bacterial overgrowth. Over the first few days of taking probiotics (swallowing a large number of capsules during the day), I felt an amazing high and sense of elation shortly after taking the capsules. This was my body's way of telling me that this was exactly what was wanted at that point in time. BlackSpy was not counting on that kind of effect so a purely psychological explanation for this is unlikely. The first time I took Kefir and Kombucha cultures, I felt a total loss of appropriate as his gut adjusted to the introduction of new species, but after a day or two it felt fine and better than before.

It is my belief and experience that one should probably take as many probiotic bacteria as one is comfortable with initially (assuming no adverse die off reactions etc. at higher doses) and taper this off slightly after 6-12 months (unless one is getting plenty of probiotic bacteria from various foods and nutritional supplements anyway (e.g. green superfood mixtures etc.) It is probably wise to take as wide a variety of probiotic bacterial strains as one possibly can, rather than merely focussing on one or two strains, as the natural floral balance of the gut is highly diverse. This could include a variety of Lactobacillus and Bifidobacterium species as well as SBOs, kefir bacteria and kombucha bacteria, etc. You could even keep a 'probiotic diary' or list to document which strains you have taken, so when you come across a probiotic supplement or type of fermented food/drink, you can see whether you have taken that particular strain or strains before. This is of course optional.

Recipes for fermented white cabbage juice and kefir can be found on the recipes page.

Once you have eliminated your candida, parasites and/or bad bacteria (see remainder of this page), and you are able to tolerate green superfood mixtures in moderation, you may wish to rely on these for your probiotic requirements rather buying a dedicated probiotic. In this way, you will be providing yourself with a rich source of nutrition as well as a source of probiotic bacterial strains. One example is Garden of Life's Perfect Food. Or perhaps just ferment your own, e.g. kefir or kombucha.

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A prebiotic is a type of soluble dietary fibre that is an ideal food source for good bacteria, particularly Bifidobacterium; which is not readily broken down by the stomach or small intestine, and which is carried into the bowel where it can be fermented by the good bacteria, allowing them to multiply more quickly. Prebiotics are types of sugars that are sweet to the taste but are not metabolised like sucrose and other digestible sugars and therefore have no calorific value (to humans). Most are types of glycans, either polysaccharides or oligosaccharides, although not all glycans are prebiotics. Prebiotics are therefore sometimes used as sweeteners (food additives). The vast majority of true prebiotic fibres tend to be non-thickening, with the notable exceptions of most vegetable gums, and Glucomannan, which are used as thickeners in food, supplements and medicines. All prebiotic fibres are thickening to some minor degree as a minimum.

Bifidobacteria possess a unique Fructose-6-Phosphate Phosphoketolase pathway used to ferment carbohydrates, including oligoaccharides (e.g. FOS and GOS).

Prebiotics selectively encourage the growth of non-gas producing, probiotic bacteria at the expense of gas producing bacteria. This may help to reduce the amount of bloating in the intestines by gas-producig bacteria. In addition, some of the more thickening prebiotic fibre supplements can also help to directly slow down gas-producing bacterial fermentation in the digestive tract, on account of their glycaemic index lowering fibre properties, thus decreasing gas and bloating in the abdomen. However, whilst prebiotics stimulate the growth of friendly bacterial species, mainy Bifidobacteria species, but they are also fermented by neutral bacteria and pathogenic bacteria, to a lesser extent. In certain instances, prebiotic supplements can actually cause gas and bloating.

'All inulin-type prebiotics, including FOS, are generally thought to stimulate the growth of Bifidobacteria species. Bifidobacteria are considered as "Friendly" bacteria. This effect has not been uniformly found in all studies, both for Bifidobacteria and other gut organisms. FOS are also fermented by numerous bacterial species in the intestine, including Klebsiella, E. coli [both good and bad strains] and many Clostridium species, which are considered less-friendly bacteria in the gut. These species are mainly responsible for the gas formation (hydrogen and carbon dioxide), which results after ingestion of FOS. Most people can eat 5-10 gram of FOS without gaseous discomfort, whereas others have problems with 1 gram. The estimated optimal dose for adults is around 5-10 gram/day'

FOS also feed yeast species as much as they feed Acidophilus and Bifido species, so have the potential to exacerbate yeast or Candida infection/overgrowth and feed certain pathogenic bacterial strains such as Klebsiella which is thought to cause gut permeability (LGS). The Specific Carbohydrate Diet (SCD), a diet aimed at calming down intestinal inflammation, where there is dysbiosis worsening the condition, strictly forbids the use of prebiotic supplements, especially FOS for this reason. Many IBS sufferers find gum-based prebiotics helpful in inhibiting their IBS symptoms without the problems of wind with other prebiotics like FOS, but in cases where there is significant dysbiosis, they may elect to follow an SCD regime. The SCD diet only really seems to work when there is not so much dysbiosis in the upper section of the small intestine, as if tropical fruits and honey may cause severe bloating immediately afterwards if there are significant numbers of gas-producing bacteria in the upper small intestine (close to the stomach). In such cases one may want to consider antimicrobial treatments before eating any readily digestible foods like fruit etc.

So do prebiotics cause or inhibit wind and bloating? Clearly they encourage the multiplication of non-gas producing, probiotic bacteria, which inhibit the multiplication of gas-producing, non-beneficial species. However, that is offset by the lesser (?) fermentation of prebiotics by these gas-producing species. It depends on the amount of probiotic bacterial species in the digestive tract, the relative ease which which gas-producing bacteria can ferment that particular type of prebiotic fibre, the types of gas-producing bacteria in the GI tract, the presence of yeasts in the GI tract, and the dosage of prebiotics you are taking. Simpler prebiotic sugars may be easier for commensal bacteria to ferment than more complex sugars, e.g. short-chain FOS may cause more bloating than Inulin for example. You may need to experiment with different prebiotics, dosages and combinations of prebiotics. Some manufacturers state that there may be some symptoms of bloating and wind initially, which should disappear after a few days. In general terms, if you take a smaller dosage, then you can build up your probiotic flora gradually over time, whereupon you can likely increase the dosage if required. Taking too high a dosage will result in there being more fibre than the number of probiotic bacteria you have in your GI tract can digest, leaving excess over to be fermented by gas-producing bacteria. Clearly both types of fermentation go on in parallel. It is thus sensible to consume only as much as does not result in excessive wind. I have found this to be true more for FOS and Acacia Fibre than for GOS, which causes significantly less wind, if any, at reasonable doses. A standard adult dosage for GOS or FOS is 3-5g between 1 and 3 times a day. If you are experiencing bloating and wind with a type of prebiotic even after some time, then it is probably best to discontinue it.

Are prebiotics better than probiotics? Yes and no. Probiotic supplements are useful for targetting specific types of bacteria which may be deficient in certain parts of the GI tract. However, if the diet is not rich enough in vegetables (soluble and insoluble fibre), then taking probiotics may not be so effective, as there are insufficient food sources for the probiotic bacteria to multiply effecively. In severe cases of probiotic species deficiency, e.g. bifidobacteria, even if one's diet is rich in fibre and vegetables, it may be necessary to take a prebiotic supplement regularly to encourage the probiotic species to multiply. In such cases, prebiotics may be more effective than probiotics. Of course, taking both together is optimal.

In my experience, prebiotics work very well, unless there is a significant state of dysbiosis or commensal bacterial overgrowth, in which case prebiotics may work well up to a certain point, then achieve very little or actually sustain the dysbiosis until the unwanted bacteria are killed off with antimicrobial treatments, afterwhich point the prebiotics can work more effectively again to boost probiotic bacterial numbers. The same also applies to probiotic supplementation in my experience, species dependent of course (E.coli numbers seem to be easier to increase with probiotic supplementation than Lactobacillus or Bifidobacteria in the presence of dysbiosis).

Prebiotics supplements are generally taken together with probiotics supplements 30 minutes before a meal, but it is not that critical. They can be sprinkled into one's food also or taken in a drink with a meal. Excessive amounts may cause diarrhea (being a soluble fibre - too much fibre may cause too rapid a transit through the GI tract meaning less digestion of the chyme/stool, less fluid absorption and thus more wind as there is more undigested food for the bad bacteria to ferment).

Please note that taking prebiotic and probiotic supplements may increase one's requirement for water and one's thirst, and it is good practice to drink slightly more water than usual when consuming prebiotics and probiotics. In some individuals, if to large a dose of probiotics are consumed late in the evening, or if prebiotics are taken together with probiotic bacteria late in the evening, this may result in an excessive thirst that may prevent a person from sleeping properly.

Examples of 'true' prebiotic fibres include:

  • Oligosaccharides

    • Fructo-oligosaccharides (FOS)

    • Fructo-oligosaccharides can be taken in supplement form (found in many probiotic supplements). It is also found naturally occurring in the following foods. The percentage prebiotic fibre content by weight is quoted in brackets for the food in its raw form or otherwise stated. Barley, Wheat and Tomatoes may not be suitable for everyone.

      • Chicory root (64.6%) - less so in Chicory leaves
      • Jerusalem Artichoke (31.5%) - a root crop or tuber - not to be confused with true Artichoke, a green thistle
      • Jicama (a.k.a. Yam or Mexican Turnip)
      • Yacon tuber (a.k.a. Peruvian Ground Apple)
      • Dandelion Greens (24.3%)
      • Garlic (17.5%)
      • Leeks (11.7%)
      • Onion (8.6% raw vs 5% cooked)
      • Asparagus (5%))
      • Peas
      • Soy beans
      • Tomatoes
      • Barley
      • Wheat bran (5% in bran)
      • Whole wheat flour - cooked (4.8%)
      • Banana (1%)
      • Burdock root
      • Elecampane root

      Inulin is a long-chain molecular form of FOS which is more capable of reaching the colon intact, compared with the normal, shorter-chain FOS. Inulin is beige in colour compared with FOS which is white in colour. Those food sources above that are rich in Inulin are marked with a star (''). Inulin supplements are usually created from Jerusalem Artichoke (not to be confused with Artichoke) or Chicory Root extracts. e.g. Now Food's Inulin or Xymogen's OptiFiberSCFA.

    • Galacto-Oligosaccharides (GOS)

    • Galacto-Oligosaccharides, a.k.a. Oligogalactosyllactose, Oligolactose or Transgalacto-oligosaccharides (TOS) - are a type of largely indigestible prebiotic sugar found naturally occurring in human mother's milk. Manufactured GOS is prepared through enzymatic conversion of Lactose. It is used as an additive in some infant formulas. It reaches the colon virtually intact. Studies have shown that it is more strongly bifidogenic than other oligosaccharides. It is reputed to increase absorption of Calcium in the GI tract. FOS is thought to be the primary food source for most Bifidobacteria except for Bifidobacterium infantis which primary feeds on GOS (when available). Two GOS GOS supplements I have found include Bimuno (powder sachets) and Jarrow Formulas' Yum-Yum GOS Syrup. Both products contain approximately 3g of GOS per 5g serving, the other 2g being sugars - lactose (perhaps not great for those with lactose intolerance) and glucose syrup. Bimuno contains additionally Gum Arabic (itself a prebiotic) and the acidity regulator Trisodium Citrate. The exact values per serving are: Bimuno in a 5.5g serving - 0.1g Protein, 5.2g carbohydrates, of which 1.9g sugars (19kcal), 0.6g dietary fibre and 2.8g Galacto-oligosaccharides; Yum Yum Syrup in a 5g serving, there is 5g of carbohydrates, of which 2g sugars (8kcal), and 3g is dietary fibre (GOS). Direct comparison is still difficult! However it would seem that the Jarrow product contains less digestible calorific sugar.
  • Resistant Dextrins

    • Wheat Dextrin, e.g. Nutriose - manufactured by the French company Roquette, marketed by Novartis - 4.3kcal/g - e.g. in Benefiber or Jarrow Formulas' Fiber Perfect)

    • Resistant Maltodetxtrin (e.g. Fibersol-2) - 90% minimum content. 1.6kcal/g. e.g. in Jarrow Formulas Fermented Soy Essence and some other protein formulas.

    • Polydextrose - synthesised from detxrose plus 10% sorbitol and 1% citric acid. E-Number is E1200. 1kcal/gram. e.g. in Xymogen OptiFiber SCFA

    • Cyclodextrins, e.g. alpha- and beta-cyclodextrins. These are oligosaccharide-based dextrin chains that form a loop or circle. The circular molecular structure allows them to trap toxic molecules such as heavy metals or tricholorethane, and also attach to fat molecules. Alpha-Cyclodextrin is thus considered to be weight loss supplement. Cyclodextrins are also used as additives to liquids to prevent unpleasant odours. Cyclodextrins are also fermentable prebiotic sugar fibres. Beta-cyclodextrin is found in FiveLac and ThreeLac, in small amounts.

  • Beta-glucan - polysaccharide sugar extracted from mushrooms, fungi, the cell wall of baker's yeast, and cereal bran such as barley and oats - also an immune system booster for white blood cells. Beta-glucan supplements are a more concentrated form than in simply eating oat bran etc. I personally ate a bowl of oat bran every day for a long time and my bifido levels were still not detectable in my stool, at one point, so I would not rely simply on eating oat bran etc., although it can still be a useful source of soluble fibre and slow-release carbohydrates.

  • Vegetable gums, containing polysaccharides, particularly Acacia fibre, Galactomannan-based gums and Glucomannan

    • Acacia Fibre

    • Acacia Fibre is a type of galactose-based, relatively non-thickening, soluble fibre extracted from the gum of the Acacia tree of Senegal in Africa - often referred to as Gum Arabic or Acacia gum. Acacia gum (E number E414) consists of a complex mixture of polysaccharides and glycoproteins (oligosaccharide chains bonded to polypeptide side chains). Acacia fibre is a pure fibre with no calorific (sugaring) content for humans. It contains minor traces of 3 simple sugars, Galactose, Arabinose and Rhamnose. Acacia fibre powder is generally dervied from Acacia senegal (a.k.a. Gum Acacia or Gum Arabic Tree) and/or Acacia seyal (Red Acacia). Now Foods' Acacia Fiber contains both types and is brown is colour. Heather van Vorous, of, the marketer of Heather's Tummy Fiber, believes that Acacia seyal is inferior. Heather's Tummy Fiber consists of pure organic Acacia senegal and is white in colour. Acacia fibre is generally regarded as a superior option to FOS and tends to cause less bloating and diarrhea, although this is not always the case. It may be because it forms a gel in the intestines thus slowing down the rate of fermentation by good and bad bacteria, thus the latter producing less wind. Acacia fibre can be taken with food (if not too dry) or a glass of water.One may want to try perhaps half a teaspoon or so at a time. Heather Van Vorous suggests a different regime but the application is different and not just as a prebiotic. Acacia Fibre is considered to assist in the treatment for IBS. It is also found as an additive to some dietary supplements, whey protein milkshake powders and fibre supplements (as a sweetener). Gum arabic or Acacia gum is used as thickener, stabiliser, glazing agent and emulsifier in food products.
    • Galactomannan

    • Galactomannan is a water-soluble polysaccharide prebiotic fibre, and is thickening in nature. It is found in a number of vegetable gums and also Fenugreek seed, Tara gum, Carob gum, and also in Fenugreek (seed extract) fibre. The mannose to galactose ratio in each source of Galactomannan varies, with Carob gum having the most mannose and Fenugreek having the least per Galactomannan molecule. Galactomannan is often added to food products as a stabiliser.

