As part II of this 3 part finale in the previous article we dwelled on the dietary foods as defined in the GAPS ( Gut and Psychology Syndrome ) diet and probiotic supplements such as Fermented food and beverages.  To complete the healing picture I want to describe the benefits from Probiotic food and health delivered from the more common bacterial species, 

Probiotic bacteria benefits

Strengthening the mucosal Firewall

When we talk of probiotics we either refer to a supplement and its bacterial content or the beneficial bacteria inside our gut. We have discussed the benefits provided by our probiotic (Beneficial) bacteria in the previous articles concerning the Microbiome, where particular E-Coli strains enhance protein expression of Intestinal Epithelial Cells enhancing gut barrier integrity. Further strengthening of the barrier is afforded by metabolites secreted by probiotic/Opportunistic species Bifidobacterium infantis and Lactobacillus plantarum , Bifidobacterium lactis, Salmonella enterica serovar Typhimurium, Lactobacillus acidophilus, Streptococcus thermophilus, Bacteroides thetaiotaomicron, Lactobacillus rhamnosus and Bifidobacterium Longum.

Natural antibiotic production

Natural antibiotics called Bacteriocins are released by bacterial species as a mechanism to control pathogenic growth which include Lactobacillus acidophilus that secrete Acidocin, Staphylococcus aureus that secretes Aureocin and Escherichia coli that secretes Carnocin and many more. In fact a study conducted in 2001 identified 100,000 different antibiotic substances were produced by Streptomyces, the largest genus soil bacteria of the phylum Actinobacteria over a number of years. Interestingly enough, if pathogenic bacteria overgrow and proliferate it is the waste products from these bacteria known as endotoxins that irritate the intestines which is the trigger for Irritable Bowel Disease ( Crohn’s and Ulcerative colitis). However endotoxins from probiotic bacteria is harmless and in some instances are beneficial.

Host vitamin synthesis and increased mineral bioavailability

As we explained in the previous article probiotic bacteria such as Lactobacillus (Lactococcus lacti, Lactobacillus gasseri, Lactobacillus reuteri) and Bifidobacterium adolescentis) can synthesize vitamins K2, Biotin (B7), Cobalamin (B12), Folate (folic) acid (B9), Niacin (B3), Pantothenic acid (B5), Pyridoxine (B6), Riboflavin (B2),  and Thiamine (B1). Other bacterial species also synthesize vitamin production such as Bacillus subtilis and Escherichia coli that produce B2.  Probiotic flora also increase bioavailability of minerals including Copper, Calcium, Magnesium, Iron, Manganese, Potassium, Zinc and possibly more.  Probiotics break down, to enhance digestibility, Proteins and fats, break down and process Carbohydrates and sugars, increase digestibility of Milk and phytonutrients and bind to/ reduce blood level cholesterol.  It might be noted here that in a way the host competes with other bacteria in terms of nutrient benefit, since Lactobacillus Bulgaricus produce folic acid, but  Lactobacillus acidophilus consume it, but the net effect is still positive on the side of the host.   

Lactobacillus Acidophilus maintains a certain acidity in the body by producing lactic acid ( hence the word Acid in acidophilus ) and Hydrogen peroxide which discourages the proliferation of harmful bacteria. This species also produces vitamin K and Lactase enzymes to break down milk products ( hence the ‘Lacto in Lactobacillus). This bacteria is 0.6 * 1.5 micrometres which is 10,000 times smaller than a Pinto bean..imagine. Other probiotic species are Lactobacillus rhamnosus that thrives in acidic conditions and it to, produces lactic acid and provides benefit to our neurological pathways and treatment of any not so friendly bacteria like Candida.  Bifidobacteria longum is also a common species that are added to probiotic products, which is an anti-inflammatory, protecting cells that line the mucous membranes. It also provides other benefits including the production of enzymes that digest proteins, provides bone health properties, prevents colon cancer ( as does Butyrate from Butter ) and lowers cholesterol.

Nutrient absorption and bile

Probiotic bacteria are also critical for nutrient absorption by breaking down complex proteins into individual amino acids and breaking down fats into mid chain fatty acids. The microbiota play a role in bile acids. Bile acid synthesis is around 400-600 mg/day, and daily secretion into the intestine is around 12-18g maintaining a bile acid pool size of around 4-6g resulting in a bile recycling process occurring several times/day. Around 95% of bile acids are reabsorbed by active transport in the ileum of the small intestine, and recycled back to the liver. A part of emulsification of fats, bile acids assist in the elimination of of non recycled cholesterol, emulsifying fat soluble vitamins bringing them to the ileum absorption site, as well as the elimination of waste such as dead red blood cells known as Bilirubin ( this substance is yellow, and can cause a yellow coloring of the skin which is called Jaundice and is an indication that there is a dysfunction either in the liver or gallbladder..  

