Healing the Microbiome

Healing the Microbiome.Microbiome

What are Microbes?

A microbe or “microscopic organism” is the general term for lifeforms of differing sizes living in the human body they include, bacteria, fungi, protozoan, archaea, fungi, microscopic animals and viruses.


What is the Human Microbiome?

The microbiome has as many bacterium as human cells, some 40 trillion, occupying almost every surface in the human body. Every persons microbiome is slightly different almost as individual as fingerprints. Environment, diet and behaviour all have an effect on the microbiome as well as exposure to toxins and antibiotics.


The Microbiome in Human Health and Disease

The microbiome plays an important role in the body protecting us from disease, supporting metabolism, reproduction and immune function, aiding in the digestive process and supporting the function of body organs.

Disruption of the microbiome can impact health, several diseases have been linked to altered gut bacteria they include: Obesity, type 2 diabetes, (IBS) irritable bowel disease and inflammatory bowel disease. Microbes have a powerful influence on response to medical treatments as well as health and disease.

More than 80% of the immune system is in our gut and it protects us from foreign invasion. An amazingly complex and diverse army is busy at work in our body, day in and day out 24/7 ensuring our continued good health.

So precise, is our immune system we can fight off a cold or flu virus in a day or two without even showing any symptoms. Continuously evolving sophisticated countermeasures and recognition systems to combat a growing diversity of infectious agents in our daily world.


Our World and Environment has Changed Forever.


Our world and our environment has gone through dramatic change in the past 50 years, so dramatic a change our immune system has become overwhelmed. More and more people are suffering needlessly with autoimmune disease.

Transverse Myelitis is a paralyzing autoimmune disorder that once was considered a rear disease only affecting 1 in a million people and prior to the 1950s, there were only a grand total of 4 cases reported in the medical literature.

Today John Hopkins Hospital in the United States treats hundreds of new cases every year and the numbers are climbing.

On the rise autoimmune disease is three times more common now than it was only 4 or 5 decades ago.

Those people suffering from an autoimmune disease now are expected to get at least 7 more autoimmune disorders in their lifetime and they are expected to live 15 years less than a person who has not got an autoimmune disease.

This dramatic rise has nothing to do with better diagnostic tools or increased recognition because the change has been far too fast and far too dramatic. Scientists agree environmental toxins are now considered the largest offender and are responsible for 70% of all autoimmune diseases with only 30% being from a genetic origin. These are powerful statistics, we can all do something about our environment. In part one of Autoimmune Disease How YOU can Reverse a Growing Epidemic you will find some links to healthy living and clean green household cleaners.

Antibiotics have had a major impact on our health and our environment in more ways than we considered when they were first used in the 1920’s.


Environmental toxins and Antibiotics changed our World Forever.


The biggest change in our environment in the past 50 years is the extensive use of antibiotics and herbicides which are constantly altering the microbial landscape of our bodies and our soil. Driving our immune system to its limits and causing it to make mistakes and turn on its own body and attack itself?

Antibiotics revolutionised modern medicine in the 20th century. In 1928 Alexander Fleming identified penicillin, which was the first compound with antibiotic properties. Antibiotics helped the eradication of many diseases like tuberculosis.

Their effectiveness was so great this lead to the widespread but incorrect belief they could be used against viruses.

Abuse and overuse then followed and caused the development of “antibiotic resistance” which is now such a worldwide concern the World Health Organisation has classified it as a “serious threat” which has the potential to affect anyone, of any age, in any country.


What does Antibiotic use do to the Gut?


Dr Axe put it so well describing antibiotics as “the A bomb” causing the likes of an atomic explosion in your gut that exterminates all the bacteria in its way. The gut microbiome is made up of approximately 40 trillion bacteria, along with fungi, archaea, viruses, and protozoans, which are largely responsible for your overall health.

Normal gut bacteria play a vital role in the body:

  • Protection against pathogens,
  • Nutrient metabolism,
  • Immunomodulation,
  • Drug metabolism
  • Maintenance of the structural integrity of the gut mucosal barrier.

According to the World Journal of Gastroenterology:

“A major concern of antibiotic use is the long term alteration of the normal healthy gut microbiota and horizontal transfer of resistance genes that could result in a reservoir of organisms with a multidrug resistant gene pool”.