      • Fenugreek Fibre

      • Fenugreek Fibre is an extract from the Fenugreek plant (seed), a soluble, taseless fibre, mainly consisting of Galactomannan (with 1:1 ratio of galactose to mannose). Best taken 5-10 minutes before a meal with 8+oz of water (1-2g of Fenugreek fibre), it forms a gel in the stomach which binds to sugar and fat, allowing for slower release of glucose into the bloodstream during the course of digestion, supporting healthy blood sugar levels. One example of a Fenugreek fibre product is FenuLife by Beyond A Century (BAC). Another is Xymogen's OptiFibrerSCFA, which also contains a number of other fibre sources. Fenugreek is also demulcent, containing mucilage, which may help to dissolve mucoid plaque and sooth the GI Tract.
      • Guar gum is the ground endosperm of the bean from the Indian Guar plant. It is often used as a thickener in baking.

      • Tara gum

      • Carob gum

    • Glucomannan

    • Glucomannan is a water-soluble polysaccharide prebiotic fibre, derived from the roots or corm of the Konjac plant. It is able to absorb 200 times it's weight in water and is extremely thickening. It is similar to mucilage globules. It help to loosen and remove fat from the walls of the colon. It is used for various conditions such as obesity as an appetite suppressant, IBS, constipation, high cholesterol and Type 2 Diabetes. Glucomannan supplements are extremely thickening and must be taken with sufficient water or they can cause severe side effects. It has been banned from some pharmaceutical products in Australia, probably because some patients were taking their medication without knowing to take sufficient water. I believe the optimal dosage is 1g or less, not more as often suggested by manufacturers. Dosage recommendations are generally 2g for use with Diabetes, to consume 20-30 minutes before a meal, with water, to reduce the Glycemic index of the meal, or 1g on an empty stomach 1 hour before a meal to relieve constipation. It is sometimes used to remove mucoid plaque although it may not be the most effective remedy for this.

Examples of bifidogenic compounds (i.e. non-sugars/fibres which are still beneficial bifidobacteria growth factors - prebiotic in many senses) include:

  • Propionic acid (e.g. produced by Propionibacteria freudenreichii in Emmental cheese or extract in Securil probiotic supplement)

  • Metabolin - Metabolites of Propionibacterium sherman - ideal food source for Propionibacteria (e.g. in Jarrow Formulas' Fiber Perfect) - which in turn produce propionic acid, a bifidogenic.

  • Gluconic acid (e.g. from royal jelly, honey or kombucha)

  • Pantethine (Active Vitamin B5) - growth factor for Lactobacillus bulgaricus and Bifidobacteria (according to Dr Atkins)

  • Polyphenols - in green tea and ginseng (tea)

  • Yeast extract - contains nutrients for bacterial culture media - but also high in Glutamate

There are other non-digestible sugars (soluble dietary fibre) besides FOS, TGOS and Acacia Fibre, that are prebiotic in nature and can assist with bowel movements on account of their soluble fibre content. These are discussed on the Mucoid Plaque page.

Not all forms of fibre are resistant to digestion by our bodies and readily fermentable by probiotic bacteria in the small and large intestine. However, a healthy fibre intake, from vegetable sources, is essential for a healthy flora balance, bowel movement regularity and to prevent mucoid plaque build up. Some less fermentable fibre sources (i.e. less prebiotic fibres), which are high in mucilage, are better suited for removing mucoid plaque, as their scraping and grinding action continues unabated in the colon.

Examples of fibre compounds with a partial or low fermentability include:

  • Cellulose - a polysaccharide - one of the most abundant fibres/sugars in aerial plant parts.

  • Hemicellulose - a polysaccharide

  • Lignans - a phytoestrogen - found in high concentrations in Flax seeds and Sesame seeds, but also in cereals (especially Rye), Pumpkin seeds, Soy beans and broccoli.

  • Plant waxes

  • Resistant starches

  • Mucilage

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Anti-microbial supplements:

Compounds described below in the treatment of fungal overgrowth, such as Candida Albicans, are also effective against bad bacterial overgrowth and will actively kill off bad bacteria. Examples include Cat's Claw and Pau D'Arco, which ard particularly good at eliminating mycoplasma and other bacterial infections. These are taken on an empty stomach, ideally as far away from meals as possible. Usually between 2 and 3 times a day. Please also the section below on the Anti-Candida Diet.

If it is necessary to take anti-microbial supplements to kill off harmful systematic or localised bacterial overgrowth (which is something your practitioner should help you determine), then make sure also that you are taking a probiotic and that it is taken just before or with a meal, and at least 2 hours away from any anti-microbial herb or supplement described above. Good anti-microbial herbs and supplements will mainly target the bad bacteria and candida in the body, but they will inevitably kill off some of your beneficial bacteria in your small and large intestine. This is why probiotic supplementation is important to maintain the good bacterial levels, whilst targetting harmful microorganisms and reducing their numbers.

The laboratory Doctor's Data uses the following compounds to treat pathogenic bacterial overgrowth, which differ slightly from those compounds they usually suggest to use to treat yeast overgrowth. These are compounds that are generally found to work for treating bacterial infections, and a pathogenic bacterial, if present in the stool, is cultured from one's stool sample and tested with these compounds to determine which particular compounds the bacterial strain in your GI tract is sensitive to (i.e. which can be used to kill them) and which they are resistant to. This is in broad terms relatively useful, but it should be remembered that bacterial susceptibilities can change with time and with treatment with a particular compound, so in a sense it provides us with a snapshot. In addition, the list of compounds is by no means exhaustive or complete, but represents a selection from the subset which Doctor's Data happen to be using. There are many herbs that are equally as good or better than those in this list. Natural agents tested - Berberine, Black Walnut, Caprylic Acid, Cat's Claw, Citrus Seed Extract, Goldenseal, Oregano and Uva Ursi. Prescriptive (synthetic) agents tested - Amoxicillin, Ampicillin, Augmentin, Ciprofloxacin and Trimeth-sulpha. At the time of testing, my Enterobacter cloacae overgrowth was sensitive only to Caprylic Acid, Citrus Seed Extract, Uva Ursi, Ciprofloxacin and Trimeth-sulpha (of the agents tested in the laboratory). I am not recommending the use of prescriptive (synthetic agents) except in extreme circumstances or as a last resort. More information about the Doctor's Data Stool Analysis test can be found on the Identification page.

Please note that whilst certain kinds of antibiotics, such as Flagyl or Doxycycline (or other antibiotic recommended by The Marshall Protocol) may well be effective in the short term in eliminating bad bacterial overgrowth or protozoan parasite overgrowth, they may potentially clog up the cell membranes and also deplete the body's natural probiotic defences, which make up the majority of the body's immune system.

Certain herbs contain chemical compounds such as quinones, hydroquinones and hydroxyquinones. These are a plant's natural antibiotics. Hydroquinone is also natural antioxidant. Herbs such as bearberry have been used to fight off urinary tract infections.

A patented, proprietary blend (marketed as Cantron and Protocel) including Tetrahydroxyquinone is used to treat cancer, a variety of viral infections including AIDS, as well as CFS. It's ingredients are tetrahydroxyquinone, rhodizonic acid, sodium, potassium, croconic acid, catechol (or pyrocatechol), triquinoyl, leuconic acid, inositol, and copper. It is claimed to be one of the most potent antioxidant formulas.

It should be noted that if one has a localised bacterial infection, for example, that have penetrated a hair follicle, that form acne or boils, that has not yet penetrated the blood stream. This is examined in the section below entitled External Application of Oils

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Yeasts, fungus and moulds:
Candida albicans:

Above are photographs of Candida albicans. Candida is a type of yeast, mould or fungus that is present all around us, but that is provided a very attractive breeding environment in those with a poor digestive system. There are a large number of tupes of Candida strain, but the generally most common variety that affects human digestive health and the immune system is Candida albicans. Other signficant strains of Candida include Candida parapsilosis, Candida tropicalis, Candida krusei, Candida glabrata, Candida guilliermondii, Candida rugosa, Candida lusitaniae and Candida dubliniensis.

A photograph of a budding Candida albicans cell is shown at the link below.

More Candida pictures can be found at the link below.

Fungal spores cover every exposed surface except for certain climates with extreme temperatures. These fungal spores are dormant and bud when the conditions are right, e.g. moisture. This is where mould 'comes from' when food is left refrigerated for too long and 'goes off'.

Under normal circumstances, Candida species entering the body through food and drink are destroyed in the stomach by the acidic pH. However Candida species may survive the body's defense of stomach acidity, on account of its low stomach acid content (in those afflicted individuals), and pass through and settle in the large or small intestine. Here it is warm, pH neutral and low in oxygen. They feed on all the simple carbohydrates that drop down to them from the stomach, and multiply at an alarming rate. They tend to burrow into the walls of the intestine, and release spores into the intestine and also into the blood stream. The highest concentration of candida is usually found in the colon (large intestine), but can also be found in the small intestine and the blood stream as a whole (spreading to certain organs etc.). In the GI tract, candida will also tend to burrow into the mucoid plaque layer and also embed themselves in the GI lining, as well as being present in the food/faeces continually. Clearly, if large amounts of mucoid plaque are present, then removing it will also help to remove/access candida effectively for elimination.

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Biochemical Markers for Candida:

There are three main biochemical markers formed by yeast/fungal organisms, usually but not necessarily in the gut. These are arabinose, beta-ketoglutaric acid and citramalic acid. Citramalate can also be formed by anaerobic bacteria.

Arabinose is an aldopentose (monosaccharide) sugar found in several fruits, e.g. apples, cherries, grapes, plums, and of course in juices made from these fruits. Elevated levels in urine above the reference range may indicate a high dietary intake of these fruits. However, arabinitol (which is converted into arabinose) has also been documented to be produced by Candida. When found in elevated levels in the bodily tissues, Arabinose can link with lysine and arginine, which may theoretically block some binding sites for coenzyme Pyridoxal-5-Phosphate (P5P - active B6), Biotin or Lipoic Acid. at the lysyl residue in apoenzyme proteins. This would impair enzymatic processees, such as the transamination of amino acids (in spite of a 'normal' intake of vitamin B6). So a high urine level of arabinose, without an associated dietary intake of the above fruits, strongly suggests the presence of Candida overgrowth.

Arabinose, beta-ketoglutaric acid and citramalic acid levels can be identified in a urine test such as the Optimal Nutrition Evaluation (ONE) by Genova Diagnostics. Please see the Identification page for more information. There are of course more direct methods of identifying bad bacteria, for example, stool analysis or live blood microscopy, but if one is evaluating amino acids and organic acids, then the results can provide some useful markers for bad bacteria and Candida.

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A biofilm is an aggregate of microogranisms whereby the cells are stuck to each other and/or to a surface. These adherent cells are frequently encased in a self-produced matrix (slime) of Extracellular Polymeric Substance (EPS). Biofilm EPS is a polymeric mixture of DNA, proteins, polysaccharide sugars, fibrin and often minerals such as Iron and also heavy metals. Cells inside a biofilm undergo a phenotypic shift in behaviour. Biofilms can form on non-living surfaces (e.g. in natural, industrial and hospital settings), but in the context of living organisms, they are particularly pertinent in the pathogenesis of respiratory, gastrointestinal and vascular infections, where they exist on the mucus membranes or walls of the surfaces concerned. Biofilms can also trap a variety of viruses.

As discussed above, a number of specific types of bacteria can exist in biofilms and are implicated in sinusitis (nasal infections) as well as intestinal overgrowth (particularly Candida albicans and Pseumonas aeruginosa) and conditions such as Lyme Disease. The presence of biofilms can make such organisms very hard to eradicate with antimicrobial herbs and antibiotics alone, as the organisms are effectively hiding behind a protective barrier. It can also render them very hard to detect. Intestinal biofilms may also contribute to poor intestinal absorption of nutrients.

Biofilm protocols can be necessary in eradicating biofilm loving pathogenic organisms. can be quite involving and typically involve taking:

  • Lactoferrin - a strong binder of Iron that helps to dissolve the Iron matrix in biofilms

  • Monolaurin - non-ionic surfactant to dissolve the biofilms and kill pathogens and viruses

  • Cistus incanus ssp. tauricus - tea - e.g. Fitne Bio Cistus Tee - helps to breakdown biofilms in the mouth to inhibit plaque formation but also is alleged to help reduce biofilms in the GI tract and systematically. Mildly antimicrobial.

  • Targetted Enzymes - to help dissolve the Fibrin in the biofilms, e.g. Nattokinase, Lumbrokinase, Serrapeptidase, Lysozyme; and also Enzyme blends such as Kirkman Laboratories' Biofilm Defense and Klaire Labs' Interfase (and Interfase Plus); and Dr Niedermaier's Regulat

  • EDTA - taken orally will help to dissolve intestinal biofilms by binding with the heavy metals and iron in the biofilms, e.g. Bio-Chelat or Interfase Plus. It will also help to bind with heavy metals generically in the GI tract, particularly when biofilm organisms are killed and their endotoxins are released into the GI tract. Other chelating agents may work to a lesser extent at actively dissolving biofilms but may be useful.

  • Bentonite clay - of the intestinal absorbants - this is probably the most effective at dissolving biofilms by drawing in their minerals.

  • Silicon

  • Allicin - e.g. enterically coated or free dried garlic

  • Vitamin C - buffered (if taken in quantity) or straight - can help with antioxidant properties and buffer the acid byproducts of breaking down biofilms.

Clearly, if you break down biofilms, you need to kill the pathogens that are exposed and so such a biofilm protocol must be performed in conjunction with antimicrobials, and also intestinal absorbants to absorb the toxins produced (endotoxin release) when you kill the pathogens. These are described on the Detox page.

A number of good internet resources on biofilm protocols can be found, in particular, Dr Marcus Ettinger's web site and also Dr Dietrich Klinghardt's web site in the Lyme Disease section.

Fungal infections of the nasal passages are also an important cause in many cases, and this may well include the Candida albicans species.

According to Dr Jacob Teitelbaum, oral antimicrobial supplements and antibiotics can be quite ineffective against sinusitis, on account on the inability of these circulating antimicrobial compounds in the bloodstream to penetrate the biofilms on the tissue surfaces of the respiratory linings. This is where nasal sprays can apparently be quite effective. Nasal rinses (with salt water) can also be effective in clearing excess mucus and also some of the biofilms from the nasal passages, and to allow the antimicrobial nasal sprays to work most effectively.

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Yeast - Saccharomyces cerevisiae:

Saccharomyces cerevisiae is a species of budding yeast. It is used in brewing and baking, where it is known as 'yeast' or 'brewer's yeast'. It is found occurring in small quantities on the surface of some fruits and vegetables. Saccharomyces cerevisiae, or 'yeast', is no a probiotic yeast species. It serves no beneficial role in the human body. Its Latin name literally means 'sugar mould'.

Yeast is found in the GI tract in minute quantities in healthy individuals - i.e. its presence is rare. In general terms, an overgrowth of intestinal yeast is prevented by sufficient levels and diversity of beneficial flora, intestinal immune system defence (secretory IgA) and the correct intestinal pH. The probiotic species Lactobacillus create an unsuitable environment for yeast colonisation by producing acids such as lactic acid, which lowers the intestinal pH. Lactobacillus bacteria can also release antagonistic substances to bad bacteria and yeasts such as Hydrogen Peroxide, Lactocidin, Lactobacillin and Acidolin.

However, in certain circumstances, it may spread and multiply to dysbiotic quantities (i.e. moderate to high quantities), where it becomes a problem and is considered abnormal. Yeast grows in colonies and is not typically dispersed uniformly throughout the stool in the colon. This may result in it being undetectable or present at low levels when stool samples are examined only by microscopy, and indeed when attempts are made to grow the culture from a stool sample, as there is a large chance of missing the colonies, even if a large amount of yeast has cultured in stool in in the colon in general.