Non-recycled cholesterol is typically cholesterol esters, the form found in most foods, although the  liver can convert it to cholesterol this is an additional step, which the body will avoid if there is another possibility, such as reabsorption.  Since bile contains cholesterol the body reabsorbs this cholesterol and eliminates the rest. This is where our microbial symbionts become part of the equation.  Anaerobic bacteria of the Genus Eubacterium (phylum: Firmicutes ) that reside in the colon ( cecum) are responsible for this elimination process by converting cholesterol to Coprostanol. As part of its energy production process the Eubacterium uses the converted product as a terminal electron acceptor involved in the energy producing electron transport chain that uses electron transfer, accepting electrons and oxidation to drive the cellular energy process.

Aromatic amino acids

Probiotic bacteria manufacture some very important ‘aromatic’ amino acids Phenylalanine, Tyrosine and Tryptophan using a 7 step metabolic route called the Shikimate pathway. Only our own microbiota can achieve this since they are the only community that have this pathway. All 3 amino acids are essential to human health. Phenylalanine and Tyrosine are needed to produce neurotransmitters epinephrine,norepinephrine and dopamine that control the way we perceive and interact with our environment, while Tryptophan produces niacin and serotonin for healthy sleep and stable mood patterns.

Indigestible Oxalate metabolism

In nature, many plants ( vegetables and Fruit ) contain oxalates to protect themselves from infection or being eaten ( the oxalate content tears up the teeth of the bug ), Foods such as Spinach, dates,grapefruit,orange,avocadoes,carrots,celery,nuts are high on the oxalate index. Even chocolate or at least milk chocolate which has certain amount of calcium in it. The good news is that if you have a healthy microbiome bacteria that reside in the colon ( large intestine ) including Oxalobacter formigenes, Eubacterium lentum ( strain ), and Enterococcus faecalis, they all metabolise oxalates ( there are in fact 18 identified microbial species known to degrade oxalates including Lactobacillus, and Bifidobacterium ). Environmental pH levels are important since for example Oxalobacter formigenes provides optimal oxalate degradation at a pH level of 6.4 ( slightly acidic ) so if body pH imbalance exists this could have an affect on oxalate metabolism.

Microbes to men and women

A well nourished gut flora contains around 150 microbial species that has over 9,000 glycoside hydrolase enzymes and 2,000 polysaccharide lyases thus providing an estimated 60,000 carbohydrate degrading enzymes. Within the microbial communities it is known that there is cross feeding that occurs between species and its this nutritional interaction that ultimately shape the microbes metabolic capacity, where one species will digest a substance and secrete a metabolite (chemical fingerprints of cellular processes ) such as lactic acid, acetic acid or butyrate which are then ingested by other microbial species to achieve optimal energy for the host. Propionate is a microbial fermentation metabolite that is promoted by dietary intakes of Arabinoxylan,  a substance found from the outer shell of wheat and rice, and available as a dietary fiber supplement, or Polydextrose which is a synthetic sugar fiber and only partially fermented by our gut microbes.

Dietary Probiotics

The market is inundated with many probiotic products.  Like the the hundreds of vitamin and mineral pills sitting on shelves at the pharmacies who knows what is good or bad. In my opinion synthetic vitamins and minerals cannot be used effectively by the body anyway..we don’t have the blueprints for them. Vitamins and minerals in a whole food format mimics the nutrients found naturally in food so they are more likely to be accepted by the human body and some of it will be absorbed.  There are many documented studies showing benefit from supplementary probiotics, but if these studies are animal based they typically would not be helpful since bacterial strains are different in animals so it’s an apple vs orange comparison. Many studies use volunteers that already have a diseased condition, and indeed the results have produced improvements using supplementary probiotics. If you want to try supplementary probiotics there are many on the market for you to research. But be diligent because some low quality products contain dead bacteria and some do not actually contain the strains that are written on the would you know any different unless you had the means to analyze it, so you have to rely on reputable brands. I personally believe that making your own probiotic food is best,  

