In this final chapter in the series I would like to discuss the topic of prebiotics and a supplement called synbiotics which is a combination of both probiotics and prebiotics which you can guess is a version of natural fermented foods. In my closing notes I want to mention other autoimmune conditions such as Multiple Sclerosis and Type 1 Diabetes

Prebiotic foods

It has transpired that the body contains a secondary digestive system just like our ruminant cousins that have a double stomach to ferment hard to digest foods like grass.  Although, some are aware of the fermentation process that occurs in the colon, we never considered it to be a secondary digestive system but that’s what it is, since it benefits the hosts digestive gut system and the flora that resides there. The colonic bacteria like to feed on indigestable foods that are referred to as Prebiotics.  The prebiotic family include Polysaccharides, Oligosaccharides (Inulin), Fructooligosaccharides (FOS), Galacto Oligosaccharides (GOS) and Trans Galactooligosaccharides (TOS).

Polysaccharide ( complex sugars ) digestion and hydrogen exhaust

Polysaccharides are various monosaccharides ( simple sugars like carbohydrates) bound together by a glycosidic bond ( e.g RNA consists of Adenosine which is a glycosidic bond of ribose sugar and Adenine) that increases water solubility. Examples of these complex sugars are starch and glycogen ( storage sugar in the liver for energy ), cellulose and chitin (a substance that lobster skeletons and fish scales are made from). Since the human host is incapable of digesting these compounds the microflora use digestive fermentation in the colon resulting in Carbon dioxide and hydrogen gas ( lactic acid and ethanol are also fermentation metabolites).  Fermentation is a necessary digestion process in the colon since it is an anaerobic ( without oxygen) dark space. A single celled Archaeon called Methanobrevibacter smithii recycles hydrogen and combines it with hydrogen to form methane ((human flatulence), This process, is not to embarrass the host, but to increase nutrient energy extraction providing soluble fiber that attenuates sugar absorption, reducing insulin spikes, normalises blood lipid levels and once fermentation is completed various short chain fatty acids (SCFA) are produced which have health providing properties to the host. Of particular interest of SCFA’s is  Butyrate which not only provide an energy source for colonic cells, but it has anti-inflammatory and anti-carcinogenic properties thus inhibiting proliferation of tumor cells ( as can be shown in vitro), and inducing apoptosis of human colorectal cancer cells. So any food stuff that is fibrous and/or fermented foods enhance butyrate production or you can consume ‘already made’ butyrate which is contained in Butter and clarified butter ( Ghee ).  It is also of interest that consuming indigestible fibres from plant foods like green leafy vegetables like Kale, chard, dandelions is a great way to cleanse the colon to avoid such conditions like diverticulitis.


Oligosaccharides which are carbohydrates that have 3-10 stacked simple sugars linked together and found naturally in many plants. The stacked molecule can be fructose (FOS), galactose (GOS), or a chain of galactose (TOS).  These plants include chicory root, Jerusalem artichokes, onions, leeks, garlic, legumes, wheat, asparagus and banana, containing a dietary fibre Inulin as a means to store energy and regulating cold resistance by changing the osmotic potential of its cells, to withstand winter cold and droughts. Interestingly, Inulin is extracted from chicory root to serve the processed food industry to replace sugar, fat and flour. In its natural form it serves nutritionally as a soluble fiber promoting growth to the intestinal microbiota.  These stacked sugar compounds are equally beneficial to the host and microbiota, processed directly as energy or used for cell wall structures or to nourish the probiotic colonies.

Fructooligosaccharides (FOS)

FOS foods include beets,leeks, whole rye, bananas, soybeans, burdock roots, asparagus, maple sugar, and whole wheat.  Bananas contain one of the highest levels of FOS

Galacto Oligosaccharides/Trans Galactooligosaccharides (GOS/TOS)

GOS/TOS foods are natural by products of milk produced as lactose enzymatically converted in the gut.


We covered these in a previous article of this series that include plant lignans, tannins, and flavonoids.