[Source: Doctor's Data Comprehensive Stool Analysis/Parasitology x1 Report]

Yeast, as mentioned above, is used in brewing and in baking. Baking kills the yeasts and in most brewing applications, the yeast is killed off by the increasing alcohol concentrations. Yeast extract (where yeast has been killed off) has a number of uses in food, either as a source of B-vitamins but also as a flavouring. However, the downside is that yeast, particularly yeast extract, is high in glutamate, and in general terms should be avoided (even in its dead form). The issues associated with elevated free glutamate levels and neurological damage and excitotoxicity are examined on the Nutritional page.

Certain true fermented foods which contain yeast(s) as part of the mother/starter culture, i.e. kefir and kombucha, when eaten raw/uncooked, may contain significant amounts of yeast, but their numbers are probably counterbalanced to some degree with high numbers of probiotic bacteria and probiotic yeast cultures where applicable. Ultimately it depends on how bad a yeast overgrowth you already have in your GI tract as to whether it will be beneficial, neutral or detrimental overall to consume such products. Kombucha is not such a lactic (probiotic) culture and is not really consumed for the bacteria and yeasts but more for the glucurate and enzyme (and often alcohol!) content. For example, In Kombucha, Saccharomyces cerevisiae exists in a symbiotic relationship with number of acetic acid bacteria. In addition, Kefir grains, used to produce milk or water kefir, contain both Saccharomyces delbruecki and Saccharomyces cerevisiae yeast species. Yeast growth should not be part of fermented vegetables like sauerkraut until yeasts or fungi growth appear on the top of the ferment during the fermentation process. However, if an individual has a very low beneficial bacterial count in his GI tract, or rather a high acidophilus count and a low count of other critical bacteria, and has a high sugar or simple carbohydrate intake, and possibly a variety of other factors that affect one's beneficial bacterial balance, then he may set himself up for yeast overgrowth, despite (and because to a large extent) consuming seemingly large amounts of kefir. This is something to consider when consuming these types of fermented drink. I personally consumed water kefir daily for several months but it did nothing to help my dysbiosis and probably exacerbated my yeast overgrowth which was present at the time I started drinking the kefir.

If you have abnormally high yeast levels in your stool, then it would be wise to desist in taking these fermented foods and instead rely on a non-yeast containing probiotic supplement (and perhaps fermented vegetables), and taking anti-microbial herbs. Protocols for eliminating yeast overgrowth are almost identical to those for eliminating Candida overgrowth. Please see below for more information.

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Eliminating Candida:

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Fungicidal Herbs and Plant Extracts:

Candida can be killed off using a variety of different natural herbs and extracts, for example:

  • Grapefruit Seed Extract (GSE) (Citrus paradisi) - a good all round killer of candida which doesn't kill off too many of the beneficial bacteria either)

  • Olive Leaf Extract - also a good anti-viral herb; olive oil has some of its beneficial properties

  • Caprylic Acid - one of the saturated fatty acids found in Coconut Oil - which in itself can be consumed and has anti-fungal properties. Coconut oil is 5-10% triglycerides of Caprylic acid. If you use Coconut oil rather than a Caprylic acid capsule, then try to buy organic virgin coconut oil (i.e. not chemically treated - 'pure coconut oil' is chemically treated). Be aware of the calorific content and also addition burden on the pancreas/liver of consuming excessive oils. MCT Oil is composed of 55% triglycerides of Caprylic acid (i.e. not actual Caprylic acid) and does not require the involvement of the gallbladder and pancreas to be digested (as it does not contain any LCTs like Coconut Oil). MCT oil is approximately 10x more antimicrobial than coconut oil. Lauric acid is one of the main constituents of coconut oil. The vast majority of lauric acid is made up of triglycerides of Lauric acid (3 molecules of Lauric acid bound to every one molecule of Glycerol). A tiny proportion of Lauric acid in coconut oil is in the form of monoglycerides, that it is, one molecule of Lauric acid bound to a single Glycerol molecule. These monoglycerides of Lauric acid are known as Monolaurin. It is reputedly more antimicrobial, antifungal and antiviral than any of the other Coconut oil components, because of its non-ionic surfactant properties, which also helps it to dissolve biofilms that many pathogens hide behind. It can however be purchased in its pure form, as monolaurin granules (e.g. Lauricidin), which is significantly more antimicrobial than MCT oil.

  • Curcumin Phytosome - more readily absorbable than regular Curcumin extract which tends to stay in the GI tract. Especially if mixed with phosphatidyl choline e.g. Vital Nutrients product.

  • Pau D'Arco (Tabebuia heptaphylla) - tree barks in general tend to be anti-viral and anti-bacterial to act as a tree's natural self-defence mechanism, but Pau D'Arco tree bark is particularly effective in this capacity

  • Samento (a.k.a. a less toxic form of Cat's Claw or Uncaria tomentosa: anti-viral, anti-bacterial, anti-fungal and anti-parasitic. Part of the Lee Cowden Protocol. Particularly good for intracellular infections such as Lyme Disease.

  • Cumanda - anti-viral, anti-fungal, anti-parasitic, anti-bacterial. Part of the Lee Cowden Protocol. Particularly good for intracellular infections such as Lyme Disease.

  • Banderol - anti-viral, anti-fungal, anti-parasitic, anti-bacterial. Part of the Lee Cowden Protocol. Particularly good for intracellular infections such as Lyme Disease.
  • Berberine Sulphate, a quaternary ammonium salt - found in varying concentrations in Goldenseal (Hydrastis canadensis), Barberry root (Berberis vulgaris), Oregon grape root (Berberis aquifolium, Mahonia aquifolium), Amur Cork Tree bark (phellodendron amurense), Daruharidra (Berberis aristata) and Goldthread (Coptis chinensis).

  • Neem leaf (Azadirachta indica)

  • Lapacho

  • Enterically coated Garlic (Allium sativum) - Allicin is the active ingredient, e.g. Vital Nutrients Garlic 6000 (Allicin 6000mcg, Thiosulfinates 6000mcg, Alliin 13,200mcg). One clove of garlic typically yields 4000-12000mcg of Allicin.

  • Limonene - from Orange Peel

  • Quassia

  • Cinnamon bark (Cinnamomum cassia)

  • Oil of Oregano (Origanum vulgare) or Hyssop (Wild Oregano); or Oregano leaf. Dried oregano can be sprinkled on your food also. Be aware of it's hot properties as a herb and its corresponding effect on the body according to Traditional Chinese Medicine.

  • Undecylenic Acid (derived from Castor Oil)

  • Peppermint Oil (Mentha piperita)

  • Clove bud / Cloves - taken ground or as a tincture.

  • Uva Ursi (Arctostaphylos uva ursi)

  • Aloe Vera (Juice)

  • Liquorice (Licorice) Root (anti-viral and anti-fungal, and much less anti-bacterial)

  • Humate derived products

  • Graviola (anti-fungal and anti-parasitic)

  • Rosemary Oil

  • Geranium Oil

  • Mastic Gum

  • Sodium Bicarbonate (baking soda) or Potassium Bicarbonate - may cause diarrhea by released CO2 pressing on walls of intestine

  • Many more

The first five plant extracts in the list above are generally the most effective against Candida albicans and other yeasts, subject to an individual culture's particular resistances and sensitivies.

The laboratory Doctor's Data uses the following compounds to treat dysbiotic yeast/candida overgrowth, which differ slightly from those compounds they usually suggest to use to treat yeast overgrowth. These are compounds that are generally found to work for treating yeast/candida infections, and the yeast/candida, if present in the stool, is cultured from one's stool sample and tested with these compounds to determine which particular compounds the yeast strain in your GI tract is sensitive to (i.e. which can be used to kill them) and which they are resistant to. This is in broad terms relatively useful, but it should be remembered that yeast susceptibilities can change with time and with treatment with a particular compound, so in a sense it provides us with a snapshot. In addition, the list of compounds is by no means exhaustive or complete, but represents a selection from the subset which Doctor's Data happen to be using. There are many herbs that are equally as good or better than those in this list. Natural agents tested - Berberine, Caprylic Acid, Goldenseal, Oregano, Tanalbit (the Tannin formula), Undecylenic Acid, Uva Ursi. Prescriptive agents tested - Fluconazole, Itraconazole, Ketoconazole, Nystatin. Of this list, at the time of the test, my Saccharomyces cerevisiae overgrowth was sensitive only to Berberine, Caprylic Acid, Goldenseal and Nystatin (of the compounds tested in the laboratory). I am not recommending the use of prescriptive (synthetic agents) except in extreme circumstances or as a last resort. More information about the Doctor's Data Stool Analysis test can be found on the Identification page.

Research and studies pertaining to Cat's Claw can be found at the link below.

Cat's Claw and Pau D'Arco have been shown to be particularly effective against mycoplasma (as well as Candida). However which herbs work best may depend on what resistances the particular culture you have in your system have built up and what they are still sensitive to, at that given point in time.

There is some debate as to whether it is more effective to take a herbal supplement as a tincture or as a dried/crushed herb in capsule form. A tincture will generally be stronger as the active ingredients are easily extracted into the alcohol or glycerin over many months than the same herbs would be in your stomach with water and digestive juices over a period of up to 24 hours. However, it is easier to gain benefit from dried leaves than it is from the harder parts of the plants such as seeds or roots, which are often harder to extract the active ingredients from. This is discussed elsewhere on this web site, as it affects a number of other types of supplement, for example, for assisting digestion, or liver function etc. Please see the Inefficient Liver Function page for more details.

Pau D'Arco is probably best taken as a tincture (buying a ready made tincture or making your own by soaking the powder in Vodka for 4-6 weeks prior); or alternatively as a tea, and boiled from fine ground Pau D'Arco, rather than buying it in capsule form. Reputable suppliers of Pau D'Arco including Herb Care and many others. Good suppliers of capsule based anti-Candida products products include Nutri's GSE/Berberine, Thorne Research's Olive Leaf Extract, and Pure Encapsulations' Caprylic Acid (gradual release), for example.

Most sources of Grapefruit Seed Extract are taken in capsule form. One exception is Citricidex. This is a liquid concentrate, from Grapefruit Seed and Rind. It is sometimes used as a natural disinfectant. It is extremely strong and needs to be diluted with water prior to drinking, as otherwise it may cause severe irritation to the mucus membranes of the throat and beyond. If you ingest insufficiently diluted or worse still, neat Citricidex, it will likely burn your throat and cause you to have the most uncomfortable hoarse sensation in your throat. This may also apply to some of the oils mentioned above, which should be diluted in a glass of water prior to ingestion. Coconut Oil seems to be alright to consume as is, although one may wish to add it to food etc.

Aloe vera juice, as well as soothing the intestinal lining and curing Leaky Gut Syndrome (see below), also helps to kill off candida and parasites to a small extent, as it is an antiseptic. Aloe vera juice also helps to reduce inflammation of the gut lining in IBS/IBD sufferers, and contains glyconutrient sugars (complex carbohydrates) and may help to boost the immune system. Maximum dosage 4 fluid ounces twice a day. Dosage suggestions often start at 15-25ml, twice a day.

Aloe vera plants can be grown at home, and a leaf squeezed or thrown into a blender or juicer as desired. One can purchase Aloe Vera juice and also Aloe Vera Gel (often in capsule form) and Aloe Vera Concentrate (e.g. Now Foods 40:1 Aloe Vera Concentrate) for further dilution. Aloe Vera products are usually made from the inner gel (a.k.a. inner fillet), but some contain both inner gel and the outer leaf (i.e. whole leaf). The outer leaf contains a high concentration of Aloin, a powerful laxative. Many commercial aloe vera juices are whole leaf (less processing and thus cheaper to produce) but are passed through charcoal filters to remove the Aloin, but also removing many other nutrients - such preparations are best avoided. Inner gel is highest in beneficial compounds. If you do buy a whole leaf produce, then if you are only consuming small quantities, it is unlikely to have a significant laxative effect. Some Aloe Vera juices have added Polysaccharide extract, which boosts the already high beneficial polysaccharide content. However, one might speculate as to whether whole leaf juice manufacturers do this to mitigate the losses through charcoal filtration of the whole leaf juice. If you can buy organic aloe vera juice, all the better. Examples of Organic Aloe Vera Juice (Inner Fillet) with low preservative counts include Lily of the Desert Aloe Vera Juice (Inner Fillet) and Country Life's Real Food Organics, Liquid Aloe Vera (Inner Fillet).

Aloe Vera gel bottles tend to be marketed for external use. All purchased Aloe Vera juice bottles contain preservatives, usually Citric Acid, Potassium Sorbate and Sodium Benzoate. Some cheaper brands of Aloe Vera juice taste of benzoic acid (a phenolic/benzene type of smell), e.g. Holland & Barrett.

Examples of a composite anti-Candida supplements include Renew Life's CandiGone, Nutri's Berberine & Grapefruit Seed Extract, Rainbow Light's Candida Cleanse, Mt Capra's CandidaCleanse, Dida, Gaia Herbs' Candida Supreme Vital Cleanse, Now Foods' Candida Cleanse, etc. These adopt the 'throw everything at it' approach, as opposed to alternating or using different herbs adaptively, as discussed in the Dosages section below.

Nutri's Berberine and Grapefruit Seed Extract (GSE) (two capsule dosage) - typically contains:

- 200mg Berberine
- 200mg Grapefruit Seed Extract (Citricidal)
- 150mg Gentiana Luteac Extract (Gentian) 4:1 conc
- 100mg Hydrastine canandensis Extract (Goldenseal - 5% Hydrastine)
- 100mg Artemesia annua (Chinese Wormwood)
- 100mg Picrasma excelsa Extract (Quassia)
- 100mg Juglans nigra Extract (Black Walnut Hull)
- 100mg Allium sativum Extract (Garlic - 0.8% Allicin)

A low dosage alternative is Thorne Research's Citricidin which contains 50mg of GSE per capsule.

An antimicrobial supplement useful for combating bacteria (as well as candida) is Vital Nutrients' Herbal Biotic. This contains (per 2 capsules):
- 100mg Chinese Goldthread (Coptis chinensis) Root Extract - one of the 50 fundamental herbs of Traditional Chinese Medicine (TCM) - anti-parasitic
- 50mg Forsythia suspensa Fruit Extract - one of the 50 fundamental herbs of TCM. Antibacterial and anti-inflammatory.
- 150mg Japanese Honeysuckle (Lonicera japonica) Flower Extract - used in TCM. Antibacterial and anti-inflammatory.
- 200mg Garlic Bulb Extract - 200mg - antimicrobial
- 200mg Myrrh Gum Powder - antibacterial and antiviral.
- 250mg Echinacea purpurea Herb/Root Extract - supports immune system
- 200mg Citrus Bioflavonoid Complex 60% - antiinflammatory antioxidants & support immune system
- 10mg Zinc (citrate) - supports immune system
- 10,000iu Vitamin A (acetate)- supports immune system
- 400mg Vitamin C (pure ascorbic acid)- supports immune system

Vital Nutrients describe Herbal Biotic as 'powerful combination of immune enhancing herbs, bioflavonoids, and vitamins that can be used to support immune function'. It is normally taken with meals, e.g. 2 capsules twice a day, as opposed to an empty stomach like most regular antimicrobial herbs and formulations.

Nutri-West's Exspore product contains a wide variety of antimicrobial ingredients and cofactors at low concentrations, including Caprylic Acid, Citrus Seed Extract, Pau D'Arco, Cloves and more.

