Introducing your microbiota

For every human cell that makes up your body, there is somewhere between 3 and 10 microscopic organisms that call your body home. You are host to more than 4,000 species of microbes, mostly bacteria, but with a smaller number of fungi, archaea and viruses as well, totalling anywhere up to 100 trillion individuals. They live on the surfaces of your body that protect your insides – this includes not only your skin, but also the surfaces that line your mouth, nose, ears, throat, stomach and intestines, nestling into and colonising your every nook and cranny.

Your collective resident microbes are referred to as your microbiota. Many of the microbe species contribute to your health and functioning, while others contribute nothing but are not harmful, and a few are pathogenic, which means they can cause disease given the right conditions.

Let’s add one more species into the mix (you – the Homo sapiens) and together you and your microbiota become a holobiont; a collective of species, living side by side and cooperatively running the body that sustains you all.

Your genes, more than meets the eye

In 2000, the Human Genome Project (HGP) identified and decoded the ~22,000 genes of the human genome. It was hoped that this development would reveal the cause of many diseases, but unfortunately it turned out that very few diseases are the direct result of a specific gene variant or set of gene variants. Instead, studies that look for associations between gene variants and certain diseases have identified gene variants that affect only a predisposition to a given disease. These are natural variations that under normal circumstances would not usually lead to ill-health, but when faced with a less than ideal environment, could result in the person developing the disease.

But the human body in fact has many more genes contributing to its function and condition than just the human genome. The HGP technology was used for another project which completed in 2012, the Human Microbiome Project (HMB), to identify and decode the genes of our microbiota, of which there turned out to be 4+ million.

Taking into account the genes of the microbiome helps to explain the dramatic increase in the number of chronic inflammatory and autoimmune diseases with significant genetic component which occurred too rapidly to be attributed to the human genome alone. In contrast, our microbial genomes have a tremendous capacity for rapid adaptations which can influence health and disease.

What we have learned from the HGP and HMP is that while individual humans are about 99.9% identical to one another in terms of their human genome, they can be 80-90% different from one another in terms of the microbiome of their hand or gut.

When things go wrong – dysbiosis

While some variation is caused by where you live, who you live with, your age and gender, whether your diet contains more plants, protein or fat, and your level of activity and exercise, these are natural variations that assist with your chosen lifestyle. However, a number of factors can negatively affect your microbiome, and with either acute attack or constant assault can lead to the microbiome being thrown off balance and unable to recover, which known as dysbiosis. Factors contributing to dysbiosis can include:

  • Refined sugar and grains
  • Genetically Engineered (GE) foods (food “products” on supermarket shelves)
  • Herbicides and pesticides
  • Eating animals that have been fed antibiotics and/or GE feed
  • Gluten
  • Pasteurised foods
  • Antibiotics
  • Nonsteroidal anti-inflammatory drugs (NSAIDs)
  • Protein pump inhibitors
  • Chlorinated and/or fluoridated water
  • Stress
  • Pollution

Dysbiosis has been linked with gastrointestinal disorders, colorectal cancer, allergies, asthma, sinusitis, autoimmune diseases, type 2 diabetes, obesity, anxiety, depression and obsessive-compulsive disorder (OCD). While some of these diseases and disorders can be improved or reversed by implementing the strategies in the next section to help re-balance the microbiome, unfortunately not all can.

How to restore order

Gut health can be improved by increasing and balancing beneficial bacteria in the gut, improving the environment and providing food for those beneficial bacteria to thrive, and reducing inflammation of the gut lining and providing adequate building blocks for its constant repair.


  • Eat real food and avoid processed food – mostly vegetables, root vegetables, fruits, nuts, natural nut butters, seeds, sprouted seeds, pulses, brown rice, quinoa, oats, olive & coconut oil, butter, lean meat, fish, eggs
  • Eat more pro-biotic foods – yogurt, kefir, sauerkraut, kimchi, miso, kombucha, pickles, olives, apple cider vinegar (ensure they contain or have been made with active or live cultures)
  • Eat more pre-biotic foods – garlic, onions, leek, asparagus, unripe bananas, oats, apples, flaxseed, green peas, lentils, raw honey, white cannellini beans, artichokes, carrots, cabbage, kiwifruit, tomatoes
  • Use almond, coconut, check pea or brown rice flour instead of wheat flour for baking
  • Sourdough bread with cultures on the ingredient list instead of regular bread (if properly made gluten has been converted by the cultures)
  • Pay attention to your fibre intake, the higher the better – soluble fibre, insoluble fibre and resistant starch all assist in feeding and cultivating good bacteria
  • Make bone broth and consume daily – helps to strengthen and maintain function of the gut wall
  • Eat slowly and don’t overeat


  • Take a broad spectrum, high strength pro-biotic every day
  • If you’re unable to make bone broth or don’t like it, supplement with L-Glutamine
  • If you have digestive problems, try digestive enzymes to see if it helps you

Cut out:

  • Avoid, wherever possible, the foods, additives, medications and environmental factors that contribute to dysbiosis listed above
  • Eliminate any other foods or factors that you know or suspect are problematic for you
  • Reduce alcohol
  • Specifically avoid sugar, artificial sweeteners, dairy (except butter and cultured dairy), refined grains (brown rice, oats and quinoa are good), white rice and white potato, pasta and other processed carbohydrates, oils other than olive and coconut, soft drinks and fruit juices

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