Various lacto fermentation products

When vegetables are fermented using a simple lacto fermentation process using just salt as a ferment starter the vegetables will naturally contain  Lactobacillus plantarum, L. pentosus, L. brevis, L. acidophilus, L. fermentum, Leuconostoc fallax, and L. mesenteroides.  Korean Kimchi harbors bacterial strains that include Lactobacillus plantarum, L. pentosus, L. brevis, L. fermentum, L. casei, Leuconostoc mesenteroides, L. kimchi, L. fallax, Weissella confusa, W. koreenis, W. cibaria, and Pediococcus pentosaceus.  European sauerkraut contains L.mesenteroides, L. Plantarum, L. brevis, L. rhamnosus, and L. plantarum.  Taiwanese Yan-tsai-shin that is fermented broccoli using Sugar, soy sauce, and sesame oil as the ferment starter contains W. paramesenteroides, W. Cibaria, W. minor, Leuconostoc mesenteroides, L. Plantarum, and E. sulfurous. Chinese Paocai that is fermented Cabbage, celery, cucumber, and radish that uses Ginger, salt, sugar, hot red pepper as a fermented starter contains L. pentosus, L. Plantarum, Leuconostoc mesenteroides, L. brevis, L. lactis, and L. fermentum.  In Spain and Italy they ferment olives using salt as the ferment starter which contains L. plantarum, L. brevis L.  pentosus, P. cerevisiae, and L. mesenteroides.

Common bacterial strains in fermented vegetables ( as shown above)

From the list of beneficial bacterial strains Lactobacillus plantarum is a strong bacterial strain that survives throughout the intestinal tract to the end of the colon, and thrives in  temperatures of 86-96 deg F (30-35.5 deg C). This strain secretes antibiotics Lysine and Lactolin providing growth control of pathogenic flora simulating growth for beneficial flora residency. They have the ability to reduce inflammatory TH2 redressing TH1/TH2 balance, fungal infection, IBS, infection, systolic blood pressure, leptin levels, interleukin 6 ( pro-inflammatory cytokine and anti-inflammatory myokine which are involved in muscles and exercise), pneumonia risk and kidney oxalate levels.   Lactobacillus fermentum enhances the uptake of cholesterol to strengthen cell walls and cellular membranes and has antimicrobial and antioxidative properties secreting acetic,lactic,succinic acids and putrescine to maintain acidity in the intestinal tract. This is intended  to control pathogenic growth ( suppression of Enterococci and Staphylococcus aureus), .withstanding PH levels drops from 4 to 2.5 ( very acidic as in the stomach) itself, and its antioxidant properties has a positive influence on reducing oxidised LDL cholesterol.

Lactobacillus brevis also found in dairy has a positive influence in periodontal disease and oxalate levels. Leuconostoc mesenteroides is a facultative anaerobe meaning this organism can exist in oxygen or without oxygen which produces lactic acid and carbon dioxide also lowering intestinal PH.  An intriguing study was completed in 2008 by Kekkonen et al to analyze immune system cytokine stimulation from 11 different probiotic strains from Streptococcus, Lactobacillus, Bifidobacterium, Lactococcus, Leuconostoc and Propionibacterium genera. Cytokines analyzed were TNF-α, IL-12, IFN-γ and IL-10. Of the 11 genera strains Streptococcus and Leuconostoc were the best best inducers of Th1 type cytokines IL-12 and IFN-γ.

Common bacterial strains found in dairy

The most common probiotic bacterial Genera are Lactobacillus and Bifidobacterium. Many more genera inhabit the human gut including Eubacterium, Fusobacterium, Peptococcaceae, Rheumanococcus and Streptococcus which are opportunistic strains meaning they can be beneficial or pathogenic ( In a balance environment they are beneficial, if not they become pathogenic).  If you pick up a bottle of kefir or organic yoghurt and the bacterial cultures are written on the bottle you will inevitably find Lactobacillus Acidophilus, a  facultative anaerobe as well which was first discovered by Ilya Metchnikoff, and like most beneficial flora have a controlling effect on pathogenic flora by acidifying the intestine. However, this species goes a stage further possessing the ability to rid the body of a nasty pathogen Candida Albicans which we have discussed in earlier articles. It also is capable of inhibiting pathogenic E.Coli, Helicobacter pylori, Salmonella, Shigella and Staphylococcus.  This species produce digestive enzymes such as lactase,lipase and protease to break down casein, fats and protein, as well as inhibiting antibiotic yeast infections. Other species such as L.Casei, L.Rhamnosus, and L.Bulgaricus all enhance immune system function among other benefits.

The colonies of Bifidobacterium are in charge of host waste processing and micronutrient extraction from food before excretion. They prevent from endotoxins reaching the bloodstream as well processing bile and liver chemicals keeping a watchful eye on the intestinal liver conduit. Case Adams in his brilliant book ‘Probiotics, protection against infection’ informs us that as we age this species which is the largest colony in the colon (90%) diminish, despite the natural amalgamation of species including B.Infantis, B.Longum and B.Brevis. Therefore it is crucial for older people like me to regularly consume probiotics.  B.Lactis as the name suggests is commonly found in fermented dairy has anti inflammatory effects toward the immune system providing modulation and the reduction in ear inflammation Otitis Media, and normalizing bowel movements and many other benefits.