- Caprylic Acid (Medium Chain Triglyceride) 250mg
- Citrus Seed Extract 7.5 mg
- N-Acetyl Glucosamine 7.5 mg
- Pau DÕArco (leaf) 12.5 mg
- Tillandsia (plant) 12.5 mg
- Thyme (herb) 10 mg
- Basil (herb) 10mg
- Goldenseal (root) 5 mg
- Cloves (flower buds) 7.5 mg
- Aloe Vera (leaf) 12.5 mg
- Beet (root) 12.5 mg
- Cinnamon (bark) 12.5 mg
- Garlic (bulb) 25 mg
- Oregano (oil) 1 mg
- Co-Enzyme Q-10 500 mg
- Niacin 2.5 mg
- enteric coated Lactobacillus bulgaricus & Lactobacillus bifidus 5 million units
- Molybdenum (as chelate) 25 mcg
- Manganese (as chelate) 1 mg
- Zinc (as chelate) 5 mg
- Black Walnut 10 mg

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Tanalbit by Intensive Nutrition / Scientific Consulting is a tannin-based antifungal combination formula. It contains zinc tannates derived from Babul bark, Swedish birch bark and methylated Quebracho extract. The tannates are complexed with purified casein (a milk protein) and L-Proline (a biosynthetically derived compound from the amino acid L-glutamate). Tanalbit also contains hyrolysed chitin extract and lotus rhizome extract (Japanese mushroom extract). It is know to be an effect Candida albicans fighting supplement, for those colonisations that are not resistant to it.

Tannins, particularly the polyphenols known as Flavorids, present in Green Tea, and slightly less so in White Tea, are anti-microbial and anti-viral, and may provide a similar action to the tannins describes above in Tanalbit, but to a significantly lesser degree. The other thing to be wary of with Green Tea is the Caffeine content, which tends to elevate one's blood sugar and thus provide Candida and other microbes with more food. Decaffeinated Green Teas are available. Tea drinking may over the long term also result in kidney stones.

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Cellulases and Proteases:

Approximately 80-90% of the outer cell membrane of Candida albicans is comprised of a number of sugars (fibres), namely Chitin, Beta-Glucans and Glyco[manno]proteins. Chitin is a polysaccharide, or more specifically, a long chain polymer of N-AcetylGlucosamine, a glucose derivative. Chitin is very similar in structure to Cellulose. Cellulose makes up the cellular structure of many plants. The enzyme Cellulase is a fibre-digesting enzyme found in insects and certain animals which is used to digest the most abundantly found natural sugar (fibre) in nature, cellulose. The enzyme Cellulase is not naturally produced by humans. However, because Chitin is deemed to be similar in structure ot Cellulose, then many supplement manufacturers claim that it is able to actually digest the cell walls of Candida albicans, thereby killing it. Many claim therefore that supplementation with Cellulase and Hemicellulase is deemed to be beneficial in fighting Candida overgrowth as well as breaking down any undigested fibre (cellulose) in the digestive tract. A report examining the cell wall structure of Candida albicans can be found here. Approximately 25% of the total mass of Candida albicans is made up of proteins, mainly concentrated inside the cell wall. When the cell walls of Candida are digested, then the contents of the cell will spill out into the digestive tract. It is thought that by combining Cellulase with Protease in supplement form, the body can digest the majority of this toxic protein waste from the dead Candida and to reduce the amount which is absorbed into the blood from the digestive tract, thus reducing the die off reaction sometimes experienced when killing off Candida. It is likely that anyone who is treating Candida is taking a wide spectrum digestive enzyme supplement anyway, but most of the enzyme based Candida formulas contain both types of enzymes. A few examples of such enzyme-based Candida formulas include:

  • Enzymedica's Candidase

  • Mt Capra's CandaCleanse (also containing a variety of antimicrobial herbs)

  • Renew Life's CandiZyme

  • Global Health Trax (GHT)'s Acive Digestive Enzymes

  • Immune Care's Candigest and Candigest Plus

  • Many others

Both types of enzyme can also be found in 'regular' digestive enzyme supplements, e.g. Renew Life's DigestMore Ultra, etc. The difference is that normal digestive enzymes are generally taken with meals, whereas enzymes that target Candida are taken on an empty stomach.

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Anti-microbial foods and condiments:

You can also assist the process by eating more olive oil and garlic which is anti-fungal in nature. Garlic does break down in the small intestine, and so is not really that effective in the large intestine. Enterically coated garlic capsules are available which release in the large intestine (colon). Garlic is also good for eliminating parasites.

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FiveLac is a Japanese supplement based on lacto-bacteria. Formerly known as ThreeLac (but now with 5 strains of probiotic bacteria). It is distributed in the USA by Global Health Trax. Although there are no documented clinical trials, it appears to help in fighting off Candida, as does taking other probiotics. It probably just acts to assist rather than the sole source for killing candida. It comes in boxes of 60 sachets, and in general, one sachet is taken per day (on an empty stomach), before a meal. It is discussed in the Probiotics - Soil Based Organisms section above.

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Mushroom Extracts to boost the immune system:

A number of Japanese mushroom extract products can be found on the market. It is likely that the polysaccharides that these mushrooms contain, e.g. Mannose, Galactose, Fucose, Glucose, Xylose, N-acetyneuramic acid, N-acteylgalactosamine and N-acteylgucosamine, help to stimulate the body's Natural Killer (NK) cells, which in turn fight off the Candida overgrowth. It is likely also that other strategies to boost the immune system will also help to fight off Candida albicans overgrowth. Please see the Immune System page for more information on the exact mushroom species in question.

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Colonic Irrigation:

Please note that colonic irrigation/hydrotherapy alone is not an effective means of ridding the GI tract of harmful bacteria, parasites and candida. It of course helps, but should not be used as a sole method of elimination. Colonic hydrotherapy only works on the large intestine. These organisms are often present in both the large and small intestine, and in many cases are present through the bloodstream and entire body (systematic). So reducing the numbers of harmful microorganisms in the large intestine through colonic hydrotherapy will certain help a little. If you chose a bad practitioner who uses anti-biotics or anti-microbial agents in the warm water, it may indeed serve to kill off your beneficial bacterial balance, increasing your likelihood of fungal overgrowth later. Colonic hydrotherapy can however be useful in eliminating mucoid plaque from the large intestine, which is discussed above in the mucoid plaque section.

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Prescriptive Agents:

Please note that I do not personally endorse the use of prescriptive agents to eliminate Candida in the first instance. Examples of such prescriptive (artificially synthesized) agents include:

  • Nystatin
  • Nizoral
  • Diflucan
  • Fluconazole
  • Itraconazole
  • Sporex

Whilst they may well work in many cases, they are synthesized chemicals and are probably much worse (in relative terms) for the liver than the natural herbs and glyconutrients described above. Certain strains of Candida may also build up a resistance to their continued usage, as with any type of antimicrobial, which is why in general one should alternate or change antimicrobial according to the changing resistance of the candida. These types of medications should only really be used as a last resort, after a methodical, natural approach has been tried. The use of antibiotics is of course not encouraged, as this may fix the problem short term, but will make it much worse than it was to start with in the long term (and often result in a predisposition to candida overgrowth afterwards as there is little probiotic bacteria to inhibit its growth).

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An article by Susie Cornell on page 32 and 33 in the Multiple Sclerosis Resource Centre's New Pathways May/June 2003 newsletter illustrates that digestive problems and heavy metal toxicity are often serious issues in Multiple Sclerosis sufferers. The pdf of the May/June issue can be downloaded from the Multiple Sclerosis Resource Centre web site or at the link below.

Energetic therapies may also assist in boosting the immune system to deal with such unwanted bad micro-organism overgrowth. Please see the Energetic Therapies page for more information.

Viewing this file requires Adobe Reader. If you do not have this, please download it from the following link. A very rudimentary 'candida saliva test' is described at the link below. It appears to work, although there appears to be no actual scientific evaluations conducted or support for this type of test."

A number of general articles about Candida and treating Candidiasis are listed below. A general review of some of the available methods of fighting Candida is shown at the link below.

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Dosages and Treatment Management:

Anti-candida supplements are best taken on an empty stomach, as far away from meals as possible (e.g. 2 hours after last meal, 2 hours before next meal), normally between 2 and 3 times a day. Your practitioner will be able to advise you of frequency and dosage for your current level of candida overgrowth. Make sure also that you are taking a probiotic and that it is taken just before or with a meal, and at least 2 hours away from any anti-microbial herb or supplement described above. Good anti-microbial herbs and supplements will mainly target the bad bacteria and candida in the body, but they will inevitably kill off some of your beneficial bacteria in your small and large intestine. This is why probiotic supplementation is important to maintain the good bacterial levels, whilst targetting harmful microorganisms and reducing their numbers.

What about dosages? This varies according to a number of factors. The dosage should be determined by your practitioner according to the level of candida in the body and other related conditions and invaders, and tweaked accordingly during your treatment.

For example, a typical dosage of Olive Leaf Extract would be anything between 1-3 capsules, 2-3 times per day. Thorne Research's Olive Leaf Extract typically contains olive leaf extract (20% oleuropein) - 500 mg per capsule.

Please note that when beginning a regime to kill off candida, you need to start gently and build up. You are likely to kill off the proprotion of the fungus population in your intestines that are most easily killed off by whatever it is you are taking in the first couple of weeks. Thus if you overdo it and are too enthusiastic, you may well kill off a huge number of fungi in a short period of time. As candida tends to absorb heavy metals and other toxins in your GI tract, by killing off too much at once, you are likely to experience an intense die off reaction (i.e. the release of endotoxins), as the released toxins float around and are reabsorbed back into your bloodstream from the intestines. This is experienced differently by different people, but most commonly the patient experiences intense headaches, like the worst headache you have ever had in your life! If you do indeed experience a die off reaction, then it is best to ease off the dosage slightly (or completely) for a few days, and then slowly build back up again. Once you have made significant progress in your treatment, you can take higher dosages with no adverse effects whatsoever.

The first time I started consuming moderate amounts of Aloe Vera Juice (this was around the time of first taking the probiotics as described above), I suffered huge headaches, probably some of the worst I have ever experienced. These were due to taking slightly too much Aloe Vera Juice in one go, and was a die of reaction of candida in the small intestine and colon dieing and releasing toxins such as mercury which were reabsorbed into the blood stream. A similar effect was noticed when first eating sizeable amounts of Coconut Oil on rice cakes (a thick spreading, a similar amount that some people use when spreading butter).

I have noticed that when taking antimicrobial herbs, it is wise not too take too high a dosage as the last dose of the day, before one's dinner, as it may tend to elevate one's body temperature which may make falling asleep at bedtime more difficult. This is perhaps due to the energetic properties or the herbs themselves (i.e. hot energy - according to Traditional Chinese Medicine (TCM))); and/or the result of killing large numbers of pathogenic organisms and the toxins released by them which must be processed by the liver (releasing heat); and indeed the energy expended in the liver as the liver works hard to remove all the antimicrobial herbs and oils from one's system. If you are taking antimicrobial herbs three times a day, and the dosage is quite aggressive, then it is wise to take a slightly reduced third dosage each day; or simply reduce all dosages to the same lower level, which is more comfortable for the body to manage (the more sensible and cautious approach).

Along the same lines, if you have tested your culture with a laboratory test or kinesiological test, and determined that only certain herbs or extract work against it (at that point in time), it is recommended to stick to one or more of those agents that the culture is sensitive to and not both adding additional herbs that you know they are resisistant to. This is because these other herbs in all likelihood will have no or minimal effect on the yeast or bacterial overgrowth. In addition, you really want to be taking as few herbs as possible that have not been approved by your TCM practitioner, as any you do take may play havoc with your internal energy balance and potentially build up large amounts of damp heat in the body, which you must then later work very hard to get rid of. So taking herbs you know don't have much effect but which may slowly affect your health is hardly a sensible strategy.

In addition, antimicrobial herbs are generally targetted at bad bacteria and yeasts, but they will to some degree tend to discourage or kill beneficial bacteria, so the less you take the better from the perspective of your beneficial flora. There is certainly little to gain and a little to lose if you take antimicrobial herbs that your Candida, for example, is relatively resistant to. However it clearly is not the same as taking an antibiotic, which is designed to kill everything, very quickly, indiscriminately. Antibiotics should be for emergency use and not prescribed willy nilly, and handed out like sweets, as they currently are by many GPs and medical practitioners (who have little knowledge of other, much older methods).

It is quite possible to have a die off reaction from killing off beneficial bacteria as well as pathogenic bacteria and yeasts. In addition, the above herbs are generally aggressive towards the body, and have certain toxic properties, so that taking them will in all likelihood put a strain on your body's biochemical functioning. I have himself noticed that taking significant or high dosages of antimicrobial herbs make him feel more tired and reduced his mitochondrial function significantly, and slowed or stopped his general recovery. There is a fine line between helping the body and battering the body. In some cases, a given herb will work to kill off bad bacteria or yeasts, but until you remove a bigger underlying issue that is impacting your immune system, your body won't be able to actually effectively fight off the bad bacteria or yeasts itself. Such an issue might be viral, for example. Pouring antimicrobial herbs down your throat before such issues are resolved may well only make you worse, not better. Muscle testing should be able to help in this capacity as well as a variety of laboratory tests. It is not skillful or shrewd to take an all or nothing 'macho' or 'compulsive' approach to treating your dybiosis and taking large dosages of random herbs and wearing yourself out, perhaps with little actual success in reducing your dysbiosis.

In certain cases, the extent of Candida or Parasitic overgrowth may cause a large degree of degree of inflammation in the intestinal lining, and even in the organs, such as the liver and abdominal lining, depending on the extent of their proliferation. In such cases, it may be necessary to back off on the anti-microbial herbs and supplements for a while and to take a natural anti-inflammatory, for example, an enzyme-based supplement. There may of course be other contributory factors to inflammation - especially to the red blood cells - for example dehyration, oxidative stress, vitamin A/C/E deficiency and/or improper Essential Fatty Acid intake/balance.

Some practitioners recommend taking one type of anti-fungal herb or supplement at a time, and taking it for a month or two, then re-testing, and if necessary, changing the dosage and type of herb. Others recommend taking several types at once. Others still recommend an alternating regime, whereupon you would take one type of herb for a week, then change to another for the following week, then change back again - so you have a rotation of two or three types of herb or supplement, going back to the first herb or supplement every 2 or 3 weeks. It appears that in some cases, the targetted harmful microorganisms become 'immune' to the course of the herb that has just been taken, but are 'vulnerable' to the next herb. After that second herb or mixture has been taken for a week or so, the targetted harmful microorganisms gradually become 'immune' to that herb that they were once 'vulnerable' to, and the herb they had been 'immune' to a few weeks earlier, they are now once again 'vulnerable' to. This principle seems to apply to both anti-fungal and anti-parasitic herbs in many cases. The effectiveness of the current and next herb to be taken can be tested kinesiologically or by other means. A sequential approach is a crude approximation and a form of guesswork as to what type of herb the Candida will be susceptible to next.

If you are eating a sensible anti-candida regime and supplementing correctly, it shouldn't really matter too much if you alternate anti-microbial herbs or not. Where many people go wrong is that one particular part of their diet is too high in candida nourishing food, so that even though they are taking anti-candida supplements, the overall effect is ineffective. Some people find that their sleep is affected if they take more than a certain amount of antimicrobial herbs or supplements and probiotics. In such cases, the dosage must be tailored to provide a comfortable cleansing work rate, so that 'normal' sleep can be obtained during treatment.

