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5 Ways to Create a Healthy Gut Microbiome

Humans possess an “extended genome” of millions of microbial genes called the “microbiome”. This complex symbiosis influences metabolism, physiology, and gene expression.

Microbes are found throughout the human body, including the gastrointestinal tract, skin, saliva, oral mucosa, and mucous membrane that covers the eye. The diversity in locations makes estimating their overall number difficult. The majority of the bacteria reside in the colon, with previous estimates of about one hundred trillion bacteria, followed by the skin, which is estimated to harbour one trillion. This means that humans are more bacteria than we are human cells and it has been proposed that humans are complex biologic “super-organisms”.


The diverse microbes in the human gut play a fundamental role in the well-being of their host. Modulation of the gut microbiota is an area of growing interest, and it has been suggested to have the potential to reduce risk factors associated with chronic diseases.

Advances in microbiologic analysis are now beginning to implicate the gut microbiome in intestinal diseases such as the irritable bowel syndrome, inflammatory bowel disease, and colon cancer, along with other diseases like type 2 diabetes and obesity. This understanding of the intestinal microbiome is therefore likely to play an important part in the prevention and treatment of diseases and health care regimens.

Evidence suggests that our immune responses and ability to adapt to stress is dependent on the diversity and complexity of gut microbiome.

The trillions of microbial symbionts (good bacteria that live in symbiosis with us) in the human intestine help nutrient absorption through the fermentation of dietary fibre and provide protection from invading pathogens. They also help to develop and regulate the immune system. The naturally occurring microflora in the gastrointestinal tract has profound effects on immunological development of the body. It encourages the immune system to respond more quickly to harmful pathogens by inhibiting them from  multiplying.

Recently it has been discovered that the microbiome plays a key role in controlling the gut-brain axis, which is the pathway for communication between the microflora and the brain, and regulates the immune system, digestion, and how the body responds to stress, among other things.



Gut dysbiosis may contribute to a myriad of ailments, including allergies, celiac disease, gastric cancer, autism, obesity, anorexia, IBS, Crohn’s Disease, and type 2 diabetes.



Results have demonstrated that the gut microbiome isn’t resistant to change and can rapidly respond to an altered diet. Good bacteria are nourished by fruits and vegetables, whereas bad bacteria are fed by meat, processed food, dairy and eggs. Studies have shown that high-fat, low fibre diets destroy the gut microbiome. Studies have also shown that a month on a plant based diet results in an increase in the population of the good microbes, and a decrease in the disease-causing bugs.

On a diet based on animal products, it has been shown that the disease associated species increase. Certain gut flora can take carnitine (from red meat), or choline (from dairy, seafood and eggs) and convert it into a toxic compound called TMAO which may lead to an increase in heart attacks, strokes, death and revascularisation. Increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids, and the outgrowth of microorganisms capable of triggering inflammatory bowel disease. Findings suggest that exposure to animal foods could favour a pro-inflammatory intestinal environment, encouraging endotoxemia development, systemic inflammation and insulin resistance.

Plant-based dietary patterns may promote a more favourable gut microbial profile. These diets are high in dietary fibre and prebiotics. All plant foods are prebiotics because they contain a non-digestible fibre that is used for energy by beneficial bacteria that live in your intestines. Plants give your microbes something to chew on, to break down, and extract the nutrients from. They literally feed the little bacteria what they love and need to survive.

The gut profile of vegans appears to be unique in several characteristics, including having a reduced amount of harmful species and a greater abundance of protective species. Reduced levels of inflammation may be the key feature linking the vegan gut microbiota with protective health effects. A diet characterised by high consumption of fruits and vegetables and low consumption of meat leads to a highly diverse intestinal flora and a greater abundance of Prevotella over Bacteroides which prevents obesity.

So what foods are best to eat?

Any whole, fresh, fruits and vegetables and soaked nuts and seeds. Some great examples are papaya, pineapple, kiwi, watermelon, oranges, apples, and berries. In fact, the addition of wild blueberries to your diet can alter the balance of gut microbe and promote beneficial microbial populations”. Other foods include celery, cucumber, tomatoes, capsicum, cilantro, parsley, kale, spinach, arugula, soaked macadamias, almonds, and walnuts.