When that delicate balance is disturbed the gut mucosal barrier can be penetrated allowing organisms to break through into the blood stream causing an attack from the ever present immune system to a presumed pathogen that should not be present.

This can happen anywhere in the body, it may be the joints resulting in arthritis, or the pancreas causing diabetes, the brain resulting in dementia and it can also cause cancer.


Where ever the immune system attack occurs in the body is where the damage is done.


Some people have a predisposed weakness or heredity for example, diabetes and all that is required is a trigger. That trigger could be what appears to be a normal protein, in disguise. Some undesirable toxins can mimic normal proteins or attach themselves to normal proteins and hitch a ride through the body, adhere themselves to any part of the body and cause surrounding cells to alter. In the case of diabetes it is the pancreas cells that have been damaged by the immune system.

An unhealthy gut can bring on metabolic disorders and cause you to put on weight. Antagonists such as gluten, casein and soy can also cause problems because they have very similar proteins to normal body proteins and your immune system can find it hard to decipher one from the other. Neurotoxic bacteria called lipopolysaccharides can also enter the bloodstream and cause widespread inflammation in the liver, heart and kidneys. Or less serious issues headaches, depression, acne, rosacea (red skin on the face) eczema and asthma.


How you can cure your disease using “The 21 Day elimination diet”.


The 21 day elimination diet excludes everything but fresh fruit and vegetables – 2/3 of your plate, fresh meat and fish, no more than 1/3 of your plate. Preferably organic, preferably fresh from your own garden.

The health of the gut microbiome is significant in preventing disease and your DIET is the number ONE WAY to ensure it.

For foods that nourish the microbiome check out part two of Auto-immune disease how you can Reverse the Growing epidemic. Those foods include:

  • Prebiotics – onions, garlic, leek, asparagus, dandelion greens, raw chicory root and Jerusalem artichoke.
  • NOTE: You can get chicory or dandelion coffee from your health food shop to replace regular coffee while on the 21 day elimination diet. 


  • Probiotics – One of the best probiotic foods is live-cultured yogurt, especially handmade. Kefir. Similar to yogurt, this fermented dairy product is a unique combination of goat’s milk and fermented kefir grains. Sauerkraut, Dark Chocolate, Microalgae, Miso Soup, Pickles, Tempeh.


  • Fermented foods – Kefir is a fermented milk product (cow, goat or sheep milk) that tastes like a drinkable yogurt. Kombucha, Sauerkraut, Pickles, Miso, Tempeh, Natto, Kimchi.



Just consuming more fruit, a large variety of vegetables, lean meats and fish you will skyrocket your nutrient intake dramatically because they are more nutrient dense and have more easily digestible fibre than the regular western diet.



Dosages and More on The Master foods of repair for the Gut.



1/ Activated Charcoal


Activated charcoal removes toxins, bacteria, viruses, impurities, heavy metals, parasites, toxic gases, food poisoning, pesticides, herbicides, drug overdose, snake venom and much more.

It is very mild on the gut and is can be taken before every meal if required. If you’ve been invited out and you suspect the food you are eating is contaminated or just not right for you take activated charcoal with you everywhere you go and before you eat have 2 tablets. Some people with IBS have even managed to eat dairy without any adverse effects. Activated charcoal has been used for thousands of years and has no adverse effect on the body.

Recommended dosage: 1 tablet per day or before every meal.


2/ Next I recommend Colostrum to fully repair the Microbiome.


Colostrum contains high concentrations of leukocytes, protective white blood cells which can destroy disease-causing bacteria and viruses.

Extremely easy to digest colostrum is very high in concentrated nutrition especially for the gut. Loaded with antibodies to fight infection, colostrum seals holes in the gastrointestinal tract with a protective barrier preventing foreign proteins from penetrating the gut wall and causing harm to the body. The ultimate healthy start to life this food is your healthy restart to a new revitalized you.

You can get bovine colostrum from your health food shop which is perfect for human consumption.

Recommended daily allowance: In an acute situation: 1 tablespoon of colostrum powder daily. Or 4 tablets daily. For maintenance and balance 1 teaspoon of colostrum powder daily or 1 tablets daily.


