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How To Restore Your Gut Microbiome

Written by

Deborah Freudenmann BHSc

The human microbiome is a collection of trillions of microorganisms which populate your intestines. Your microbiome is essentially its very own complex ecosystem. Although the microbiome consists of a diverse range of microorganisms (bacteria, archaea, fungi, protozoa and viruses), it is primarily populated with bacteria which are located in your gut.

Your microbiome is a complex ecological community, which communicates, cross feeds, combines, evolves with you and your environment. The symbiotic relationship between your body and your gut is important to understand. You depend on your gut microbiome and your gut microbiome depends on you. One cannot thrive without the other. The micro-organisms living in our gut perform a wide range of useful and health promoting activities, however they can also be responsible for the development of different diseases.

In the modern world, your human microbiome is often exposed to harmful factors. Poor dietary and lifestyle habits as well as increased stress levels decrease the diversity and effectiveness of your microbiome’s functions. All of these factors lead to an increased chance of developing various chronic conditions.

For maintaining your long-term health, prioritisation of your microbiome’s health is necessary.

The Negative Impacts of Our Modern World

As industrialisation swept through the world, developing nations began witnessing changes in individuals’ microbiota. Organisms such as H. pylori, and the ratio between Prevotella and Bacteroides species, have acted as indicators of a healthy gut. Over time, these ratios have changed, corresponding to altered gut function and poor health.

Currently, the mechanisms that maintain perfect balance in our gut remains unknown. As each individual’s microbiome is unique, it makes it difficult to track the exact links. However, it is widely known that when the microbiome is pushed beyond its functioning capacity, due to altered microbial population or diversity, the individual enters an alternative state—a pre-disease or a disease state. This state is defined by a host vulnerable to disease and health complications.

Returning to a healthy and balanced gut microbiome it requires a holistic approach, with specific steps to help re-build its diversity.

What is dysbiosis?

Dysbiosis is a term to describe microbial imbalance that most often affects your gut or intestinal tract. As you know, the gut is host to many different microorganisms and not all of them are friendly or good. This only becomes an issue when there is an overgrowth of these bad microorganisms – bacteria, parasites, fungi, yeasts or other organisms which lead to dysbiosis. Having too many of these intestinal pathogens can result in intestinal inflammation contributing to digestive diseases, small intestinal bacterial overgrowth, irritable bowel disease and candida overgrowth.

A study on the use of ozonated water and rectal insulation in patients with intestinal dysbiosis was conducted. The study confirmed the validity of the treatment with ozonated water combined with rectal insufflation to control the symptoms linked to dysbiosis and favouring the restoration of proper environmental homeostasis in the gut microbiome.

Therefore this treatment combination is useful in microbiome imbalances along with a nourishing diet, healthy and active lifestyle, and clinically proven, strain-specific probiotics that nourish the present bacteria. Further steps like reducing antibiotic overuse and the heavy intake of processed foods is crucial.

Nourishing your gut microbiome

Individuals should maintain a diet rich in prebiotics, probiotics, fiber and polyphenols to support the diversity and function of the gut microbiota.

Unfortunately, the standard Western diet, lacks sufficient microbiota accessible carbohydrates. This lack of nutrients subsequently disrupts the balance of the gut as it cannot feed the beneficial bacteria. In turn, insufficient diets contributes to the onset of various inflammatory chronic diseases.

Adding MCAs to one’s diet can combat this, thereby improving your metabolism and immunity. The foods listed below have been shown to improve microbial diversity and improve overall gut health.

  • FOS (fructooligosacchrides) and Inulin 
    • Garlic
    • Jerusalem Artichoke
    • Leek
    • Onion
    • Asparagus
    • Rye
    • Tomato
    • Honey
    • Wheat
    • Bananas
  • Resistant Starch
    • Cooked then cooled potatoes
    • Bananas
    • Cashews
    • White Beans
    • Lentils
  • Fibre
    • Flaxseed
    • Fruits 
    • Whole grains
    • Chickpeas
    • Raspberries 
  • Polyphenols
    • Blueberries
    • Strawberries
    • Peach
    • Plum
    • Cocoa
  • Other Prebiotic Foods
    • Kiwis
    • Beetroot
    • Green peas
    • Snow peas
    • Red kidney beans
    • Soy beans
    • Watermelon
    • Grapefruit
    • Fennel bulb
    • Savoy cabbage

A modern microbiome supportive lifestyle

A weak gut microbiome means its suffering from inadequate microbial diversity, which needs to be restored.

Simple lifestyle changes benefit the gut microbiota, like adding aerobic activity into one’s daily life.

A recent study found overweight women that participated in a 6-week endurance program increased their count of beneficial bacteria Akkermansia and decreased the pathogenic Proteobacteria population. The women achieved these positive changes without any dietary changes—exercise alone improved their microbiome.

Reducing stress is another effective method of improving gut health. Within the past decade, various researchers have found links between bacterial diversity and the adrenals. Studies have shown increased stress levels reduce the number of the beneficial bacteria Lactobacillus. Additionally, researchers have found individuals with higher stress levels experience bacterial translocation—a sign of a weakened digestive system. Proving that reduced stress levels is vital for the flourishment of a healthy gut microbiome.

Recent studies have even shown that having poor dental health contributes to a strong imbalance within the gut. Individuals with higher levels of periodontal gingivitis have greater risk of their microbiome becoming dysbiotic.

Other lifestyle changes proven to create positive change include owning a pet, getting sufficient sleep, staying hydrated, and quitting smoking.

Are probiotics important?

As research has shown that dietary and lifestyle changes impact individuals’ gut health the most, they should make up the foundation for any treatment plan. However, if your gut falls into an altered state of balance, clinically proven probiotic strains should be taken to support the regeneration of their core bacteria.

Some of the most researched strains for restoring gut microbiota include:

  • Lactobacillus rhamnosus is a strain of bacteria that dramatically influences the diversity and populations of the resident microbiota. It promotes the growth and function of 5 of the 6 strains that make up the core group of bacteria in a healthy, stable microbiota.

  • Saccharomyces cerevisiae is a microorganism that is responsible for reducing the antibiotic-associated loss of bacteria and restoring microbiota. It also increases populations of bacteria that are fundamental to healthy microbiome function.

  • Bifidobacterium animalis ssp lactis is a strain of bacteria that prevents the growth of pathogens while regulating the expression of carbohydrate metabolizing enzymes. Thus, it allows commensal bacteria to flourish and further support the gastrointestinal environment.


Together, these microorganisms exhibit a positive impact on the host by improving barrier integrity, modulating the immune system, and interacting with the nervous system.

Furthermore, probiotics have been proven to reduce metabolic disease, gastrointestinal disease, and colon cancer. Ultimately, these three strains produce the required effects to rebuild diversity and improve the functionality of the gut microbiota.

Final words

In the modern world, protecting and restoring gut microbial composition and function is necessary for a healthy life. It’s essential to help clients understand the importance of healthy dietary habits and lifestyle practices, in conjunction with ozone therapy and clinically proven probiotics, to support the gut microbiota.

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