If you want to read more about bacterial strains you can visit the website of  the: ‘American Type Culture Collection’, which also list the majority of Probiotic supplements sold in the US.

Supplemental Probiotic function

I believe it is safe to say that probiotic supplementation, for the most part, has a transitory effect on the existing permanent resident colonies of bacteria. This means the net effect is to inhibit gut disruption from the normal balance, and if normal balance is upset the benefit of probiotic supplements is to inhibit pathogenic growth providing a time window for beneficial bacteria to reclaim more colonial turf and grow to normal numbers to achieve balance. It is important to note that probiotic supplements do not reseed or feed the permanent residents, but simply encourage the beneficial flora to grow and discourage the pathogenic flora to grow.  Early childhood colonization is crucial to establish permanent microbial residency so as the beneficial flora take a permanent controlling position.  If early childhood colonization is not established for reasons of a C section birth and/or no breast feeding or inheritance of a dysbiotic gut from the parents, then there is profound risk that as the child develops he/she may well develop associated aberrant conditions such as allergy, asthma, bedwetting, behavioural abnormalities ( ADHD,ADD), cognitive dysfunction ( Autism), schizophrenia, epilepsy. The average physician may not administer the correct treatment and plying the child with antibiotics further damages the gut. The child reaches adulthood still with the dysbiotic gut and now possibly experiencing fibromyalgia, thyroiditis, rheumatoid arthritis, Crohn’s disease, Celiac disease and other adult autoimmune conditions.  


Both Probiotics and Prebiotics have beneficial effects on the body.  There are other products on the market which contain both probiotics and prebiotics called Synbiotics,  that are used by veterinarians….why not ? cats, dogs and horses also have a gut ecosystem. A US company known as Kendy Nutraceuticals carry such a product ( this is for humans not animals) claiming 45 billion CFU/ capsule. Each capsule contains a blend of  Saccharomyces Boulardii ( a probiotic yeast that is supposed to reduce symptoms of Crohn’s disease, reduce Clostridium difficile, inhibit H.Pylori and stimulate T cells), L.Acidophilus, Bifidobacterium, Streptococcus Thermophilus and prebiotic Inulin.  Manufacturers claim that this prebiotic/probiotic combination improves the survival of the probiotic organisms especially when they transit through the stomach.

Pros/cons of Synbiotics

There is however, something to be said about synbiotic preparations.  The majority of probiotic supplements are freeze dried before encapsulation thus putting the little creatures to sleep ( suspended animation I suppose), however, as soon as the capsules come into contact with heat or moisture, the microorganism will awaken and you can bet they are going to be hungry. This is one reason why I am skeptical about commercial probiotic products, because if this happens the product will contain a lot of dead microbes that have starved to death.  Having said that even if the synbiotic product does contain some prebiotic substance like inulin for the miniscule creatures to munch on, it might extend their life by a few seconds, so that has little benefit as well.

My preference

For the reasons explained above, this is why I prefer food based probiotic supplementation, since these are natural synbiotics, because the prebiotics are in there, in abundance, for live microorganisms to feed on, and you are certain that they are alive when they transit the body.  Similarly diary based ferments that contain Lactobacilli and Bifidobacteria are quite happy fermenting in a dairy environment feeding on lactose, GOS/TOS (Galacto Oligosaccharides/Trans Galactooligosaccharides).

CFU (Colony Forming Unit)

This is a unit of measurement that estimates the viable bacteria or fungal cells in a sample. In general, microorganism proliferation comes from a clump of cells rather than one cell, so future growth occurs in chains such as Streptococcus or in clumps as in Staphylococcus. A standard size Petri dish measures 3-1/2” x 5/8” (100mm x 15mm) which can accommodate between 30-300 CFU.   For convenience, the results are given as CFU/mL (colony-forming units per milliliter) for liquids, and CFU/g (colony-forming units per gram) for solids.  As an example, if 200 colonies are counted within 1 millilitre solution diluted 1000 times from its original strength then the original solution before dilution contained 200,000 CFUs/ml. I will leave it to you to figure out what the CFU measurement is for the human microbiota.

