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What is the gut microbiome?

The gut microbiome influences almost every facet of our health, from mood, metabolism, skin, energy levels, mental health, immune health and even our susceptibility to certain chronic diseases (Magne et al., 2020). Arguably the discovery of the microbiome is one of the most important scientific discoveries of this century due to the impact it has on health and wellbeing. Although the research has exploded over the last 15 or so years there is still a lot that is yet to be discovered.

The gut microbiome consists of a symbiotic colony of trillions of bacteria along with fungi and viruses that weighs approximately 2kg in the gastrointestinal tract (Magne et al., 2020). Each person’s microbiome is unique, just like our fingerprints. The composition of our gut is influenced by a number of factors such as geographic location, mode of birth, duration of breastfeeding as an infant, the number of times you’ve had antibiotics and other diet and lifestyle factors. Generally, microbial diversity is associated with better health and wellbeing.

Why is gut health important?

A gut microbiome with a good balance of healthy bacteria produces a number of nutrients and bioactive compounds in the body. Some of these include short chain fatty acids such as butyrate, vitamin D, vitamin K and B vitamins such as biotin, cobalamin, thiamine, folate, niacin, pyridoxine and pantothenate. These vitamins are cofactors for hundreds of different functions in the body and influence intestinal health (Hossain et al., 2022).

Around 95% of serotonin (Terry & Margolis, 2016) & 50% of dopamine (Xue et al., 2018) is produced in the gut. Melatonin & GABA are also produced in the gut. This is part of the reason why good gut health is fundamental to our sense of well-being & happiness. Dopamine plays a key role in reward and motivation, regulation of emotions and much more (Xue et al., 2018). Sufficient levels of serotonin helps regulate mood, focus, sleep, and more. Both are referred to as happy hormones, deficiencies are implicated in depression, anxiety, ADHD and other mental health issues, plus play a host of other roles in the function of the body (Pourhamzeh et al., 2021).

Clearly it is important to look after our microbiome if we want good health and longevity, below are 6 key ways to do this.

1. Time in nature improves the gut microbiome

Get outside! Research proves that getting into nature improves the health of our microbiome and stress levels. Doctors in Japan have been prescribing time in nature as a part of a preventative health care routine since the 1980’s (Hansen, 2017). Time spent in nature is known as forest bathing or Shinrin-Yoku in Japan. A literature review of 14 scientific research studies shows that after spending quality time in nature was an effective way to reduce “blood pressure, lower pulse rate, increase the power of heart rate variability (HRV), improve cardiac-pulmonary parameters, and metabolic function, inducing a positive mood, reducing anxiety, and improving the quality of life of pre-hypertensive or hypertensive participants” (Yau et. al, 2020).

A 10 week study done on preschool children shows that spending more outdoor time in nature increases the beneficial bacteria Roseburia and elevates serotonin levels. Roseburia increases butyrate (Sobko et al., 2020), butyrate is associated with a host of health benefits including reducing inflammation, improving intestinal health, antioxidant properties, reduces the risk of colon cancer, immune modulation and gene expression (Bedford & Gong, 2018).

Another study found that those living in rural areas had healthier microbiomes than their city counterparts. This may be attributed to spending more time in nature and less exposure to poor indoor air quality and pollution. Rural dwellers had more beneficial gut bacteria, such as Bifidobacterium and Faecalibacterium (Das et al., 2018).

2. Stop consuming artificial ingredients

Many think that if food additives are in products sold in supermarkets that they are safe, unfortunately that is not always the case.

Food dyes

For example, some artificial dyes are derived from petroleum or coal tar such as red dye 124 and yellow 102. These dyes are allowed in Australia however are banned in other countries due to safety concerns. Colour 124 aka scarlet is banned in the “US, Canada, Norway, Sweden & Japan” due to associations with “DNA damage and tumours in animals… (and) can produce bad reactions in asthmatics” (Okafor et al., 2016). Colour 102 aka tartrazine is an artificial yellow dye associated with adverse reactions such as “allergies, asthma, skin rashes, hyperactivity, and migraines” in some consumers. It has been banned in parts of the EU (Ramesh & Muthuraman, 2018). Both 102 and 124 require the warning label “may have an adverse effect on activity and attention in children” in a number of European countries (National Health Service UK, 2020) (Arnold et al., 2012), however no warning is required on products sold in Australia. In fact, these colours are in a number of Australian foods including one of the most popular ice blocks aimed at children.

Even in small quantities artificial food dyes can have a negative impact on the gut microbiome. For example, food dye 171 ‘Titanium White’ helps bacteria that are known to cause an inflammatory response to proliferate, reduces short chain fatty acid production and cause an over production in the antimicrobial peptide defensin. These three things cause intestinal dysbiosis, systemic inflammation and may increase IBS and other bowel issues in those with less-than-optimal microbiome health (Jarmakiewicz – Czaja et al., 2021).


Emulsifiers are another common additive that can have a negative impact on gut health. Research shows that they can negatively influence the epigenetic expression of bacteria, increase pathogenic bacteria, and increase inflammation in the gut resulting in the development of enteritis and metabolic syndrome (Jarmakiewicz – Czaja et al., 2021). Emulsifiers stop oil separating in long life products and are commonly found in plant milks, ice cream, mayonnaise, cosmetics, pharmaceuticals, lotions, bread and many other products. Scientific studies show that two synthetic emulsifiers in particular carboxymethylcellulose and polysorbate 80 cause intestinal inflammation, inflammatory bowel diseases and metabolic syndrome (Naimi, 2021).