There is certainly a great deal of overlap in terms of treating these types of harmful micro-organism. There is evidence to suggest that protozoa parasites can be difficult to fully eradicate if candida is also present. In addition, some people believe that it is not possible to effectively eliminate candida if heavy metals are present in the colon, however this is not a view shared by all, and it may be depent on the individual case. Candida and parasites tend to absorb heavy metals, which is which die off reactions can be quite severe when these organisms are killed off and broken down. In any case, it is probably wise to conduct a heavy metal detoxification regime if there is any significant level of toxicity in the body. If one is having problems killing off any particular type of harmful micro-organism, it is certainly worth investigating what else in going on in the small and large intestine which may be contributing to this problem, be it other types of organism, diet, toxicity or other factors.

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Oxygen Ion Releasing or 'Oxygenating' Treatments:

Oxygenating supplements as an antimicrobial treatment are discussed on the Mucoid Plaque page, on the Viral page and on the Cardiac page.

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Parallels between Candida overgrowth, cancer and acidosis:

Dr Tullio Simoncini has conduced research into the parallels between fungus overgrowth (in particular systematic candida) and cancer cell growth. He has established the similarities between the two, in terms of growth occurring in anaerobic, acidic conditions, where candida and cancer cells ferment simple sugars for energy and are killed off in an alkaline environment. He postulates that systematic candida and cancer are one and the same thing. Whilst I am not totally convinced of this theory, there are many parallels and much common ground. It is an area which demands further study. His book on the subject can be read at the link below. His main web site is listed at the second link.

Related articles to the proposition that fungus overgrowth is strongly related to the development of cancer are shown below.

Dr Mercola article 'Fungus Causing Cancer -- A Novel Approach to the Most Common Form of Death'

My personal opinion is that whilst both candidiatis and certain specific cases of cancer share some common causes, e.g. poor immune system function, acidosis, a diet high in simple carbohydrates etc. and toxins, this is not to say that one candida is a cause of cancer or that cancer is a cause of candida. I keep an open mind but does not wish to join the dots in this instance. There are many different types of cancer, and it would be foolish to generalise about the causes (or main cause) in each particular instance.

Please see the Other Approaches section of the links page for some unorthodox approaches to treating candida and mycoplasma infections.

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Ringworm is a collective name for certain tinea types of fungi which causes a ring-like red rash (hence the name) on the skin, scalp, groin, nail or feet (aka athlete's foot - occurring on the feet or between the toes, e.g. which may be red or white in appearance).

Ringworm usually occurs only on the surface of the skin, but the best treatment is a combination of internal anti-fungal herbs or supplements combined with the external application of an anti-fungal agent (e.g. tea-tree oil, aloe vera gel or Caprylic Acid etc.)

Tea tree oil is usually extremely expensive, and is very potent, and most forms available use a base oil to dilute it with and are perhaps around the 15% concentration mark. Tea tree oil should be applied to the athlete's foot afflicted area 3 times a day until it is gone. A cotton swab or bud may be effective in applying it. It depends on the type of bottle you have.

It is of course important to keep the area in question on the foot dry at all times during treatment, and avoid excessive sweating of the feet, to avoid conditions which stimulate the fungal growth. If you fail to do this, then the treatment may not work.

Other methods of treating athlete's foot include pre-soaking or applying a solution containing surgical spirit (methylated spirits or pure alcohol) and aspirin (e.g. 5 aspirin to 1/2 cup of alcohol), before applying the tea tree oil. The aspirin locally dilates the blood vessels and pores and allows the tea tree oil to be more effectively absorbed into the skin. One application should hopefully be enough, but monitor the area and repeat as necessary. Another method is to use vinegar instead of tea tree oil, applying it topically to the afflicted area. Finally one may choose to create a footbath solution out of vinegar and salt. Recommendations include 1/2 cup of vinegar, 2tbsp of salt and enough water to cover the feet. A stronger concentration will clearly not hinder the process. Avoid the above if there is cracked skin present as it may hurt!

Ringworm is generally not something that contributes significantly to CFS, but may be a sign of an impaired immune system, perhaps being strained by other microorganisms, toxins or mitochondrial inefficiency.

Please note that ringworm has nothing to do with the parasite roundworm discussed below, nor the harmful yeast candida (besides being another type of fungus), described above. It has been included for completeness and also because of its incorrect association with 'worms'!

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Leaky Gut Syndrome and Food Allergies:

As described above, Candida can often burrow through the intestinal lining and make its way into the blood stream, and spread around the entire body (systematic). In especially bad cases, enough burrow through the GI (intestinal) lining that the intestinal lining becomes semi-permeable, allowing particles of semi-digested food into the blood stream. Such particles of semi-digested food are attacked by the immune system, causing fatigue and flu-like symptoms, and in addition may cause allergic reactions in the body. This condition is known as 'Leaky Gut Syndrome' or LGS.

Digestive complications can thus arise from damage to the intestinal wall lining, by excessive immune system response to certain food types in the digestive tract; or the action of fungal species such as Candida albicans; or even the excessive use of anti-inflammatory drugs such as Ibuprofen. The result can be a semi-permeable intestinal lining, whereby semi-digested food is allowed to pass directly into the blood stream before proper digestion has occurred, causing food sensitivites and excessive pressure on the immune system which seeks to attack the 'invading' molecules in the blood stream which should not really be there in that form.

LGS is one potential downstream consequence of too much (non-IgE mediated) immune system regulated inflammation in the digestive tract, caused by excessive Eosinophil hyperactivity and inflammatory cytokines being released by them. This is one feature of severe cases of Celiac Disease (Gliadin Protein Intolerance). For a detailed analysis of Food Allergies and Food Intolerance, please see the Food Allergy, Intolerance and Sensitivity page.

LGS is also caused by the use of anti-inflammatory drugs such as Ibuprofen (which patients may well take because of their poor protein digestion and ongoing muscle/joint injuries. Natural anti-inflammatories can be used such as Nutri's Prozyme, which is enzyme-based). In such cases, as if the immune system wasn't overloaded already in fighting off the fungus, it now has semi-digested food to handle in the blood stream. This often creates food allergies, which mysteriously disappear once the candida has been killed off and the intestinal lining restored.

LGS and other negative side effects of pathogenic microorganisms is discussed in the section above entitled Effects of Pathogenic Organisms.

To cure leaky gut, one needs to reduce the inflammation and irritation of the gut lining and also to provide enough building materials to rebuild the gut lining. One also needs to ascertain the original cause of leaky gut and remove that causative factor or it will prolong or prevent recovery.

  • Natural anti-inflammatories to help reverse the irritation to and sooth the GI lining, such as aloe vera (juice), fermented cabbage juice, nettle tea, licorice root, marshmallow root, slippery elm, quercetin, vitamin C, curcumin (not phytosome), essential fatty acids such as GLA (Omega 6 - from Evening Primrose Oil or Borage/Starflower Oil) and DHA and EPA (Omega 3 - from fish oil), amongst others. The Omega 3 and 6 EFAs are also useful for repairing cellular membranes from oxidative/free radical damage.

  • Aloe vera juice also tends to speed up the rate of healing and cell growth by up to four times (according to some sources). It is of course important to remove the cause of leaky gut (i.e. stop taking ibuprofen or kill off the candida first) before effectively treating the actual intestinal membrane and helping it to heal back to its normal state. Aloe vera is also an antiseptic and anti-fungal and perform both functions at once. Chinese herbs to repair the small intestine epithelium include spleen qi tonics such as Liu Wei Di Huang Wan (Rehmannia 6) or Bu Zhong Yi Qi Tang and special formulas that reduce small-intestine inflammation.

    Curcumin is the principal curcuminoid compound found in the popular Indian spice Tumeric, that is part of the ginger family. If one is to take Tumeric, then one should consider the hot energy component which may throw the body out of energetic balance if taken regularly. Taking a curcumin supplement may be preferable for long term use.

  • The main amino acid that makes up the intestinal walls is L-Glutamine, and supplementation with this amino acid will help. Other nutrients to provide support for the regeneration of the GI lining, such as:

    • N-Acetyl-D-Glucosamine (NAG)

    • Zinc (also promotes stomach acid production)

    • beta-carotene (Vitamin E)

    • Pantothenic acid (Vitamin B5)

    • Phosphatidyl Choline (or Lecithin - from Soy, Sunflower or Eggs) - useful for cell repair from oxidative/free radical damage

    • Gamma Oryzanol (rice bran oil extract including sterols and ferulic acid)

    • Fermented fish (e.g. Stabilium 200 and/or Proper Nutrition SeaCure)

    • Dr Niedermaier's Regulat (cascade fermented vegetables and nuts containing digested proteins and fats)

    • Quercetin dihydrate

    • Arabinogalactan (Western Larch Heartwood)

Examples of useful products include (there are many others):

  • Identify the original cause of the LGS. If it was on account of prolonged use of synthetic anti-inflammatories such as Ibuprofen, then one should desist immediately and consider why one was taking so much in the first place and seek more effective and natural means of combatting the muscle inflammation etc. (e.g. enzyme-based anti-inflammatories). If there is any significant amount of candida in the body, one should consider commence a programme to eradicate this overgrowth.

Some information on LGS can be found at the links below. contains some good information in general, although the treatments section is focussed soley on nutrition and not on standard accepted treatments for LGS (from my experience).

Some food allergies that may be induced by leaky gut syndrome or the presence of candida or for other reasons are listed at the link below.

When it comes to adjusting one's diet to accommodate for temporary food allergies, some choose to buy 'gluten free' and 'lactose free' processed foods. These include rice milk, soya milk, gluten free museli etc. Unfortunately, the labelling on these foods can be confusing, as simply buying gluten and lactose free food does not necessarily mean that they are that good for you, or are not full of simple carbohydrates, and ultimately are not exaccerbating your candida and LGS problem, which may well be the cause of your food allergies in the first place. For example, gluten free museli usually contains large amounts of sugar. Rice milk is very high in simple carbohydrates. Rice milk and soya milk (are other soya products) are highly processed also, and may not be compatible with an anti-candida diet. Please note that I am not criticising gluten and lactose free foods, but merely the highly processed forms and breakfast cereals. For more information, please see the Anti-Candida Diet section below.

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Parasites can come from a variety of sources, from animals, soil (absorbed through skin or mouth), contaminated food, unwashed fruit or vegetables, raw meat or fish (e.g. poor quality sushi), mosquitoes, contaminated water sources (sometimes unfiltered tap water) and certain sexual practices (contact with infected person).

Parasites, mainly Protozoa (single cell parasites - a single Protozoa being known as a Protozoan), are not uncommon in the average adult. Parasites can get into the intestine in the same way as candida, in unwashed vegetables, raw fish, undercooked meat, etc. especially if the stomach acid is very weak.

A list of all the different categories of parasitic organism can be found on Wikipedia at the link below.

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Protozoa are microorganisms classified as unicellular Eukaryotes.

In the context of CFS, pathogenic protozoan species can be sometimes be found in the colon and small intestine, but also can spread throughout the body through the bloodstream.

They are single cell organisms that are physically much larger than bacteria.

Protozoa do not tend to erode the intestinal wall as much as candida, although they do frequently spread throughout the body. Probably the most famous protozoan parasite is the malaria causing Plasmodium falciparum, infections mainly occurring in tropical locations. However, there are many other types of protozoan that are frequently found in the segment of populations in temperate regions that is suffering from CFS and related disorders.

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Giardia lamblia

Giardia lamblia (shown above) is a protozoan parasite of a genus of anaerobic flagellated protozoan parasites of the phyllum Metamonada, in the supergroup Excavata that colonise and reproduce most notably in the small intestine. Their lifecycle alternates between an actively swimming Trophozoite and an infective and resistant/dormant Cyst. Giardia lamblia is one of 40 identified Giardia species. Giardia have 2 nuclei, each with four associated flagella or tail-like projections. They lack mitochondria and Golgi apparatus, but do contain mitosomes (that mature iron-sulphur containing proteins).

A published study by Galland, L. and Leem, M. (1990) in the Journal of Nutritional Medicine 1:27 found that 28% of people with CFS where infected with the parasite Giardia lamblia.

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Cryptosporidium is a protozoan parasite in the phylum Apicomplexa. It affects mainly the intestines and is spread often through contaminated water and can particularly affect campers, backpackers who drink unfiltered water, swimmers (in lakes, streams, rivers etc.) and also those who like anal sex. It is one of the most common waterborne parasites. A number of notable outbreaks occurred in the USA and UK in the last 20 years affecting many hundreds, thousands and even hundreds of thousands of people. The disease associated with the Cryptosporidium protozoan parasite is known as Cryptosporidiosis or 'Crypto' for short, which is an infectin of the Epithelium. One of the main symptoms is Diarrhea in those individuals with functioning immune systems, along with nausea, vomiting, malabsorption and dehydration. In those with severely impaired immune systems, such as HIV (or possibly CFS), the infection can be very severe and perhaps even fatal.

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Roundworms (Nematodes)

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Roundworms (Nematodes) are very small wandering worms that hatch from eggs, and which can travel in the bloodstream and settle around the body.

The following links have some general information on Roundworm (Nematodes).

A limited study presented at The Third International Clinical and Scientific Meeting on ME/CFS in 2001 found that approximately 63% of CFS patients (in the study grouop, without controls) was infected with the roundworm species Cryptostrongylus pulmoni.

Tapeworms and Roundworms, depending on the species, can burrow through the intestinal or stomach wall and get into the blood stream. Tapeworms and roundworms frequently carry many harmful varieties of protozoa also. Parasites of all forms put a constant strain on the immune system, as does candida, which is usually impaired in afflicted patients.

A small number of possible Roundworms are examined below.

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Crytostrongylus pulmoni

An example of a common roundworm parasite in sufferers of CFS and also other multisystemic diseases is Cryptostrongylus pulmoni.It is estimated to affect up to 66% of CFS patients (identified in the sputum coughed up from the lungs), based on double blind studies carried out to date by Dr Lawrence Klapow. It is known to infect the lungs, bloodstream and lymph nodes (particularly in the lumbar region of the lower back.) C.pulmoni is a hormone secreting nematode which means that it may act to disrupt the endocrine system, secreting interfering and unwanted hormones into the bloodstream. These two hormones are:

  • Hippocampal Cholinergic Neurostimulatory Peptide (H.C.N.P.) - a neuropeptide that affects the hippocampus, the part of the brain associated with memory functions. The presence of this hormone can cause symptoms such as memory loss.

  • Vasoactive Intestinal Polypeptide (V.I.P.) - a hormone that affects the hypothalamus and therefore the HPA-axis, affecting pituitary function and the production of Cortisol Regulating Hormone (CRH). It also affects blood pressure, particularly blood flow to the brain, and that can cause hypertension (high blood pressure) and other cardiovascular disorders.

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Toxoplasma and Toxocara

Two examples of parasites include those derived from household pets, toxoplasma and toxocara, which are described below.

Up to 1/3 of the world's population is infected with the protozoan (unicellular) parasite Toxoplasma gondii, although it is believed to uncommonly cause clinically significant disease. There are 3 main genotypes of Toxoplasma gondii which vary according to their pathogenicity, Type II causing most cases of Toxoplasmosis. Only 10-20% of toxoplasmosis cases in humans are noticeably symptomatic. It is estimated that 20% of the population of the UK has the toxoplasma parasite in their brains, but only 10% of American adults. The protozoa are freqently found in cats, particularly in their faeces and fur (in particular the fur around the anus), and also in rats, but can also be caught from undercooked meat.