Typical probiotic supplement contents

Because the body is so wonderfully adaptive, and it is never too late to fix the gut problem, although it might take more time as the individual gets older.  There are various home made probiotics that you can choose from, alongside a healthy diet that will achieve gut healing, but the use of commercial probiotics have the same suspicions of efficacy as multivitamins  and other synthetic products so I would be very cautious in their use. It is also my belief that probiotic supplementation is medicinal, and in the case of a healthy gut I do not see a need to take it on a daily basis, but if you are in the habit of eating say fermented vegetables as a side dish, than I see no problem and at least you are maintaining gut health.   From various studies on the human microbiome ( estimated # of publications in 2010 was around 1350) we know the following :

  1. The Microbiota consists mainly of  Bacteroidetes and Firmicutes Phyla (90%), and   Actinobacteria ( 10%) in the small and large intestine.  The same colonies exist in the stomach in addition to  Proteobacteria ( Escherichia, Salmonella, Helicobacter) and Fusobacteria ( associated with Ulcerative colitis and periodontal disease)  which are both pathogenic.  Bacteroidetes are commensal or opportunistic flora while Firmicutes are both commensal and beneficial.  A 100 years ago the annual sugar consumption was 3-4 pounds (approx 1.3-1.8 kilos)/person. Now it is in the range of 150 pounds ( 68 kilos)/person, so It is no wonder that bacterial species like Bacteroides fragilis and Bacteroides melaninogenicus are feasting daily on their favourite food, glucose, causing them to overgrow to unhealthy levels.   Lactobacillus makes up only about 1% of the total probiotic flora and is part of the beneficial family of Firmicutes , while Bifidobacterium which constitutes the majority of the total probiotic flora is part of the beneficial family of Actinobacteria..
  1. Out of the 1000-1130 bacterial species that have been isolated from human microbiota , only 160 unique species reside in each individual.
  2. A common bacterial species “core” is shared among at least 50% of individuals Seventy-five species are common to >50% of individuals and 57 species are common to >90% of individuals
  3. Total number of genes that are encoded by bacterial colonies are approximately 50 times the number of mammalian genes ( there are approx 23,000 host mammalian genes).
  4. To date the number of bacterial genes that  have been identified number 536,112, but we also know that 2,375,655 bacterial genes exist in about 20% of the population, and 294,110 exist in around 50% of the population.

Ayurvedic Medicine’s  answer to healing the gut

Finally, as a side note Dr John Douillard informs us that ayurveda medicine advocate a herbal fruit blend to heal the gut called ‘Triphala’.  This combines  Amalaki (extract of the indian Gooseberry), that repairs intestinal damage, Bibhitaki ( fruit from an Indian tree called Terminalia bellirica), that is supposed to pull excess mucus from the intestinal wall, and Haritaki (an indian fruit that resembles an almond called a myrobalan), that tones the muscles involved in bowel movement.  You can buy the Triphala powder from one company called ‘Organic Traditions’.  I have no doubt it works so this can be helpful toward  healing the gut.

Closing notes

Appropriate treatment

In this series I have not covered every variation of Autoimmune conditions but the treatment modality is still the same toward healing the gut, detoxing vital organ systems like the liver, kidney and lymphatic systems and avoiding stress and prescription medication.  Since we are all unique, the outcome will not always be the same; some treatments may take longer than others. As Dr Bergman always says that it is crucial that you get your nervous system checked by a licensed Chiropractor since any dietary/lifestyle changes that you make will be ineffective if the signalling and blood supply is dysfunctional to a particular organ which needs chiropractic adjustment and/or correction. This is very relevant for autoimmune conditions that involve joint pain like Fibromyalgia, arthritic pain such as Rheumatoid arthritis, and arthritis in the spine as in Ankylosing spondylitis.  This is also important in conditions that affect the peripheral nervous system as in Guillain Barre syndrome and Axonal and Neuronal neuropathy.

