Your Microbiome – Part 1

Your Microbiome – Part 1

By Sandrine Clayton

Sandrine explains the details of your micro biome and how, with a little tender low and care, your inner flowers can crowd out the weeds of illness.

Our immune system is mainly developed in the gut which hosts an array of micro-flora, bacteria and yeast.  The term ‘microbiome’ describes the community of these micro-organisms inhabiting our bodies with the power to encourage good health or lead to a variety of illnesses.  An apt analogy is a beautiful garden with abundant flowers (beneficial bacteria) and hopefully not too many weeds (bacteria that cause imbalances).  For good health, it is vital to replant the ‘seeds’ of healthy micro-flora which are constantly being depleted and to keep the gut healthy by preventing the ‘weeds’ from growing.

Often, imbalances in the body that lead to disease start at a very early age.  While still in the mother’s womb, an unborn baby gets its first colonisation of flora, good or bad, from the mother’s amniotic fluid via the placenta1.  A baby born through the vaginal canal then receives more healthy and/or unhealthy micro-flora depending on its mother’s health, which provides additional colonisation of the gut.

This little baby is then fed his mother’s first milk, colostrum, which is a highly concentrated food with the perfect nutritional composition for newborn babies.  Colostrum is rich in protein, fat and concentrated antibodies. This helps protect the infant from gastrointestinal infections2 and further develops the infant’s micro-flora due to certain strains of immune-boosting bacteria and yeast.  Colostrum and breast milk are high in a particular fat called MCT (medium chain triglycerides) and contains lauric acid, a beneficial fatty acid also found in coconut oil.  Lauric acid has anti-bacterial, anti-viral and anti-microbial properties, which essentially means it is a great ‘weed killer’ and keeps the gut healthy for the ‘good flowers’ to grow.

The preferred fuel of the weeds in our inner garden

is glucose. For all humans, whether newborn babies or old-age pensioners, the optimal fuel is fat, not glucose.  Unfortunately, in our modern industrialised diet we over-consume starches such as grains, rice, potatoes and processed foods that are all high in carbohydrates.  Whether one is ingesting a sweet treat or a bowl of pasta, the end result is the body converts this carbohydrate to glucose, which in turn effectively feeds the weeds.

Think of your immune system as your own private army, ready to fight a huge array of invasions from bacterial infections to viruses, pathogens and parasites.  Keeping one’s immune system strong is key to longevity and a healthy life.  We are sadly brought up to believe a pill or a treatment can fix us while it is our body’s immune system that heals us.  Since our immune system is mainly made in the gut, the health of our gut is of prime importance.  It stands to reason that the foods we ingest impact the health of our gut and therefore our overall wellbeing.

Certain foods cause terrible damage to the gut.

Anti-nutrients are substances that oppose the action of other nutrients and can have a negative impact on health as a result. They all act in different ways in the body; preventing absorption, binding minerals, creating inflammation or interfering with our protein-digesting enzymes resulting in poor digestion that can severely impact our health. These are the most common anti-nutrients:


Lectins are found in all plants but are concentrated in grains (cereals) and to a lesser extent legumes and dried beans.  They can harm digestion by damaging the lining of the intestines8. They have been linked to autoimmune disorders9  and leaky gut, and can disrupt the balance of micro-flora in the digestive tract.


Gluten or gliadin is the protein found predominantly in wheat but also in other grains such as barley, bran, bulgur, farina, kamut, rye, semolina and spelt. Gluten found in wheat is one of the worst offenders in damaging the lining of the gut and then causing a huge array of secondary issues.  Studies3 reveal the sad truth that nearly all humans are sensitive to this particular protein.  Modern wheat has been so genetically hybridised that it is capable of producing more than 23,000 different proteins, any one of which can trigger a potentially damaging inflammatory response. The list of symptoms caused by eating gluten is vast and ranges from Celiac disease, IBS, Crohn’s disease, neurological disorders,4 premenstrual syndrome (PMS), infertility and miscarriage,5 and a number of autoimmune disorders6.