The parasite chiefly affects the Central Nervous System. The parasite is found to affect the brain chemistry of rats, to influence their behaviour so that they are more likely to be caught and eaten by cats, thus transferring the parasites to the cat. Infected rats tend to lose their fear of cats. The parasites can be easily transmitted to humans by stroking fur or handling faeces or anything that has been contaminated with cat faeces (e.g. soil) and then touching the face or mouth. It is thought that the parasite when present in humans may influence similar fearless behaviour. Although humans are not predated by cats, symptoms are thought to include fearlessness, for example, male 'loners' and female sexual predators. It is likely that many other people fit these stereotypes who are not infected however!

Toxoplasmosis may be treated with a combination of antimicrobial treatment and probably biofilm treatment protocols.

It is estimated that anywhere up to 25% of the population of the UK has or has had the Toxocara parasite. This parasite is a tape worm and is found in dogs. The larvae or eggs can be frequently found in dog faeces or dog fur (fur near anus especially). Virtually all dogs are thought to have the parasite.

It is recommended to regularly worm dogs to keep the parasites in check. The parasites can be easily transmitted to humans by stroking fur or handling faeces or anything that has been contaminated with dog faeces (e.g. soil), and then touching the face or mouth. Children are most often those affected. The parasite develops from a larva into a tape worm up to several meters in length. This tape worm is not specialised to function in the human gut, as it has evolved for hundreds of thousands of years in the canine gut. When introduced in the human gut it tends to wreak havoc. Segments of the worm break off, and can crawl around of their own volition (containing both male and female sex organs) and seek out new environments, elsewhere in the body. They may break out of the gut and into the blood stream, where they may end up in the liver, spleen, lungs or even the eye. Some people who complain of eye problems actually have a worm in their eye. Some may go blind as a result if the worm is not killed off. The 'crawlers' are also able to crawl out of the colon and out of the anus!

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Tapeworms: Larger parasites, such as can grow to several metres in length (sometimes even 10 metres!), lay eggs and can break off independent worm segments from their length, whereas single cell parasites do not and reproduce by mitosis (cell splitting).

The following links have some general information on Tapeworms.

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Anti-Parasitic Treatments:

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Remedies for killing off parasites (of all types) include the three herbs and spices:

  • Wormwood
  • Black Walnut
  • Cloves

Normally the green outer hull of the black walnut is used. These are normally taken together on an empty stomach, ideally as far away from meals as possible (e.g. 2 hours after last meal, 2 hours before next meal), usually 2-3 times a day. Your practitioner should be able to advise you of dosage and frequency depending on the extent of your parasite overgrowth. The wormwood and black walnut kill off the adult parasites (enterically coated garlic can also be used), whereas the cloves are used to kill the eggs. If you have large parasites and you only kill the adults, then they will come back again once the eggs have hatched. Be aware that these herbs are toxic, so that it is best to take only what is required to kill off the parasites, and no more. You do not want to cause 'collateral damage' or suffer from 'friendly fire'. This applies to candida treatment also.

For example, if one is treating for protozoa, then one would take a combination of wormwood and black walnut on an empty stomach 2-3 times a day. If one is treating for tapeworm or roundworm, then one would take a combination of wormwood, black walnut and cloves. An example dosage would be 1-3 capsules of Nutri Wormwood and Black Walnut, 2-3 times a day, and 1-3 capsules of cloves, 2-3 times a day if necessary. An additional anti-parasite and anti-candida capsule could be taken in addition, for example, Nutri Berberine and Grapefruit Seed Extract (not to be confused with Grape Seed Extract which is an antioxidant), at a dosage of 1-3 capsules, 2-3 times a day. Clearly the dosage depends on what is actually present and in what quantity in the body, which should be determined by your practitioner, and the dosage adjusted accordingly during your treatment.

Other exampes of herbs commonly used to fight parasites in conjunction with the above include:

  • Graviola - a fruit from the Brazilian rainforest, is strongly anti-fungal and anti-parasitic, and is used to treat cancer patients, to kill off cancer cells and tumors.

  • Kamala - a more mild herb used for killing tape worms.

  • Fenugreek (Trigonella foenum-graecum)

  • Fennel Seed (Foeniculum vulgare)

  • Garlic (Allium sativum) - Enterically Coated

  • Berberine Sulphate, a quaternary ammonium salt - found in varying concentrations in Goldenseal (Hydrastis canadensis), Barberry root (Berberis vulgaris), Oregon grape root (Berberis aquifolium, Mahonia aquifolium), Amur Cork Tree bark (phellodendron amurense), Daruharidra (Berberis aristata) and Goldthread (Coptis chinensis).

  • Samento (a.k.a. a less toxic form of Cat's Claw or Uncaria tomentosa: anti-viral, anti-bacterial, anti-fungal and anti-parasitic. Part of the Lee Cowden Protocol. Particularly good for intracellular infections such as Lyme Disease.

  • Cumanda - anti-viral, anti-fungal, anti-parasitic, anti-bacterial. Part of the Lee Cowden Protocol. Particularly good for intracellular infections such as Lyme Disease.

  • Banderol - anti-viral, anti-fungal, anti-parasitic, anti-bacterial. Part of the Lee Cowden Protocol. Particularly good for intracellular infections such as Lyme Disease.
  • Artemisinin - extract from Sweet Wormwood - it reacts with Heme inside RBCs and creates Superoxide radicals that kill intracellular parasites. First used by the Chinese to treat malaria parasite infections. Also kills intracellular bacteria such as Borrelia (Lyme Disease).

  • Chaparral

  • Undecylenic Acid - from Castor bean oil - highly antifungal but also anti-parasitic

  • Limonene - from Orange Peel

  • Olive Leaf Extract

  • Turmeric

  • Propolis (from bee's hives)

  • Quassia (from wood)

  • Caprylic Acid - one of the saturated fatty acids found in Coconut Oil - which in itself can be consumed and has anti-fungal properties. Coconut oil is 5-10% triglycerides of Caprylic acid. If you use Coconut oil rather than a Caprylic acid capsule, then try to buy organic virgin coconut oil (i.e. not chemically treated - 'pure coconut oil' is chemically treated). Be aware of the calorific content and also addition burden on the pancreas/liver of consuming excessive oils. MCT Oil is composed of 55% triglycerides of Caprylic acid (i.e. not actual Caprylic acid) and does not require the involvement of the gallbladder and pancreas to be digested (as it does not contain any LCTs like Coconut Oil). Monolaurin (e.g. Lauricidin) is the monoglyceride of the fatty Lauric acid combined with Glycerol (in Coconut oil, 3 Lauric acid molecules are bound to one glycerol molecule). It is reputedly more antimicrobial, antifungal and antiviral than any of the other Coconut oil derivatives, and good at dissolving biofilms, on account of its non-ionic surfactant qualities.

  • Grapefruit Seed Extract

  • Pumpkin seed

  • Pippali seed (Piper longum)

  • Neem seed

  • Rosemary leaf and stem

  • Thyme leaf and stem

  • Marshmallow Root

  • Many more

An extensive list of foods, herbs and plant extracts for treating parasites can be found at the web site listed below. The microbes section also contains useful information on related topics. Some herbs are more targeted at protozoans, and others at worms, so it is wise to target the right kind of herbs at the right type of parasite.

I have noticed that when taking antimicrobial herbs, it is wise not too take too high a dosage as the last dose of the day, before one's dinner, as it may tend to elevate one's body temperature which may make falling asleep at bedtime more difficult. This is perhaps due to the energetic properties or the herbs themselves (i.e. hot energy); and/or the result of killing large numbers of pathogenic organisms and the toxins released by them which must be processed by the liver (releasing heat); and indeed the energy expended in the liver as the liver works hard to remove all the antimicrobial herbs and oils from one's system. If you are taking antimicrobial herbs three times a day, and the dosage is quite aggressive, then it is wise to take a slightly reduced third dosage each day; or simply reduce all dosages to the same lower level, which is more comfortable for the body to manage (the more sensible and cautious approach).

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Examples of Combination Herbal Formulations:

Nutri's Wormwood and Black Walnut (two capsule dosage) typically contains:

100mg Wormwood (Artemesia annua)
100mg Fennel Seed (Foeniculum vulgare)
100mg Black Walnut Leaf
100mg Fenugreek (Trigonella foenum-graecum)
100mg Garlic (Allium sativum)

Nutri's Berberine and Grapefruit Seed Extract (GSE) (two capsule dosage) - also useful for Candida/bacterial treatment - typically contains:

200mg Berberine
200mg Grapefruit Seed Extract (Citricidal)
150mg Gentiana Luteac Extract (Gentian) 4:1 conc
100mg Hydrastine canandensis Extract (Goldenseal - 5% Hydrastine)
100mg Artemesia annua (Chinese Wormwood)
100mg Picrasma excelsa Extract (Quassia)
100mg Juglans nigra Extract (Black Walnut Hull)
100mg Allium sativum Extract (Garlic - 0.8% Allicin)

Panaxea's Gut Bug Formula contains a number of Chinese Herbs to fight Gastointestinal Parasites, Blastocystis Hominis, Amoebic/bacterial parasites, Amoebic dysentery and Bacillary dysentery. It is also designed to clear hot energy, remove damp energy and regulate qi, according to Traditional Chinese Medicine (TCM). The active ingredients are:

- Radix Sophorae Flavescentis (Ku Shen)
- Endothelium Corneum Gigeriae Galli (Ji Nei Jin)
- Caulis Sargento Doxae (Hong Teng)
- Radix Stemonae (Zhi Bai Bu)
- Semen Arecae Catechu (Bing Lang)
- Fructus Quisqualis (Shi Jun Zi)
- Radix Glycirrhizae (Gan Cao)
- Sclerotium Poriae (Fu Ling)
- Pericarpium Citri Reticulatae (Chen Pi)
- Rhizoma Dioscoreae Oppositae (Shan Yao)
- Testa Dolichoris (Bian Dou)
- Rhizoma Atractylodis Macrocephalae (Bai Zhu)
- Radix Saussureae Lappae (Mu Xiang)

Paracidin, by Premier Research Labs, is a herbal blend designed to remove parasites, eggs, worms and flukes from the liver, gallbladder and blood. It contains the following ingredients: Indian Clove (bud) (Eugenia Caryophyllata), Pumpkin Seed (Curcubita pepo), Indian Neem (leaf) (Azardirachta indica), Tumeric (rhizome) (Curcuma Longa), Wormwood Herb (Artemesia absinthium), Sida Cordifolia (root), Gentian Root (Gentiana Lutea), Turkey Rhubarb Root ( Rheum officinale), Oregano Leaf (Origanum vulgare), Rehmmania Glutinosa (root), Senna Leaf (Cassia spp.), Yucca Root (Yucca filamentosa).

Parastat, by Quantum, is a general intestinal cleaner and anti-parasitic herbal prearation. It contains Holarrhena antidysenterica (bark and seed), Nopal Cactus (pad), Noni (fruit, seed), Turmeric (rhizome), Green tea extract (leaf) (50%), Fo Ti Tieng (root), Self Heal (leaf), Turkey Rhubarb Root, and digestive enzymes - protease, lipase, amylase, cellulase, intertase, lactase, maltase.

Energetix offer two different anti-parasitic herbal tinctures, Core Artemesia Blend and Core Para-V. Tinctures are often a more concentrated and higher quality manner of preserving fresh herbal ingredients than dry capsules.

Core Para-V (V for vermifuge properties) contains Black Walnut Hulls, Sweet Annie, Wormwood and Clove Oil.

'The high tannin content of Black Walnut Hulls paired with the broad spectrum of phytochemicals in the ingredient Goldenseal are favored by herbalists to assist in reducing inflammation of mucous membranes due to microbial stress. Additional phytochemicals contained in Sweet Annie, Wormwood and Clove Oil have all clinically shown to help fight a variety of infections including bacteria, fungus, viruses and parasites. Core Para-V Blend can be combined with a variety of synergistic energetix remedies to assist any healing strategy that targets parasitic infection.'

Core Artemesia Blend contains Black Walnut, Wormwood, Pumpkin Seed, Papaya Leaf, Clove Oil, Senna, Tansy and Pomegranate.

'Black Walnut's high tannin and high iodine content are the medicinal components known by traditional healers to expel unwanted microbes, especially parasites, from the bowels. The extremely sharp and bitter properties of both Wormwood and Pumpkin Seeds, coupled with additional ingredients such as Senna, Tansy and Pomegranate, have all been chosen for their reported success in cleansing the gastrointestinal tract. Additional synergistic botanicals such as Garlic and Turmeric assist the expulsion of these opportunistic microbes by providing immune support, thereby creating an environment that is inhospitable to parasites. Core Artemisia Blend is a formulation of botanical ingredients that have been used medicinally by herbalists in cases with heavy parasitic burden of all types. This can be used in any healing strategy to assist the body in addressing parasitic toxicity to bring any individual back to a state of health.'

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External Application of Oils:

Some practitioners recommend the use of various plant-based oils to rub onto the abdomen, to absorb anti-parasitic oils through the skin, which can directly be absorbed into the blood stream and be directed to the targeted organs and parts of the GI tract. Absorption of compounds into the blood stream is known to be much more efficient on the skin than it is when the same compounds are ingested and pass through the GI tract. Such oils include Castor Oil (from Castor Beans), Allicidin (from Garlic) and Limonene (from Citrus Fruits, e.g. Lime Oil, Orange Peel). Extracts from these oils may also be found in anti-parasitic supplements. One may also wish to consider any of the oils or oil extracts of the anti-parasitic herbs mentioned above.

Such a strategy may also be effective against localised bacterial infections (i.e. boils) where the bacterial infection has not yet entered the blood stream, but the exact oils used may be slightly different, e.g. coconut oil, tea tree oil, garlic oil etc. The external application of epsom salts can also help to stimulate enzymatic and lymphocyte activity to fight localised bacterial infections. This could be either using a Epsom Salts or Magnesium Sulphate cream (e.g. by Kirkman Laboratories) or an Epsom salts bath or soak, or simply applying concentrate Epsom Salts solution the skin, drop by drop and allowing it to soak in.

Using oils externally to target certain regions or organs of the body to fight parasite infections (rather than using the digestive tract) may be similar to using an enema or anal syringe in its purpose (of getting the anti-microbial herbs and oils directly to where they are needed). Dr Schulze is one of many herbalists and doctors who recommends the external application of oils as well as internal consumption in order to attack tumors from all sides, for example.

One may also wish to consider ingesting small amounts of these oils, in water, or even inhaling them (a few drops using steam inhalation), although ingestion is likely to be more effective in targetting the GI tract.

Castor Oil is a triglyceride vegetable oil obtained from the Castor bean/seed. It is colourless to pale yellow with a mild or no odour.

Allicidin is the most powerful chemical compound found in garlic and is stabilised in its concentrated form. It is anti-microbial and may help to boost the immune system.

Limonene is a monoterpene, found in the essential oils of citrus fruits (e.g. Orange Peel, Lime Oil etc.) and many other plant species. It is used as an anti-microbial, but is also used in some Co-Enzyme Q10 supplements to assist in mitochondrial function, as it prevents Q10 crystallisation.

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Diatomaceous Earth (D.E.):

Diatomaceous Earth is 'a naturally occurring, soft, chalk-like sedimentary rock that is easily crumbled into a fine white to off-white powder, sometimes even light brown powder. This powder has an abrasive feel, similar to pumice powder, and is very light, due to its high porosity. The typical chemical composition of diatomaceous earth is 86% silica (as silicon dioxide), 5% sodium, 3% magnesium and 2% iron. Diatomaceous Earth consists of fossilized remains of diatoms, a type of hard-shelled algae [one of the most common types of Phytoplankton].'

