The Microbiome & Internal Balance

    The human microbiome, which is comprised of all the microorganisms (the microbiota) that live on and in humans, plays an essential role in determining good health.

    Microbes cover every surface of our bodies, inside and out. They’re on our skin, inside our noses, mouths, whole respiratory tract, plentiful in our digestive tract, reproductive system, and so on. These microscopic life forms consist of thousands of species and outnumber our own 50 trillion cells by about 10 to one.


    Our microbiome can be considered as a newly discovered, still largely unexplored system, with numerous functions essential to human life. Very few microbes actually cause disease and, in fact, many are essential for homeostasis (internal balance) which is important for good health. They are key to a healthy immune and digestive system.

    As a society, we have become too clean, overly conscious of hygiene! For example, forgetting that babies do require some exposure to various organisms to develop immunity, we over sterilise their bottles and toys, thereby killing the beneficial flora or microbes, leading to Candida overgrowth (thrush).

    We also misuse antibiotics, killing our own microbiome, once again causing overgrowth of Candida and leading to yeast infection. Candida albicans is also a normal part of our microbiome, but needs to be kept in check, and in balance, by our innate intestinal flora or gut microbes. Antibiotics (meaning against life) kill our normal flora, leaving fungi, yeasts, parasites and viruses flourishing, while disturbing our inner balance and immune system health.


    More and more research shows the possible connections to the human microbiome, dysbiosis (microbial imbalances) and chronic Western diseases, including arthritis, gum disease, obesity and cardiovascular (heart and blood vessel) disease – all of which have renegade inflammation at their core. Inflammatory bowel diseases (IBD), from irritable bowel syndrome (IBS or spastic colon), to Crohn’s disease and ulcerative colitis, are directly linked to dysbiosis inside the digestive tract. Evidence is pointing to the microbiome and imbalance in gut microbes as well as an imbalance in lifestyle, with chronically high levels of stress as a trigger for IBD. Instead of crippling immune systems with immunosuppressive drugs, I recommend prescribing an improved set of bugs (gut microbes or probiotics) to patients with IBD!

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    Most of the micro-organisms living in and on us are beneficial, with only some potential pathogens.


    The beneficial ones are called probiotic microorganisms. Lactobacillus acidophilus bacteria reside mostly in the small intestine, and Bifidobacterium bifidum bacteria are found in the large intestine (colon).

    Probiotics improve the environment of the intestinal tract. The regular use of probiotics is important in healing many chronic gastrointestinal problems and allergies. Some experts feel that children with allergic tendencies need several times the amount of probiotics than those without GI problems, due to the frequency of dysbiosis (overgrowth of yeast, harmful bacteria, etc.) and ‘leaky gut syndrome’ (increased intestinal permeability).

    Well-known probiotics include Saccharomyces boulardii, Lactobacillus acidodiphilus and Bifidobacterium bifidus. These restore normal gut flora, improve immune system function, and assist in digestion and absorption of food.


    Also helpful are the prebiotics, inulin and fructo-oligosaccharides (or FOS, found in artichokes, onions, garlic, bananas, and specific supplements). FOS and inulin are non-digestible oligosaccharides that help promote the growth and activity of friendly bacteria in the intestinal tract. These are called ‘prebiotics’ because they are thought to help promote probiotic colonisation and growth. Research has shown that both FOS and inulin enhance the growth of lactic bacteria, especially Bifidobacteria, and inhibit the growth of a variety of undesirable organisms.


    The major benefits of adding probiotic organisms to the diet:

    • Support of the immune system.
    • Improved resistance to allergies.
    • Reduction in yeast and other infections.
    • Inhibition of disease-causing organisms.
    • Improved digestion, increased nutrient absorption and vitamin synthesis.
    • Reintroduction of healthy bacteria into the digestive system. This is especially helpful to restore balance where Helicobacter pylori plays a role in peptic ulcers.
    • Detoxification and protection from toxins.
    • Prevention of diarrhoea from various causes.
    • Reduction in the risk of irritable bowel syndromes.
    • Cancer-protective effects.
    • Probiotics act in various ways to restore and maintain gut health:
    • Microbial antagonism – keeping the microbiome in balance by working against potential disease-causing organisms or microbes.
    • Anti-toxigenic effect – neutralising toxins.
    • Increase in the activity of the intestinal disaccharidases – enzymes promoting carbohydrate digestion.
    • Support of the immune system.

