Thursday 11 December 2014

The key is the gut

Bacterial, Fungal & Parasitic Overgrowth


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

Bad Bacteria, Mycoplasma & Lyme Disease
     Overview
     Lyme Disease
     
     
Enterobacter cloacae
     Chlamydia pneumoniae
     Biochemical markers for Clostridia and Pseudomonas
     PROBIOTICS
           General
           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
                 Background
                 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
           Afternote
     PREBIOTICS
     Antimicrobial Supplements

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

Leaky Gut Syndrome (LGS) and Food Allergies

Parasites
     General
     Protozoa
           Overview
           Giardia lamblia
           Cryptosporidium
     Roundworms (Nematodes)
           Overview
           Crytostrongylus pulmoni
           Toxoplasma and Toxocara
     Tapeworms
     Anti-Parasitic Treatments
           General
           Examples of Combination Herbal Formulations
           External Application of Oils
           Diatomaceous Earth (D.E.)
           Bismuth
           Mebendazole
           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.

http://articles.mercola.com/sites/articles/archive/2003/10/18/bacteria-gut.aspx

'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.

http://en.wikipedia.org/wiki/Probiotic

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.

http://www.drmyhill.co.uk/wiki/Fermentation_in_the_gut_and_CFS

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.

http://en.wikipedia.org/wiki/Gut_flora

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.

http://en.wikipedia.org/wiki/Antibiotics#Antibiotic_classes

http://en.wikipedia.org/wiki/Broad-spectrum_antibiotic

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.

www.unc.edu/depts/tcf/badbug_index.htm

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.

www.naturalnews.com/022692.html

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.

http://en.wikipedia.org/wiki/Germ_theory_of_disease

www.unhinderedliving.com/germtheory.html

www.rawpaleodiet.org/pleomorphism-1.html

www.drlwilson.com/Articles/antibiotics.htm

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

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Imbalanced Flora:

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General:

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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D-Lactate:

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.1.1.2.3). The other LDH enzyme is a Cytochrome c-enzyme found in the liver (EC.1.1.1.27). 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).

http://en.wikipedia.org/wiki/Lactate_dehydrogenase

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.

www.cfids-cab.org/rc/Sheedy.pdf

http://jn.nutrition.org/cgi/content/full/135/7/1619

www.biolab.co.uk/docs/dlactate.pdf

http://www.drmyhill.co.uk/wiki/Fermentation_in_the_gut_and_CFS

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.

http://en.wikipedia.org/wiki/Streptococcus

http://en.wikipedia.org/wiki/Enterococcus

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:

http://jn.nutrition.org/cgi/content/full/135/7/1619

'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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        General:

        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.

        http://en.wikipedia.org/wiki/Hydrogen_sulfide

        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:
         
              Overview:

              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.

              http://en.wikipedia.org/wiki/Lyme_disease

              American Lyme Disease Foundation:

              http://www.aldf.com/

              Sarah Myhill:

              http://www.drmyhill.co.uk/article.cfm?id=361

              TO BE UPDATED!

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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.

              http://en.wikipedia.org/wiki/Mycoplasma

              http://bacteriality.com/2007/08/15/l-forms

              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.

              www.gulfwarvets.com/mycoplas.htm

              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.'

              www.keac.nl/news4.htm

              http://en.wikipedia.org/wiki/Peroxynitrite

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

              www.immuno-sci-lab.com/mycoplas.html

              www.shasta.com/cybermom/asimple.htm

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

              http://www.vimeo.com/2585394

              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.

              http://precedings.nature.com/documents/164/version/1/files/npre2007164-1.pdf

              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.

              http://trevormarshall.com/BioEssays-Feb08-Marshall-Preprint.pdf

              '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.

              http://en.wikipedia.org/wiki/Vitamin_D

              '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.

              http://www.marshallprotocol.com/forum39/9348-4.html

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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.

              http://en.wikipedia.org/wiki/Enterobacter_cloacae

              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.

              http://en.wikipedia.org/wiki/Chlamydia_pneumoniae

              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.

              http://cpnhelp.org/home

              http://cpnhelp.org/contents

              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.

              http://www.davidwheldon.co.uk/NAC.html

              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.

              http://cpnhelp.org/?q=simple

              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).

                http://en.wikipedia.org/wiki/Metronidazole
          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.

          http://en.wikipedia.org/wiki/Clostridia

          www.textbookofbacteriology.net/clostridia.html

          '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.

          http://en.wikipedia.org/wiki/Pseudomonas

          www.patient.co.uk/showdoc/40000416

          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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          General:

          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).

          http://en.wikipedia.org/wiki/Probiotic

          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'.

                http://www.bifantis.com/

                http://www.aligngi.com

              • 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.

                http://en.wikipedia.org/wiki/Lactobacillus_reuteri

                http://www.naturesway.com/

                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).

                http://www.culturelle.com/

                http://en.wikipedia.org/wiki/Lactobacillus_GG
          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.

          http://drbenkim.com/best-probiotic-health-benefit.htm

          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.

          http://en.wikipedia.org/wiki/Escherichia_coli

          http://en.wikipedia.org/wiki/Mutaflor

          http://www.drmyhill.co.uk/wiki/Fermentation_in_the_gut_and_CFS

          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.

          www.ardeypharm.de/pdfs/en/mutaflor_drugforlife_e.pdf

          www.mutaflor.com/

          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).

          www.berlindaversandapotheke.de

          www.drmyhill.co.uk/wiki/Growing_Mutaflor

          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.

          www.metropolitan-pharmacy.de/en/home.html

          If you search on g**gle.de, 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.

          http://en.wikipedia.org/wiki/Propionibacterium_freudenreichii

          http://en.wikipedia.org/wiki/Propionic_acid

          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.

          http://www.stabilium.co.uk/index.php?cPath=23

          '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.

                http://en.wikipedia.org/wiki/Bacillus_subtilis

                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:

                http://Bio-Kult.org/probiotic/bacillus-subtilis

                '...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.

                http://Bio-Kult.org/probiotic/bacillus-subtilis/

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

                http://en.wikipedia.org/wiki/Bacillus_licheniformis

                '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.

                www.ebi.ac.uk/2can/genomes/bacteria/Bacillus_licheniformis.html

                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.

                http://en.wikipedia.org/wiki/Bacillus_coagulans

                www.lactospore.com/intro.htm


                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.

                www.flora-balance.com/Flora-Balance.htm

                www.flora-balance.com/faq.htm#f1

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                Rhodopseudomonas palustris:

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

                http://en.wikipedia.org/wiki/Rhodobacter_palustris

                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.

                http://en.wikipedia.org/wiki/Rhodobacter_sphaeroides

                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.

                http://en.wikipedia.org/wiki/Saccharomyces_boulardii

                '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.'

                http://en.wikipedia.org/wiki/Effective_Microorganisms

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

                www.efficientmicrobes.co.za/News.aspx?tid=15

                '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.

                www.scdprobiotics.com

                www.scdworld.net/product_p/a112-1.htm

                www.emearth.com

                http://www.emearth.com//PDFs/HistoryOfEm.pdf

                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

                www.scdworld.net/category_s/44.htm

                MSDSes can be found for both products below.

                www.scdworld.net/category_s/77.htm

                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.

                www.vinnypinto.us

                http://health.groups.yahoo.com/group/EM-health/?v=1&t=search&ch=web&pub=groups&sec=group&slk=2

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

                http://windintheroses.googlepages.com/em

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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.

                www.agmfoods.com/

                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.


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