Fermented foods or beverages have been shown to directly influence our microbiota and show increased antioxidant and anti-inflammatory activity, reduction of intestinal permeability, improved glycemic control and more. They populate your gut with healthy, live micro-organisms that will crowd out the unhealthy bacteria. The fermented foods I recommend are high quality raw organic sauerkraut and coconut yogurt. I personally love to make my own raw organic coconut yogurt at home. Here is a great video showing you how you can make it: https://www.youtube.com/watch?v=YQsgh9lUhoE


Raw fresh fruit and vegetable juices are another great option to include in your diet. They provide polyphenols, oligosaccharides, fibre and nitrate (beet juice), which may induce a prebiotic-like effect.

To maximise the benefits of drinking juices, you can do a juice cleanse a few times per year. This study proves that doing a 3-day juice based diet of only drinking 6 bottles of fruit/vegetable juice blends resulted in significant changes in the intestinal microbiota. Bacteroides species were significantly increased which was associated with a decrease in markers of metabolic syndrome (cholesterol, blood pressure, etc).


Did you know the way we feel also effects how our gut microbiome works? When we feel relaxed, this helps our gut bacteria to work together harmoniously. However, the Oregon State University researchers found that when someone is under stress, their gut microbiome communities become confused and behave erratically, in ways that are unpredictable and vary from person to person. Even short-term exposure to stress can impact the microbiota community profile.

Dr. Kim Huhman, Distinguished University Professor of Neuroscience at Georgia State states: ”We found that even a single exposure to social stress causes a change in the gut microbiota, similar to what is seen following other, much more severe physical stressors, and this change gets bigger following repeated exposures”.

Therefore it’s important to focus on reducing stress in your life. Practices like meditation, going for a walk in nature, deep breathing, and exercise can help. Eliminate social stresses by communicating in a loving way with someone you disagree with, or reduce and/or eliminate time spent with people who you don’t get along with.


Studies have shown that physical activity can alter the composition of gut bacteria by increasing the abundance of beneficial microbial species.

Cultivate a regular exercise regime that feels good for you. Incorporating a combination of cardio and resistance training is always a good idea. Perhaps that might be yoga and weight training, or running and hitting the weights at the gym.


There isn’t conclusive evidence proving whether probiotic supplements fundamentally alter the gut microbiome, or simply stabilise the microbiota.. Either way, they have been shown to induce health benefits like helping to prevent or treat diarrhea, IBS, ulcerative colitis, Crohn’s disease, vaginal infections and more.

There are hundreds of probiotic supplements on the shelves today and this can be quite confusing and overwhelming. As with any supplement, it’s important to do your research and choose a high quality product. There are many strains of probiotics and each give different benefits. If you have a specific health concern, do your research to discover which strain suits your condition. Alternatively, you can take a wide range of strains to cover a broad range of symptoms.

Things to consider when buying a probiotic is to seek a reputable supplement from an established brand. It helps if the product has positive customer reviews. Ensure the product has no toxic additives. These are the probiotics I personally take and recommend:

Floratrex by Global Healing Centre

Liyfbiotic by Puradyme (this is the probiotic I use to culture my coconut yogurt).

There are very few side effects associated with taking probiotic supplements, but one effect can include digestive upset. There has also been one case of bacteremia (bacteria in the bloodstream) when someone with severe inflammatory bowel diseases with mucosal disruption, was given strain of Lactobacillus GG. As always, if you’re thinking about starting a new supplement regime, do so under medical supervision.

Although we might not be able to restore our microbiome to their original state, we can use natural practices to manipulate specific microbial species to help restore our gut health and stay happy and healthy.


This blog, its content and any linked material are presented for informational purposes only and are not a substitute for medical advice, diagnosis, treatment, or prescribing. Nothing contained in or accessible from this post should be considered to be medical advice, diagnosis, treatment, or prescribing, or a promise of benefits, claim of cure, legal warranty, or guarantee of results to be achieved. Never disregard medical advice or delay in seeking it because of something you have read in this blog or in any linked material. Olivia Budgen is not a medical doctor. Consult with a licensed healthcare professional before altering or discontinuing any current medications, treatment or care, or starting any diet, exercise or supplementation program, or if you have or suspect you might have a health condition that requires medical attention.

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