3/ Follow up with Bone Broth.


Bone broth can be found all over the internet and we can learn the most about bone broth from history. Staples of all traditional diets bone broth is legendary.

In Chinese medicine, whose origins date back over 2,500 years, bone broth is used to support digestive health, as a blood builder, and to strengthen the kidneys. Then, beginning in 12th century Egypt, physician Moses Maimonides was known to prescribe chicken soup as a medicinal remedy for colds and asthma.

Nature’s multivitamin, bone broth is packed with collagen, glycine proline and glutamine all building blocks for repairing connective tissue.

I have my own personal recipe for bone broth that comes from a cook book my grandmother used. Odhams Encyclopaedia of Cookery 1950s.

What I love about this cook book is the recipes are simple, very tasty and packed with fresh ingredients. And also what I love about this recipe for bone broth is that the bones have been fried or roasted first to help remove a lot of the fat and drained. When I make my bone soup I always use cooked bones from the organic roast chicken we had the night before. Waste not want not. I have seen other bone broth recipes that also recommend roasting the bones first.



Bone Soup – Odhams Encyclopaedia of cookery 1950s. With my nutritional twist.


  • 1 chicken carcass from an organic roast chicken.
  • 2 cups, raw fresh vegetables include carrots, turnip, parsnip, beetroot or other root vegetable, diced in small pieces.
  • 1 square inch of fresh ginger diced,
  • 1 large onion skinned and diced,
  • ½ cup of celery
  • 2 cloves,
  • 4 cloves of garlic whole,
  • 50 grams of coconut oil,
  • 2 litres, cold water,
  • a handful of fresh herbs: thyme, sage, parsley and a tablespoon of rosemary leaves, (all of these herbs are powerful antimicrobial herbs).
  • 1 teaspoon of peppercorns,
  • 1 level tablespoon of homemade tomatoe ketchup, (optional)
  • salt and pepper.

Place 2 cups of diced vegetables in a roasting dish with coconut oil and cook until the vegetables have browned. (Approximately 20 minutes).

Set aside and drain.

Add 2 litres of cold water to a stock pot and add vegetables and bones and the rest of the ingredients.

Bring to the boil and simmer on a very low heat for 6 hours removing the scum as it rises.

Strain through a fine sieve and leave until cold, it is best to leave it until the following day, then any fat that settles on the top can be removed.

This stock is a great base for any soup.


Recommended dosage: 2 cups per day. For colds, flu and acute sickness, sip chicken broth ½ hourly.

If you like it thick.

Try 1 cup of cooked, fresh kumara (sweet potato) or pumpkin.

Combine 2 cups of broth and 1 cup of cooked vegetables, blend until smooth in a blender. Heat and eat.


The elimination diet has plenty of fresh vegetables and you can make your choices here  among’st the more than 100 super-foods list.

You can make smoothies from anything in the super-foods list.

(Just avoid the foods NOT on the elimination diet list for 21 days)

Substitute milk for coconut milk or cashew nut milk or unsweetened yoghurt instead of regular milk.

4/ Easy coconut milk

1 can coconut milk

1 can water

Shake. Place in container in frdge and use in place of regular milk.

5/ Easy cashew nut milk

1 cup raw cashews nuts soaked overnight

1 cup water

Blend in a blender until smooth

 Place in container in frdge and use in place of regular milk.


6/ Apple cider vinegar

Apple cider vinegar is going to be a must in your 21 day diet. You can use it for dressing on your salads and you can use it to detoxify vegetables.1 capful (capful = Lid capful) tossed in fresh salad will detoxify non organic vegetables. And 1 capful in every smoothie to aid digestion.

If you want to find out more about Apple cider vinegar and its therapeutic value check it out here.



The foods to Avoid.


1/ All Processed Food.


All processed foods have additives, sugars, preservatives and plastic packaging that none of us need if went want to be healthy again.


Surprisingly you will find by not purchasing these items you are going to save money.


Contrary to what we are lead to believe packaged processed food is not cheaper.


To make it easy, shop around the outside isles in the supermarket. You will find everything you need.