Preservatives not only stops the bacteria growing in packaged food, they also kill the bacteria in the gut. Daily exposure is common because packaged foods such as salad dressings, sauces, olives, crackers, cheese, dried fruit, seafood, fruit juice, processed meats and many others have preservatives. Even naturally shelf stable products have preservatives added, so it is important to read the labels. Preservative numbers on the ingredients list are numbered from 200 to 299 and are used to extend shelf life (Jarmakiewicz – Czaja et al., 2021). Nitrates, nitrites, BHA & BHT, potassium bromate and sulphites are some of the most commonly used preservatives in food and should be avoided where possible.


3. Reduce the favourite foods of unfriendly gut microbes

A high sugar diet has been shown to increase harmful bacteria such as E.coli and yeasts such as candida in the gut. Reduce the number of foods that bad bacteria love to eat, such as sugar, unfermented dairy and simple carbohydrates. Unfermented dairy such as milk has lactose and carbohydrates have polysaccharides – both quickly breakdown into glucose as part of the digestion process spiking insulin. Unfortunately, these foods feature heavily in the western diet. Complex carbohydrates are a much better option, although they can still breakdown into glucose it is albeit more slowly. Good sources of complex carbohydrates include quinoa, peas, beans, sweet potato, and other vegetables.

Intestinal permeability, colitis, allergy susceptibility, hypertension, insulin resistance, increase in oxidative stress and cognitive decline have been demonstrated in various animal studies with a high sugar intake. Animal models are often used in dietary studies as it is hard to control diet in long term human studies.


 4. Medications can affect gut health

There is no doubt that medications can be necessary, however some have a negative impact on the health of the gut.

Antibiotics attack not just harmful bacteria but beneficial as well which can lead to pathogenic bacteria and yeast overgrowths. Studies have estimated that between one-fifth to one-third antibiotic prescriptions are not necessary which is a contributing factor to antibiotic resistant infections (Krockow et al., 2022). Yes, antibiotics have indeed saved many lives, however the over prescription is contributing to the alarming increase in antibiotic resistant infections resulting in death.

Antacids, also known as proton pump inhibitors, are commonly used to treat reflux and ulcers. They affect the microbiome because they reduce the levels of acid in the gut and thereby the digestion of food. Long term users of antacid medications were found to increase unhealthy bacteria and reduce beneficial species as a result they can be more prone to infections (Levy et al., 2020).

Nonsteroidal anti-inflammatory drugs (NSAID) such as Advil and ibuprofen are very good at relieving pain however have a negative impact on the gut. Along with their well-known side effects NSAID’s also affect the function and composition of the gut which as a result can precipitate bacterial dysbiosis (Maseda & Ricciotti, 2020).

There are many other medications that alter the microbiome, speak to your doctor about any medications you take and the affect they might have on gut health if you have concerns.


5. Exercise increases good gut bugs

Exercise also improves gut health, multiple studies show that friendly bacteria and beneficial metabolites such as short chain fatty acids increase with regular exercise.

Research shows that moderate exercise reduces intestinal permeability and inflammation, however repeated overtly intense exercise can negatively affect the epithelial wall and mucosal thickness of the gastrointestinal system. Intestinal permeability increases inflammation levels if bacteria and food particles leak out of the digestive system and into the blood stream (Clauss et al., 2021).

Studies that have been conducted on rodents have shown that microbial composition may affect physical performance (Clauss et al., 2021).


6. Diversify diet to improve gut health

And last but not least – of course eat a diverse range of plants, pastured meat, probiotic foods, spices and herbs. Diet diversity is key to microbiome health as demonstrated by a large number of studies. Disease states such as obesity, type 2 diabetes and bowel diseases are often implicated in low diversity or missing strains of beneficial bacteria (Heiman & Greenway, 2016).

Due to the advance of agriculture and globalisation many stick to the same diets year-round and thus lose the variety that eating seasonally brings. Additionally, it is estimated that today around 75% of the food generated comes from only 12 types of plants and five types of livestock. Large scale agriculture of wheat, corn and soy often involves heavy pesticide and herbicide which is also harmful to the microbiome (Heiman & Greenway, 2016).

The good news is that in as little as a week, positive shifts can be seen when incorporating a wider range of plant foods into the diet. Foods high in fibre are fundamental in increasing diversity such as avocados, berries, beans, chia seeds, plums, and apples. Prebiotic foods such as artichokes, potatoes, asparagus, greenish bananas, garlic and traditional oats for example are also important for microbiome health as they feed the good gut bugs.

Every week aim for 40 different types of healthy foods including plants, spices and herbs, oils and wild caught seafood and pasture rasied eggs and meats.



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By nutritionist Chrissy

Chrissy is a university qualified nutritionist who graduated with honours at La Trobe University in Melbourne. One of her favourite hobbies is to read the scientific literature on how to optimise health. When she’s not reading, writing or working she’s with her 3 children outdoors, practicing yoga, jogging or cooking up a storm in the kitchen. Chrissy has overcome some debilitating chronic health issues (low mood, adrenal fatigue, insomnia, very bad acne to name a few) with the power of nutrients and correcting gut health, at 39 she now feels better than she did in her 20’s.