Diatomaceous Earth (DE) is mainly sold as either food-grade, traditionally for use with animals, or for use with filtration applications (e.g. pool-grade). 'Food-grade' DE is mined (as Diatomite) and then generally packaged and sold as is. No processing or treatment is required. The FDA has classified it as GRAS (Generally Recognised as Safe). Food-grade DE has been use in conjunction with animals for thousands of years, and can be used internally (for remineralisation, de-worming etc. - usually mixed in with the animal feed) as well as externally on the animal fur/feathers and in animal pens to kill off parasites and red mite. Food grade diatomaceous earth is chiefly marketed as a delousing/bugging product for external use on pets, for example, cats, dogs, horses, or farmyard animals such as chickens. It is rubbed into the fur and/or sprinkled onto animal's bedding, and brushed out after 48 hours. In this application it punctures the exoskeleton of a variety of larger parasites, such as red mite, lice, fleas, and absorbs their fluids, effectively dehydrating them.

According to Perma-Guard, US-based suppliers of DE, there is a significant difference between DE products on the market. Deposits where Diatom is mined/extracted can be either of Fresh Water or Salt water origin. This will affect the species of Diatoms in the DE but perhaps also the state of preservation. Fresh water diatoms, specifically Melosira Preicelanica, in the Perma-Guard product Fossil Shell Flour, are 89-95% amorphous silica, a higher silica content than many DE products. Less pure DE products may contain different Diatom shapes or Diatom fossils that are more fragile and less effective (typically from salt water deposits) and perhaps a higher concentration of crystalline silica.

Food-grade diatomite is largely amorphous silica (as Silicon Dioxide). However, a small proportion is in the form of crystalline silica. This latter form is extremely detrimental to health, and if inhaled/ingested in any significant quantity can result in silicosis.

Pure food-grade, for example, Fossil Shell Flour by Perma-Guard, contains 0.05% crystalline silica. The 'Diatom' brand of DE, conversely, is said by manufacturers to contain a maximum of 1 to 1.5% crystalline silica, which does not tell us what the average is, but it does sound considerably less pure. DE with a high crystalline silica content (typically 60% crystalline silica) and not for human or animal consumption (i.e. pool-grade not food-grade) and is commonly used in swimming pools and industrial applications as a filtration agent.

Amorphous silica is changed into crystalline silica by the action of extreme heat, which is typically through volcanic activity or through industrial heat treatment processing. Industrial heat treatment is typically used on filter-grade DE, as crystalline silica is more useful for filtration purposes, e.g. in swimming pools etc. However, some sources of food-grade DE are heat-treated to 600 degrees Celsius, for 'sterilisation', although of course this does increase the crystalline silica content. Such manufacturers do state this, and warn customers not to inhale it as it becomes harmful (a consideration which is not nearly as significant for non-heat treated DE). Such DE is best avoided, as is any DE with a significant naturally occuring high crystalline silica content, and it is probably best to try to find as pure a source of (non-heat treated) DE as possible with a low crystalline silica content.

The diatom fossils are cylinder-like shapes. The outside of the fossil cylinders is said to be negatively charged. When ingested, the fossil cylinders are said to attract endotoxins, pesticide and drug residues, heavy metals that are present in the GI tract. Some claim that they also attract bacteria, fungi, protozoa and viruses, as well. The cylindrical shape is said to trap these microbes so they can be passed out of the digestive tract - I am uncertain exactly how effective this really is in this latter application. Perma-Guard have reported that bacteria have been observed to have actually been killed by the negative electrical charge of the fossilised diatoms, under microscopy. It is possible that the DE may have some impact on both good and bacteria.

DE is extremely hard and is classified as 7 on the hardness scale. Diamonds are classified as 9. The sharp edges of the cylinders also act mechanically to cut up larger parasites such as worms inside the GI tract. As DE does not leave the GI tract, then clearly it is not able to kill worms and eggs elsewhere in the body, if present. However, the majority of such larger parasites reside in the GI tract, especially the colon.

Other applications for internal use include assisting in the removal of mucoid plaque and the movement of stool through the colon in general. Earthworks Health claim that it is possible to remove all mucoid plaque (containing hardened mucus, faeces and moulds etc.) after a few months of taking DE on a daily basis. In some respects it is perhaps more convenient to use than Psyllium and Bentonite shakes for mucoid plaque removal, as DE is not a form of soluble fibre, but is insoluble fibre, unlike Psyllium which has a tendency to clog up the GI tract and stick to the sides of the colon if too much is taken. Also DE is much easier to prepare than P&B shakes. It also has other nutritional advantages. It may not however be quite as effective as an absorbant as bentonite clay.

DE is well know for its ability to remineralise the body. It is slightly alkaline with a pH of 8.0. As it is mostly Silica, a small part of the silica is able to dissolve and be absorbed/utilised by the body, so whilst Silica makes up the bulk of DE, only a small part is soluble. This has been shown to help with keeping down cholesterol and reducing atherosclerotic plaque formation in the arteries. The silica content also has a use in helping to lower high blood pressure, and is beneficial for healthy teeth, nails and hair. The fossilised Diatoms contain a number of nutritional metal elements, as well as some heavy metals such as Aluminium, albeit in the Oxide form that is non-toxic (as do many other beneficial mineral clays and soil products) - and it is insoluble in any case and not likely to come of out the fossil matrix. Few hair mineral analysis tests test for Silica, so it may be difficult to monitor blood Silica levels in the event they become excessively elevated.

A typical dosage for human consumption of food-grade DE (for internal usage) is approximately one heaped tablespoon per day. The exact daily maximum amount is calculated by body weight (based on animal consumption figures). Some users take 2 tablespooons per day. It will likely be most effective if taken on a daily basis, for a least a few weeks at a time, and preferably for a few months. Probably best taken on an empty stomach mixed in a glass of (deionised/distilled) water, or perhaps mixed with psyllium husks into a 'P&DE' shake. After drinking it down, you may want to rinse out your mouth with water, as you don't want any abrasion on your teeth caused by the fossilised diatoms. Permaguard advised me that there are many different opinions on how to consume DE and that there have been few clinical studies or testing on human consumption of DE.

I have tried D.E. for a couple of months, and has found that it seems to work best to remove mucoid plaque when either mixed in with a thick medium (e.g. a fibre drink or 'shake'), which can give the D.E. some leverage from which to actually scrape the most effectively in the GI tract; or when taken twice a day, e.g. one tablespoon twice a day with water (between or with meals). I therefore believe that D.E. is best consumed either in a glass of water taken with food, or mixed in with a glass of water/fibre mixture, with or without an absorbant like bentonite or charcoal. If using the latter absorbants with D.E., it is best consumed on an empty stomach.

D.E. does not appear to be as efficient an absorbant or binder of heavy metals as either Bentonite Clay or Charcoal. This is probably because of the scale, D.E. working on a fossilised cellular level to trap heavy metals rather than a molecular level.

In terms of its ability to kill cestoda sulfasalazine renal dose cipro (tapeworms) and nematodes (roundworms etc.) is one of the primary reasons for taking DE. There are numerous case studies of patients taking DE and passing large numbers of worms out in their stools after a few days of daily intake. In my experience, at one time, having identified tapeworms and roundworms in my stool, I tried a course of DE at a high dosage for just over 3 weeks, and it didn't visibly appear to have done anything - no worms were observed in the stool, except when I had performed a herbal enema targetted at killing worms in the colon. Perhaps it may have weakened the worms slightly but it is hard to tell. It is possible to use DE in an enema but this is not something I have yet tried. So I would assume that DE isn't always effective against worms and it depends on the individual case. Additionally, DE appeared to be quite harsh on the GI tract, resulting in increased levels of mucus in the stools, at a dosage of 2 tbsp twice a day.

Diatomaceous earth can be purchased very cheaply, most cost effectively in bulk, but of course for human use, you probably won't need much more than 500g to start with. Whether you want to take it with meals or in between meals is up to you, but animals don't tend to complain too much if there is some 'mud' or 'earth' in their food, but you might! I have taken it on an empty stomach, together with a Psyllium and Bentonite 'shake', for colon cleansing, although in this application, the Bentonite might absorb some of the mineral content from the DE. There is no reason why you cannot take it on it's own however, mixed in with a glass of water, or together with a psyllium/water mixture.

Most suppliers are based in the US, although international shipping can be cost prohibitive. It is typically sold in pet shops or in farmyard supply stores. I am currently investigating how this product compares to other DE products on the market.

There are many diamtomaceous earth products on the market that are combined with other ingredients. One example is NanO Bio-Sim. This is said to target candida, parasites (which kind?), worms, yeast, fungi and amoebas (in the GI tract only) without causing any harm to the body. I would however take any claims to kill anything other than candida with a pinch of salt, but would like to see any research data on the subject. Bio-Sim contains diatomaceous earth as well as a small amount of sugar cane and kosher distilled vinegar to order to encourage a little micro-organism activity. The nanoised silica in the earth is said to slice up the harmful microorganisms but without harming the body.

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Some manufacturers add the heavy metals Barium and/or Bismuth to their anti-parasitic preparations, to increase the efficiency with which they kill parasites. Whilst this may indeed be effective, there is a sufficient variety of other herbs and extracts that can be used without resorting to heavy metals which are in themselves much more toxic to the body's cells than the ingredients of the herbs are, and harder to remove; even if many claim that Bismuth at low levels shows no signs of known toxicity. An example of such a product is Renew Life's ParaGone, which contains a small amount of Bismuth Citrate in each capsule, in addition to a wide and excellent variety of anti-parasitic and broad spectrum antimicrobial herbs. I would like to try it without the Bismuth, even though the standard product seems to be very effective, as taking a heavy metal like Bismuth is simply not necessary unless it is an absolute emergency. ParaGone is an example of a herbal combination product that subscribes to the philosophy of throwing virtually everything at the parasites, all in one go, rather than targetting them more accurately and effecively (i.e. anti-aircraft fire vs heat seeking missile).

According to Doctor's Data, Urine Toxics Metals report, based on various reference sources, Bismuth is only considered to be slightly toxic with ingestion of gram quantities necessary before any visible/detectable signs of toxicity occur. Only 5-10% of soluble bismuth salts are absorbed into the blood when orally ingested. Early signs of Bismuth excess may include constipation or bowel irregularity, bad breath, changes in skin pigmentation, blue-black gum pigmentation with stomatitis (inflammation of mucus linings of mouth). At sub-gram quantities, no toxic effects are (yet) documented for Bismuth. The existence of health problems due to environmental pollution by Bismuth are not documented either. Bismuth has various therapeutic uses with antimicrobial, anti-secretory and anti-inflammatory properties. Bismuth subsalicylate is used in the product Pepto-Bismol, and hydrolyses in the stomach to salicyclic acid and insoluble bismuth. Historically it ws used to treat syphilis. Bismuth has a variety of industrial uses, as well as being found in some lipsticks (e.g. pearlescent white) and paint.

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Mebendazole, a.k.a. Vermox, is a benzimidazole drug used to treat worm infestations from pinworms, roundworms, tapeworms, hookworms to whipworms. It is said to cause the slow immobilization and death of these worms by selectively and irreversibly blocking the uptake of glucose and other nutrients, starving them to death effectively. It is known as a spindle poison that induces chromosome nondisjunction. Whilst I am no big fan of taking pharmaceutical drugs to eliminate worms, many people have reputed great success with the product, including a friend of mine who had a severe roundworm infection for many years which were somewhat resistant to herbal methods after a while.

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After Note:

It is best to measure one's progress throughout the treatment and to adjust the dosages accordingly. Don't crack a nut with a sledgehammer! Co-ordinating treatment with a consultant, as with candida treatment, is highly recommended. The principles of alternating anti-parasitic herbs or mixtures may be useful in eliminating parasitic overgrowth. Please see the Candida section above for more information.

The usefulness of a blood microscopy cannot be stated enough. A live blood microscopy can reveal the presence of protozoa and eggs in the bloodstream, as well as bad bacteria and candida spores. Stool analysis is also a useful tool to investigate parasite presence in the intestines, although its ability to identify all parasites may be limited. As tapeworms can grow to very large lengths, they can be detected by ultrasound, although this is not the usual method of detection, and requires a skilled practitioner to detect one. In some patients, if one is eating too many simple carbohydrates, for example, white rice, then even a good dosage of anti-parasitic herbs will not be completely effective, and one has to reduce one's intake of such foods for a certain period of time, afterwhich one can slowly reintroduce them.

Energetic therapies may also assist in boosting the immune system to deal with such unwanted bad micro-organism overgrowth. Please see the Energetic Therapies page for more information.

In certain cases, the extent of Candida or Parasitic overgrowth may cause a large degree of degree of inflammation in the intestinal lining, and even in the organs, such as the liver and abdominal lining, depending on the extent of their proliferation. In such cases, it may be necessary to back off on the anti-microbial herbs and supplements for a while and to take a natural anti-inflammatory, for example, an enzyme-based supplement. There may of course be other contributory factors to inflammation - especially to the red blood cells - for example dehyration, oxidative stress, vitamin A/C/E deficiency and/or improper Essential Fatty Acid intake/balance.

Please note that whilst certain kinds of antibiotics, such as Flagyl or Doxycycline (or other antibiotic recommended by The Marshall Protocol) may well be effective in the short term in eliminating bad bacterial overgrowth or protozoan parasite overgrowth, they may potentially clog up the cell membranes and also deplete the body's natural probiotic defences, which make up the majority of the body's immune system.

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The Anti-Candida Diet:

I am not qualified to provide dietary advice, and people trying the above do so entirely at their own risk.

Why not try a change of diet for a week? What have you got to lose?

As an experiment, anyone who is feeling fatigued might want to try cutting out sugar, simple carbohydrates, pasturised milk and yeast containing foods completely for a week or two and notice if you feel any different. This would include avoiding sugar, alcohol, tea, coffee, bread, pasta, breakfast cereals (i.e. sugary cereal carb hit consumed with sugar-rich pasturised cow's milk), fruit juices, pasturised milk and cheese, sweets, cakes, chocolate and processed foods etc. and cutting down on potatoes and starchy vegetables like peas and sweetcorn. Instead you might want to focus on foods such as lean meats, white meats, fish, pulses (beans - not tinned beans with sugary tomato sauce), nuts, wild rice, plenty of steamed vegetables of all kinds, kefir (preferably based on live goat's milk), natural yoghurt, porridge (made with both porridge oats and oat bran), fermented cabbage juice (see recipe page), a few pieces of fruit a day maximum, and non-heat treated oils (correct omega 3:6:9 balance - see nutritional deficiencies page for more information). If you feel radically better on this new regime, then you more than likely have a significant bad bacteria or yeast problem in your GI tract. You might want to ensure you eat enough so as not to lose weight and to get enough nutritional input.

Please note that a restrictive diet alone may make you feel much better, but it alone will not kill off parasites/candida. You need to deprive the candida and parasites of their usual food sources whilst simultaneously actively killing them off using the correct supplement in the correct amount. Any prolonged diet changes should be discussed with your nutrionist or naturopathic medicine consultant. It is not the policy of this web site to offer dietary recommendations, and the author is not qualified to give dietary advice. An example of long term anti-candida diets are discussed below. If you are currently taking drugs regularly, even 'just' marijuana, and/or are hooked on junk food/sugary foods/simple carbohydrates, you are highly unlikely to completely cure yourself of dysbiosis and hormonal dysfuction. You really need to commit to a healthy regime. You need motivation. See the motivation page in the psychology section and also the drugs page if you need negative movitation and leverage.

The Anti-Candida Diet is described below.