    Digestive enzymes are also very helpful in restoring balance to the intestinal flora population. These can be found in supplement combinations containing pancreatic enzymes (amylase, protease, sucrase, malt diastase, lipase, cellulose, lactase), papain form pawpaw, bromelain from pineapple stem and cultured moulds from the Aspergillus species.

    Probiotics are helpful in restoring balance inside the digestive system. If anyone does need an antibiotic for severe bacterial infection (e.g. pneumonia or meningitis) or suffer from any allergies, be sure to include probiotics to improve gut and immune system health.

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    The 4 Rs

    To restore the internal balance (homeostasis) of your microbiome apply the principle of the 4 Rs:

    1. Remove

    Treat dysbiosis: No yeast/fermented foods for three months; investigate food intolerances and cut out: refined carbs, sugars, wheat and dairy proteins for three months; no decaffeinated or caffeinated coffee, no alcohol, no NSAIDS, no antibiotics.

    Use citrus seed extract, caprilic acid, garlic, Echinacea, oregano, barberry, golden seal, Calendula, berberine and bromelain.

    2. Replace

    Digestive enzymes and factors to lower levels of Helicobacter pylori (pathogenic bacteria found in those with peptic ulcers) and to manage pancreatitis and damage to the mucosal layer of the digestive tract. Digestive enzymes that can be used: proteases, amylases, lipases and cellulases.

    3. Re-inoculate

    • Pro- and prebiotics: Lactobacillus acidophilus, Bifidobacterium bifidus and bulgaricus: live cultures.
    • Therapeutic: 5 to 10 billion organisms two to three times a day.
    • Fructo-oligosaccharides (FOS): artichokes, onions, garlic, bananas, supplements.

    4. Repair

    Nutraceutical food supplements and herbal remedies

    • Eat rice protein basis food.
    • L-glutamine: barrier function, immune support, fuel for intestinal bacteria.
    • Vitamins: A, Bs, C, E, mixed carotenes, bioflavonoids.
    • Minerals: zinc, magnesium, calcium, chromium.
    • Essential fatty acids: GLA (omega-6 – evening primrose or starflower oil), EPA (omega-3 – cold water fish oil).
    • Glutathione (cysteine, lysine), N-acetyl-cystein – liver support, antioxidant.
    • Inulin: as substrate for intestinal flora that use the short-chain fatty acids for fuel.
    • Ginger, mint, chamomile, bromelain (enzyme found in pineapple) to assist digestion.
    • Milk thistle (Silybum marianum) for liver support.
    • For Helicobacter pylori use: probiotics, FOS, vitamins A, C, E, zinc, glutathione, EFAs, garlic, berberine (found in the herbs: golden seal, barberry, oregon grape), Aloe vera, cabbage juice.
    • Fresh ginger (2 cm crushed) and peppermint leaves (about 10, crushed), steeped in hot water, will help for nausea. Take it 15 minutes before meals to improve digestion.

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    Stress management and relaxation

    The digestive system is often called the second brain because of the many receptors for serotonin found there. Digestion and absorption of food should occur in a relaxed atmosphere. Deep relaxation exercises and meditation help you and your gut relax. Yoga refreshes your body, gives you energy and strength, and calms your mind and soul.

    Drink water and a herbal mixture

    Drink at least eight glasses of water and at least three cups of a cleansing herbal tea mixture every day.

    Balanced diet

    Follow a healthy wholesome and balanced diet with plenty of fresh fruit and vegetables, wholegrain products, beans, seeds, pulses and nuts, and garlic, onion, and ginger to prepare tasty and healthy food. Increase your intake of fibre by sprinkling psyllium seeds, linseeds, digestive or oat bran over your porridge, or adding them to salads and other food every day.


    Try to fast one day a week. Drink at least 12 glasses of water, above herbal teas and fruit juices such as apple or grape juice. If you get very hungry, eat an apple or a bunch of grapes. Fasting once a week does wonders for your health and state of mind and restores balance to the microbiome.


    Try to exercise for 15 minutes every day or for 20 to 30 minutes three or four times a week. It is not necessary to exhaust yourself. Choose an activity that you enjoy.

    Beneficial bacteria

    Increase the population of ‘friendly’ bacteria in your intestines by eating asparagus (fructo-oligosaccharides), fresh, full-cream yoghurt with live A and B cultures, or taking the friendly bacteria in food supplement form: Saccahromyces, Lactobacillus and Bifidobacterium are good examples.

    The most important thing is to realise that there must not only be a balance in gut bacteria or flora (microbiome), but also in mind, body and soul!

    Editor’s note: For more articles on probiotics, see:  Probiotics and their conversations in our bodies and The difference between prebiotics & probiotics

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