2/ Sugar – White Death


The number one food to avoid is sugar. Also known as white death sugar is addictive, deadly and toxic to the body it feeds bad bacteria and promotes yeast and candida overgrowth, all of which damage your gut. The amount of sugar the body can assimilate in a day is just 3 teaspoons for a child, 6 – 9 teaspoons for an average adult. All processed foods are high in hidden sugar to add flavour. Sugar damages and overloads your liver, increases uric acid levels causing heart and kidney disease, causes you to eat more and develop insulin resistance, obesity as well as damaging many other bodily functions.


It is not easy to avoid sugar even when you make a concerted effort because it is so addictive. Don’t be too hard on yourself if you have a relapse and dive into that bag of lollies, allow yourself time and be persistent and one day you won’t even enjoy it anymore, everything will taste far too sweet and sugary foods will not tempt you again. The secret is to persevere.


3/ Grains


Avoid grains while on the elimination diet. Certain low GI grains can be introduced later but the main ones to stay away from are processed wheat (white bread) which contains gluten a hard to digest protein. Gluten may need to be avoided completely from the diet because of its growing connection to health problems.

The problem with grains is there high glycaemic index meaning they release glucose rapidly into the blood stream causing toxicity. High glycaemic grains can cause blindness, increase cardiovascular disease and kidney failure.

Low glycaemic grains release glucose more slowly into the blood stream allowing the body time to process it properly. If you enjoy grains then only consume whole low glycaemic organic grains such as barley, buckwheat, bulgur, Oats, quinoa, rye wild rice and limit them to 10% of your diet.

If you are worried about getting your fibre, then grains are not the best source of fibre anyway we don’t process it as well as we do fruit and vegetables.

Many other foods contain more nutrients than grains so they will not be missed from your diet.


4/ Dairy


We hear a lot about dairy and the problem with beta- casein 1 cows

as opposed to casein 2 cows. Casein 2 is regarded as much healthier than casein 1 the difference being one very important amino acid or (imino acid) proline. Casein 1 cows have the proline missing substituted for the amino acid histidine, which is considered inflammatory.

Although Wikipedia class New Zealand milk as casein 1 cows this is not entirely correct because here in New Zealand all the milk goes into the same vat so to speak and we milk both friesian cows (casein 1) and jersey cows (casein 2) so I think we are pretty well protected but the problem with dairy is a bit deeper than that. While whole fresh organic grass fed cow’s milk and yoghurt are regarded as ok. Cheese on the other hand is not, because of the high saturated fat content. Saturated fat was always one of the bad guys, but we are learning today that in fact saturated fat is not the problem it was once thought. Personal responsibility for what you consume is in your hands when you do not buy processed foods and takeaways loaded with cheese you are controlling how much cheese you eat. If you’re a cheese lover. Buy good quality and limit consumption. If you are lactose intolerant then stay away but if you can handle yoghurt then I highly recommend it especially if it is New Zealand origin and organic.

In closing: Are there any more details I need to cover?


The 21 day elimination diet is going to get you right back on track.


And turn your body into a healthy optimally functioning machine. Are you prepared to take 21 days out of your life to recreate a better, stronger, happier, healthier YOU?


The 21 day elimination diet will eliminate your pain and inflammation.


And help alleviate Chronic fatigue, Mood disorders, Allergies, Asthma, Depression, Anxiety, Autoimmune disorders, Obesity, Weight gain, Migraines, Kidney and gallbladder problems, Arthritis, Nutrient deficiencies, Learning disabilities, Insomnia, Trouble sleeping, Cognitive decline, Neurodegenerative diseases, Dementia, Parkinson’s disease, Muscle and joint pain, Cancer, Chronic fatigue, more…

In some cases eczema can be eliminated in just 24 hours.



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Deborah Harper

Article by Debbie Harper

Debbie Harper is a self-published author and an accomplished blogger. She's the founder of www.happyhomesnz.com and the author of the book “The Number #1 Rule for a Long and Healthy Life”. If you like this post, you can stay up to date with the latest information from www.happyhomesnz.com by subscribing via RSS, or receive articles directly in your inbox. Then click here to download a free report on "The Number #1 Rule for a Long and Healthy Life".