There are many versions of the Anti-Candida Diet. There is no 'one size fits all' diet for everyone. A patient's exact diet will vary during the course of his treatment, and should be tailored to the exact severity of the condition. The severity of anti-candida diets varies. The diet is not a separate entity, but a part of the overall treatment, and the exact supplements/medication for killing off the candida must be taken into account when drawing up a proposed diet for a patient. A naturopathic consultant will be able to advise of the best course of action and of any diet changes and supplement requirements. Diet recommendations are also available from the National Candida Society in the UK, and from reputable books on CFS.

The purpose of an anti-candida diet is to deprive the candida of its usual food source, whilst still providing the body with all the nutrition that it requires. Whilst cutting off most/all of the candida's usual food supply will stop it multiplying, it will not actually reduce the amount of candida in the person's system. To achieve this, one needs to proactively kill it off. The supplements used for this purpose are described above. Some patients have been able to completely eliminate their candida without significantly changing their diet at all (with the exception of sugar and sweet elimination), whilst taking an anti-microbial supplement. Some patients have had to moderately change their diet for a period of a few weeks only, in combination with an anti-microbial supplement and have successfully eradicated all of their candida. And indeed, some patients have had huge trouble eliminating their candida overgrowth and require a very restrictive diet for a period of 6-12 months in combination with a variety of different anti-microbial supplements.

With regards to a highly restrictive diet, then, one can either choose to completely deprive candida of its normal food source, being simple carbohydrates and readily available energy sources, or one can choose to restrict their normal food source but not eliminate it completely. In reality there are no food sources that will completely deprive candida of digestible sugars, but it is a relative issue. Elimination is therefore never truly elimination, although it may be close to that. This is why a restrictive or elimination diet alone is unlikely to completely resolve candida overgrowth although it may well reduce it. The benefit of a restrictive diet is that the candida is kept weakened but still in the budding state, so that anti-microbial supplements can work with their maximum effect as the yeast buds and grows (albeit in a restricted manner), and can be killed off more easily. In some people, a severely restrictive elimination diet may force the yeast into its cyst form, where it may be harder to kill, and in which it can survive for many years. In such cases, when a person's normal diet is recommenced, the yeast spores then grow and the yest overgrowth starts all over again. Whichever approach one chooses to take is up to the individual to discuss with one's naturopathic consultant. An example of slightly less restrictive anti-candida diet protocol is listed below.

One thing to bear in mind is that there are two components to eliminating or restricting sources of food that encourage candida growth or prevent or slow its reduction.

  • The first is the simple carbohydrate content, which is the most important factor. e.g. Dried Fruit, because of it's smaller volume than the equivalent fresh piece of fruit, allows a person to eat an inordinately large amount of fruit in one sitting, much more than would be physically possible if one was eating the same amount of fresh fruit. This is a very efficient way of consuming far too much fruit sugar!

  • The second is the mould or yeast content of the food.

    • Mouldy foods

      Certain types of food often have a high mould content compared to others, for example dried fruits, nuts, processed meats and foods, and fruits such as melon. Processed food in general, in particular processed meats (such as sausages or mince meat) may well have higher mould levels. In addition, pre-cooked foods that are often eaten cold will contain more mould than fresh foods that are prepared, cooked and eaten on the spot. It is probably wise to only eat freshly prepared and cooked foods, fresh fruit and vegetables, and not re-heat leftovers. If nothing else, leftovers never taste that great anyway. Fruit and vegetables are best eaten when they are newly purchased/grown and fresh, rather than leaving them out for a week and eating them, when they have become limp or overripe, and likely to contain higher mould content and less 'qi'. Any food that has a small amount of white or green mould visibly growing on the surface should be thrown away - it is no good chopping off the mouldy part and eating the rest and when food gets to this stage it will have a very high internal mould content and is really inedible (it may or may not be possible to taste this). It is better to be conservative rather than to aggressive in such matters. Perhaps shop more regularly and in smaller amounts if need be.

      Clearly, ingesting a small amount of mould (which will be dead if the food has been cooked), which is likely to be largely killed off in your stomach by the stomach acid (depending on the levels of production), is probably not likely to increase your already present candida overgrowth more than actually ingesting too many simple or moderate carbohydrate food types, which will actually actively feed the candida present in your digestive tract or system-wide in your body. However, it is probably best to avoid foods that are high in mould (and spores content) in any case. Spores that get through to your large intestine may well bud and multiply as a fungus or yeast.

    • Saccharomyces cerevisiae - Nutritional/Brewer's Yeast

      There is considerable debate as to which types of yeast are harmless to consume and which will not affect your candida overgrowth and which will have a bad or allergic effect. Some favour total elimination of all yeast sources, regardless of the fact that S.cerevisiae is not the same as Candida albicans. Others favour elimination of specific types of yeast. Most recommend avoid fermented and processed foods except for true true fermented foods with lacto bacteria (i.e. probiotics). Some supplements or sources (e.g. Selenium supplements) contain only a very tiny amount of yeast.

      Sacchormyces cerevisiae is a neutral yeast (neither probiotic nor pathogenic) that consumes sugar and produces alcohol and CO2. S.cerevisiae is naturally occuring in many vegetables and plants in minute quantities. It is harvested and cultured to produce yeast in larger quantities, which is used in beer, wine and bread making as well as for use in food supplements and as a flavour enhancer. Some S.cerevisiae is present in the GI tract but normally at very low levels. In some cases, its levels (or other bacteria, parasite or fungus species) may increase to a problematic but not pathogenic level, often when sufficient probiotic bacteria are not present to suppress them.

      Brewer's yeast - The yeast is inactive in the final product in wine and beer and is dead, except in specific organic brands that are marketed as containing live yeast. Active, freeze-dried brewer's yeast is available to purchase in powder and flake form. Live yeast can also be purchased. Inactive brewer's yeast (dead brewer's yeast) is available in tablet form and is marketed as a nutritional supplement.

      Baking yeast - In bread making, S.cerevisiae is not used for its alcohol produced qualities but because it also produces CO2 which enables the bread to rise when warmed gently in the oven, prior to baking the bread to kill the yeast.

      Nutritional yeast - in the inactive (dead) form - is the type of yeast most frequently found in food sources, as yeast or yeast extract - as a flavour enhancer (high in glutamate). The yeast is dried at higher temperatures than baking yeast, rendering it inactive (i.e. killing it). As it is dead, it can no longer ferment, clearly and the vitamins and minerals are available in its matrix. Nutritional yeast is also added to some health protein powder mixtures etc. e.g. Garden of Life's Raw Meal. It is also used as a nutrient supplement to increase the intake of most B vitamins, either directly or indirectly, e.g. Garden of Life's The Vitamin Code, or live fermented B-vitamin liquids such as Max Stress B Nano-Plex.

      The main issue with yeast bread is the use of bleached white flour, which is a simple carbohydrate and which is a primary fuel for candida in your digestive tract. Modern western diets are heavily reliant on white flour and white bread in a variety of baked products (which incidentally often contain transfats - on account of the hydrogenated vegetable fat used). Some people are also allergic to the gluten in wheat flour.

      Early scientific experiments into yeast growth showed that inactive yeast was a food source for active yeast, i.e. a previously boiled yeast solution (cooled down) and added to a solution containing live yeast would serve to actively feed the live yeast. This is primarily due to the vitamin B6 (pyridoxine) content. Yeasts, moulds and fungi feed on B6 amongst other nutrients. This is why taking live yeast is not recommended by some practitioners because the yeasts that are not destroyed by the stomach acid may go on to absorb the B6 from your food or supplements in the GI tract.

      In the context of the candida diet, the rationale for excluding all forms of fermented products is that the vast majority contain naturally occurring yeast or have had yeast added to them, so that regardless of whether the beneficial and neutral bacteria in the fermented food are still alive or not (i.e. dead vs 'true live' fermented foods), there will be an elevated Pyridoxine content. Pyridoxine form of B6 is poorly absorbed in the small intestine and tends to travel a long way through the small intestine before it is effectively absorbed, meaning that elevated levels consumed, either in supplemental form or from food, may well result in feeding any yeasts or moulds in the small and large intestine.

      Ironically, sufferers of CFS or related conditions are likely to be chronically deficient in vitamin B6. However, in the biologically active form of B6, a.k.a. Pyridoxal-5-Phosphate (P5P), it is better absorbed in the GI tract and whilst it is still able to feed yeast and moulds, it does not penetrate so far into the GI tract and is less likely to cause any adverse effects with Candida overgrowth in the GI tract. P5P is not naturally occurring in fermented foods or elsewhere (in any significant quantities) to my knowledge but is available in supplemental form, e.g. Vital Nutrients P5P. If your supplements contain B6, and they most likely should, check to see it is the optimal form of B6. As to what effect it might have on Candida species in the blood (i.e. systematic mould/yeast/fungus infections) I am not sure, but if you are chronicaly deficient in B6, you still need to take it - so maybe lower dosages taken more often might help not to spike the P5P levels in the blood quite as much as high single dosages. Candida cannot make its own B6 whereas yeast can.

      When it comes to 'true, live' fermented foods or drinks, one has to look at the positive and negative aspects, and exactly what live organisms they contain. Fermented vegetables should be ok to eat on an anti-candida regime, however, the Lactobacillus acidophilus they contain, the probiotic strain, produces racemate-Lactic acid, i.e. it produces both L-Lactic acid and D-Lactic acid - the latter of which is not naturally produced in the body and may be slower to remove from the body - and which may have a negative impact on mitochondrial function if it accumulates to excess. It depends on whether you have elevated D-lactate levels or not as to whether that is a problem or not. L.acidophilus however does have beneficial effects on the GI tract if the levels are low there, suppressing other bacterial species. Kefir and kombucha contain naturally occurring S.cerevisiae (brewer's/nutritional yeast) - so this is consumed in live state (there will always be some dead yeast content), and may be not be best for those who have elevated levels of S.cerevisiae in their GI tracts as they will populate the GI tract with more. Also, such live fermented drinks will still have an elevated Pyridoxine content (B6) so may still have detrimental effects on intestinal Candida species. Fermented foods and drinks tend to be very sugary to start with, and the fermentation reduces the sugar content - clearly the longer you leave it to ferment, the less sugar there is in the food or drink, up to a point, before it goes off. Sugar content may still be an issue, even for fermented foods and drinks, although clearly much less of an issue with the original food/drink sources. For someone who has never taken any probiotics supplements before, and has dysbiosis issues, taking kefir for instance may be beneficial on the whole in the short term. This is why it was included above in the lists of foods to try for those unfamiliar with this area.

Whether the total elimination approach with respect to yeasts is the right approach or more superstitious is up to you and your practitioner to decide. A list of food types that are likely to contain mould are shown at the links below. The second link looks at different approaches to and opinions on the anti-candida diet. Please note that this site is providing this as an example, to aid understanding, and is not prescribing this diet to anyone. There are many versions of it, and the exact constituents and recommendations of an anti-candida diet are usually tailored to the individual's requirements and situation at a given point in time, and reviewed and adjusted regularly. An anti-candida diet is not intended to be a static one-size-fits-all prescriptive diet. Anyone who chooses to do so does so at their own risk.

One may wish to consider the possibility of Food Intolerance and the need to incorporate a Gluten-Free and Dairy-Free Diet into one's Anti-Candida Diet regime.

An Example of an Anti-Candida Diet Protocol is shown below. Remember that the exact quantities and make up of this diet will vary according to the individual or across the timeline of the treatment, and according to the practitioner's guidelines.

Food types to eliminate:

  • (Refined/unrefined) sugar (aka sucrose) or sugar containing foods, drinks and sweets (including soft drinks, chocolate, biscuits, cakes, ice cream, honey etc.) This includes other simple carbohydrate sugars, for example, dextrose, dextrin, glucose, etc.
  • Fruit juice
  • Alcohol, especially beer (this includes Guinness/Stout)
  • Tea, coffee
  • Wheat products (including bread, pies, pasta, biscuits, cakes etc.)
  • Starchy vegetables, such as (sweet)corn (and foods containing cornflour), peas and winter squash
  • Brewer's and baker's yeast
  • Vitamin B6 (pyridoxine) - not to be confused with active vitamin B6 (pyridoxal-5-phosphate or P5P), which does not encourage yeast overgrowth and is more easily utilised by the body.
  • Tofu, soya milk and other non-live fermented/processed soy products.
  • Processed meats and other processed food products

  • Please note that soya milk typically contains approximately 30% more carbohydrates than cow's milk, and a nominal amount of fibre. I find that unsweetened Soy Milk is quite unpleasant, and of course sweetened soy milk typically increases the carbohydrate levels. Rice milk typically contains 117% the amount of carbohydrate than cow's milk, and no fibre to boot. It is a little like eating rice but without all the fibre and with nearly all the carbohydrate. One has to ask how 'healthy' it is to drink pasturised milk and indeed an expensive vegan milk substitute. What purpose does it serve? Why the obsession with breakfast cereals and milk? Can one not simply eat a bowl of hydrated/cooked wholegrain organic porridge oats instead?

    1 Cup = 8 Fluid Ounces = 240g.

    e.g. Rice Dream contains approximately 23g of Carbohydrate per 8oz cup.

    e.g. Semi-skimmed milk typically contains approximately 11.5g of Carbohydrate per 8oz cup.

    e.g. Soy Milk typically contains 15g of Carbohydrate per 8oz cup.

Food types that are eliminated with severe cases of candida, but which can be consumed in moderation with less severe cases are listed below.

Even in less severe but significant cases, it is unwise to consume any of these carbohydrates more than once a day. Sometimes one may choose to avoid these food types completely for a week or two and notice if one feels any difference, then reintroduce later.

  • Whole grains such as oats, oatbran, barley, quinoia, buckwheat (some patients may not be allergic to buckwheat), etc.
  • Potatoes and sweet potatoes
  • Rice, preferably brown or wholegrain

Two servings/pieces of moderate carbohydrate fruit per day maximum (pretty much any fruit except bananas), as listed below.

It may be more conservative to stick with apples, which are often cheaper than other fruit too. Grapes, berries, tropical fruits and other medium carbohydrate fruits may be omitted depending on the severity of the candida case.

  • Apple, pear, avocado, grapes, lemon, mango, canteloupe, peach, plum, orange, tangerine, watermelon, berries, apricot, cherries, fresh figs (not dried figs or dried fruit), nectarine, pomegranate, etc.

Food types that should be consumed liberally (or according to your dietary preferences and tolerances):

  • Low carbohydrate vegetables, such as artichoke (not Jerusalem artichoke), asparagus, brussel sprouts, carrot, cauliflower, red/yellow/green peppers, onions, leeks, tomatoes, snap peas, turnips, cabbage, lettuce, celery, okra, olives, broccoli, and beetroot (beetroot is not strictly a low carb vegetable but the juice is useful for killing parasites).
  • All meats (i.e. chicken, pork, beef, lamb, turkey, etc.), fish and shellfish
  • Natural (live) yoghurt, live kefir, hard cheese, double cream
  • Nuts and seeds
  • Dry beans, Sprouted beans (the amount of raw sprouts tolerated may vary. They are rich in enzymes and vitamins, but may be harder to digest, especially for an impaired digestive system.)
  • (Eggs)

Please note that as a general rule, very moderate alcohol consumption in the form of spirits or wine is often not an issue in terms of digestive health for people in general, whereas beer, lager and stout are best avoided by even the very healthy on account of their yeast and grain content. Sorry lads! However, my personal approach is to avoid all alcohol, caffeine and recreational drugs (and medicinal drugs unless for specific reasons and as a last resort); and to avoid recreational drugs whether one has candida or not for toxicity, endocrine and psychological reasons.

Further reading on diet is found in the books listed on the links page and can be also found at the IHS web site below.

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