Unfortunately, wheat and gluten are used in the majority of packaged or processed products on the market.  Who would have thought that wheat would be in a bag of crisps for example?  In a Mars bar?  In soy sauce?  Ingesting even a small amount can be harmful; most people who have eaten wheat and gluten may have caused some damage to their gut7.


Phytates are found in grains and to a lesser degree legumes and dried beans, seeds and nuts. If eaten in excess they can inhibit mineral absorption10 and interfere with our protein digestive enzymes.


Saponins are anti-nutrients with a link to autoimmune disorders and impaired digestion. These are found in quinoa, amaranth, and nightshades such as tomatoes, aubergines, peppers and white potatoes. Saponins can cause enzyme inhibition and promote inflammation and leaky gut, especially for those who already have compromised digestion and suffer from certain autoimmune disorders, particularly rheumatoid arthritis.


Goitrogens are found in high amounts in soy products and brassicas such as kale, broccoli, cabbage, and brussels sprouts in their raw form.  These compounds inhibit thyroid function and hormone production.


Oxalates are found in concentrated forms in dark, leafy greens and soy. They can cause oxidation leading to inflammation and damage to tissues, including the digestive tract. People with autism and autoimmune disorders should be aware of oxalate’s ability to disrupt the digestive system.  People who suffer from kidney stones or other kidney issues should be advised to avoid foods high in oxalic acid as they can promote the formation of kidney stones.


Egg white should always be cooked and eaten in addition to the yolk.  Raw egg whites contain avidin which blocks the digestion of biotin, a B vitamin, and trypsin, another anti-nutrient that inhibits a protein-digesting enzyme.


Dairy is a food that not all of us can tolerate as it depends upon the body’s ability to metabolise lactose.  A large portion of the world’s population lacks this ability, especially southeastern Asians, American Indians, Chinese (except those of Mongolian or Tibetan origin), Japanese and a few cultures of Africa. It has been noted that where dairy is not a major part of the ancestral traditional diet the incidence of lactose intolerance is very high, therefore implying that the body did not develop over generations certain enzymes to digest lactose.

Raw, full-fat dairy from cows, sheep or goats milk is rich in beneficial micro-flora that protects against pathogens and contributes to a healthy micro-flora in the intestines.  Without these healthy bacteria, homogenised or pasteurised milk is more susceptible to contamination of harmful germs and has a much lower nutrient and vitamin content.

Casein, the protein in dairy, will often cause problems when the gut has been damaged by gluten.  Once gluten has been removed from the diet and the gut has healed, most people who previously required lactose-digesting enzymes can then safely consume dairy.


GMO foods continue to be a highly controversial topic and some studies have shown GMO foods to be allergenic, toxic and carcinogenic.  Studies show that animals consuming a diet high in GMO foods develop a range of health issues including cancer11 and organ failure.  A recent long-term study  on pigs fed a diet of GMO corn and soy revealed that their stomachs were severely damaged.12

The human gut is very similar to that of a pig and these studies not only reveal the damage done when eating these GMO foods, but sadly these sick animals are slaughtered and then enter our food chain which in turn harms consumers.


Soybeans and soy products are some of the most common GMO foods.  Soy is a phyto-endocrine disruptor, which causes havoc with our hormones13.  Soy inhibits fertility,14 blocks thyroid hormone synthesis, obstructs iodine metabolism and is linked to auto-immune thyroiditis.15 Soy contains a large amount of anti-nutrients and causes red blood cells to stick together, thus making them unable to absorb oxygen efficiently to distribute throughout the body.  Soybean products such as miso, natto or tempeh have a reduced amount of anti-nutrients as a result of fermentation.

To find out how you can improve your gut bacteria’s diversity, read Part 2 of The Microbiome.

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