Streptococcus strain fights on the side of the good guys

When I wrote the articles on the microbiome I discussed some of the beneficial and opportunistic (Commensal)  genera and species. One such opportunistic genera is Streptococcus ( from strep throat infection fame), its phylum is called Firmicutes a definite troublesome pathogenic species, what I am calling an intestinal bully.  However there is another species of streptococcus called thermophilus used in the production of cheese and yoghurt and found typically in other fermented dairy products like kefir.  Like no other species it can colonise in temperatures of 104-113 deg F (40-45 deg C) breaking down lactose, as well as immune system regulation, inhibits Clostridium difficile, another infamous bacterial bully, reduces baby colic and restores infant microflora. It can also reduce respiratory tract infections from Staphylococcus aureus, Streptococcus pneumoniae, beta hemolytic streptococcus and Haemophilus influenzae.

Probiotic Ingestion

I am not sure if many people know how supplemental probiotics help the gut, some believe it reseeds the gut replacing lost colonies or indeed feed the residential colonies.  In actual fact ingested probiotic foods and supplements are simply transitory, and may be they are just visiting old colonial friends for a few days…lol. As a child the gut requires colonisation, but once that is achieved the new permanent microbial colonies remain permanent during the life of the host. Providing you follow a healthy diet of organic fruits vegetables, seeds, nuts, grains and spices your permanent microbial residents will be quite happy for life.  If you upset this delicate balance by ingesting man made food, allowing yourself to become excessively stressed or get talked into taking broad spectrum antibiotics from the man in the white coat, then you need to redress the balance by stimulating growth of our beneficial microbial ‘housekeepers’. As we have discussed above most beneficial species of supplemental probiotics re-acidify the intestinal gut space, releasing lactic acid and nucleic acid and other nutrients to to stimulate growth of our permanent beneficial flora residents.  This allows our transitory probiotic supplements to take back control from the opportunistic/pathogenic flora and hand it back to the beneficial flora. All probiotic supplements from fermented food or other sources only remain in the gut from a few days to a couple of weeks, which should be enough time to stimulate regrowth of the permanent microbial residents and cut back the growth of the pathogenic colonies and establish balance again.


In the final part III of this series we will conclude with a discussion on synbiotics and supplemental notes.

There used to be only a vague answer to the problem of the body’s resistance, remarkable as it is. Since the memorable discoveries of Pasteur and his co-workers who found that immunity could be conferred by means of vaccination with microbes, the question has all at once become vastly clarified. The problem has become open to study by experiment. For Pasteur, who was a chemist, the fact that the undamaged organism does not allow certain morbid agents to spread within it, could be explained simply in terms of the chemistry of the environment. In the same way that plants will not grow on soil that lacks some substance indispensable to their growth, so microbes, these microscopic plants which cause infectious disease, are unable to grow in an organism which does not give them all the substances they need.

Elie Metchnikoff” (from his  Nobel Prize speech Dec 11 1908)

These microscopic organisms form an entire world composed of species, families and varieties whose history, which has barely begun to be written, is already fertile in prospects and findings of the highest importance. The names of these organisms are very numerous and will have to be defined and in part discarded. The word microbe which has the advantage of being shorter and carrying a more general meaning, and of having been approved by my illustrious friend, M. Littré, the most competent linguist in France, is one we will adopt.

Louis Pasteur (1878)

In fact, the following year Pasteur, in a memoir upon lactic fermentation1 of sugar, under the conditions of Berthelot’s experiment, placed himself on the side of Schwann and asserted that the development of special living beings was the sole cause of the fermentations pointed out, but without paying any more attention to the molecular granulations that Berthelot had done, he had the merit to distinguish among the particular living beings that which he named lactic yeast, and which he regarded as being to lactic fermentation what beer yeast is to the alcoholic. But of the development of these beings, especially of the lactic and alcoholic yeasts, what according to him, was the cause? He had the choice between two hypotheses; that of the germs of the air with Spallanzani and Schwann, and that of spontaneous generation; he chose the second, asserting that these beings were born spontaneously of the albuminoid matter of the nitrogenised matters

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)

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. Ilya Mechnikov – Nobel Lecture Dec 11 1908 Nobel
  12. Louis Pasteur quotes TODAYINSCI
  13. The blood and its third anatomical element Antoine Bechamp 1912


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