Sjorgren’s syndrome/Multiple sclerosis

Sjogren’s syndrome causing ulcers in the rectum and colon is definitely caused by colonic bacterial imbalance requiring fermented foods to correct the problem.  Multiple sclerosis (MS) that affects the myelination of nerve cells within the brain and spinal cord requires a complete dietary and lifestyle change and to ensure that cholesterol production is not interfered with, and the host consume healthy dietary fats like eggs, avocado pears, organic fatty meats, and coconut on a regular basis.  As I wrote in Part II of the articles on Alzheimer’s disease (AD) :

Myelin is composed of different cell types, but Schwann cells supply the Myelin for the peripheral nervous system, while oligodendrocytes myelinate the axons of the central nervous system. The Myelin is a fatty white substance that acts as an electrical insulator for neurons in the brain, being a major part of the ‘white matter’ in the brain. Cholesterol is an essential part of Myelin, comprised of 40% water, between 60%-70% lipids ( fats) and between 15%-25% protein. Insulating neurons in this way increase impulse propagation speeds. The body can handle a severed peripheral fibre by the regrowth of an alternative track, but if the Myelin sheath begins degrading due to lack of nutrients and/or cholesterol it is much more difficult for the body to apply repair, especially if the nutrient/cholesterol deficiency continues over time, the neurons cannot regenerate and impulse speed is impaired.

I also believe that in Multiple sclerosis the body is also very toxic including toxic metabolites being released by the pathogenic flora that are crossing the blood brain barrier that the already compromised immune system is attempting to eliminate ( the immune system working with ‘one arm tied around its back’).  As in the study on 45 MS and 9 AD autopsied patients conducted by Dal Bianco et al in 2008 stated objectively that chronic inflammation with microglia activation is thought to be involved in the formation and clearance of AD lesions and the induction of demyelination in MS and concluded :

‘Profound microglia activation, determined by a broad spectrum of markers, was found in both MS and AD cortices, and the patterns of microglia activation were closely similar. Microglia activation in MS cortex, in contrast with that in AD and control cortex, correlated with lymphocyte and plasma-cell infiltrates in the meninges. MS cases older than 64 years experienced development of AD pathology in comparable incidence as seen in the course of normal aging. The density of beta-amyloid plaques and neurofibrillary tangles did not differ between demyelinated and nondemyelinated cortical areas.’

As we know now in AD the Amyloid Beta plaques surrounding the neurons are put there as a protective measure by the immune system against a normal inflammatory response to repair the body.  Similarly, the immune system attempts the same protocol in MS because inflammation has become widespread in the body and the brain, but due to its chaotic state instead of repairing the problem it begins to damage the myelin sheaths.

Type 1 Diabetes

Finally, Type 1 diabetes is an autoimmune disease that appears in adolescence ( peak age 14 but normally before the age of 40).  Its pathology assists in its diagnosis when excess CD4+ T helper cells and CD8+ T cells which are cytotoxic cells ( autoreactive ) and autoantibody B cells, islet cell autoantibodies, insulin autoantibodies and the activation of the innate immune system are found, because the immune system is functioning inappropriately due to gut dysbiosis. In fact the immune system is destroying the Islet (beta) cells of the pancreas responsible for storing and releasing insulin. Some affected also have other autoimmune conditions such as celiac disease.  Some develop ketoacidosis which is a metabolic acidosis that the body reverts to in the event of alcoholism, starvation and diabetes. Basically it is a process called Gluconeogenesis where the individual amino acids, broken down from protein metabolism, that are normally absorbed by muscle and bone are actually taken to the liver where it breaks the protein down in a process called deamination. The body does this as a survival mechanism when it senses trouble as in this case, no insulin hormone to tell the cells to take up excess sugar in the bloodstream; it can also occur under extreme stress as well. I believe that if this problem is caught early enough and treated appropriately ( without poisonous chemicals ) this condition can be eliminated but as time passes it might be more difficult, but certainly improved.

The traits of the phagocyte have been retained most completely in the mesoderm where a large number of amoeboid cells occur to ingest the body’s own dead or weak as well as foreign particles such as senescent red blood cells.”

Elie Metchnikoff”

“Messieurs, c’est les microbes qui auront le dernier mot.” (Gentlemen, it is the microbes who will have the last word.)”

Louis Pasteur (1878)

The living being, filled with microzymas, carries in itself the elements essential for life, disease, death and destruction. And that this variety in results may not too much surprise us, the processes are the same. Our cellules, it is a matter of constant observation, are being continually destroyed by means of a fermentation very analogous to that which follows death. Penetrating into the heart of these phenomena we might really say, were it not for the offensiveness of the expression, that we are constantly rotting!

Antoine Bechamp ( Ffrom his last published works The Blood and its Third Anatomical Element 1912)

Check out the previous articles in this series :

Autoimmune Disease I

Autoimmune Disease II (Gut Flora Balance, Gut Symbiosis)

Autoimmune Disease III (Thymic recruits, Immune system Battlemap,Th1/Th2 balance)

Autoimmune Disease IV (Inflammatory mediators)

Autoimmune Disease V ((Asthma, Gut Epithelium, Chronic cystitis)

Autoimmune Disease VI (Fibromyalgia,Rheumatoid Arthritis,Allergies)

Autoimmune Disease VII ((Attack on the thyroid Hashimotos and Graves)

Autoimmune Disease VIII ((Celiac disease)

Autoimmune Disease IX ((crohns-disease-ulcerative-colitis-inflammatory-bowel-disease

Autoimmune Disease X ((Psoriasis, Vitiligo)

Autoimmune Disease XI ((Pernicious Anemia)

Autoimmune Disease XII ((autoimmune-disease-xii-finale-part-i-how-did-we-get-here-healing-food-gaps-probiotics)

Autoimmune Disease XIII ((autoimmune-disease-xiii-finale-part-ii-probiotic-benefits)


References/Acknowledgments :

  1. Myokine,  kvass, galactooligosaccharide, inulin, electron acceptor, cholesterol esters, Polysaccharide, chitin,Methanobrevibacter smithii,  Lactobacillus fermentum wikipedia
  2. Fermented Fruits and Vegetables of Asia: A Potential Source of Probiotics Manas Ranjan Swain et al 2014 Biotechnology Research Int
  3. How to Ferment vegetables Cultures for health
  4. Examination of intestinal conversion of cholesterol to coprostanol in 633 healthy subjects reveals an age- and sex-dependent pattern Peter Benno et al 2005 Microbial ecology in health & disease.
  5. Probiotics Protection against infection book 2016 Case Adams
  6. Diet, Microbiome & Health handbook of food bioengineering vol 11 book 2018 Holban,Grumezescu
  7. Healing the vaccine damaged part 3 article 2017 Eric Malouin Dr Bergman’s owners guide for humans
  8. Probiotic Leuconostoc mesenteroides ssp. cremoris and Streptococcus thermophilus induce IL-12 and IFN-γ production  Kekkonen et al 2008 NCBI
  9. Impact of Probiotics on Colonizing Microbiota of the Gut Mary Ellen Sanders, 2011
  10. Eat wheat Book 2017 Dr John Douillard
  11. Multiple sclerosis and Alzheimer’s disease. Dal Bianco et al in 2008 NCBI
  12. Type 1 Diabetes Wikipedia
  13. A Journey with Elie Metchnikoff: From Innate Cell Mechanisms in Infectious Diseases to Quantum Biology  Fabrice Merien 2016 NCBI
  14. Louis pasteur quotes Goodreads
  15. The Blood and its Third Anatomical Element 1912 Antoine Bechamp

Author : Eric Malouin


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