What’s with the microbiome?

The gut microbiome is complex ecosystem of microscopic organisms that live in our intestines including bacteria, viruses and fungi.

These microbes all play a vital role in digestion, nutrient absorption and the functioning of our immune system. They can affect our mood, weight, brain health and overall wellness.

While some are helpful and others harmful the balance of the microbes in our gut is critical.

As the host to this intricate ecosystem, we can influence its composition to change, improve and diversify our gut microbiome.

Many factors influence the health of our microbiome – the quality of sleep, exercise, stress and most significantly our diet.

A healthy well balanced, high fibre and plant rich diet is one of the single most significant factors to impact the quality of our gut health.

The field of microbiome research has attracted great interest in recent years.

Emerging research suggests the gut microbiome may play an important role in the development and progression of bowel cancer.

The composition of the microbiome has been linked to the efficacy of some chemotherapy drugs during cancer treatment.

The diversity of gut microbes may be related to the severity of chemotherapy related side effects.


10 ways to feed your microbiome

  • Eat more plants – supercharge your gut with 30 different plant foods a week demonstrated in the American Gut Project to diversify the human gut microbiome. A wide range of plant foods provides the fibres that act as fuel for gut microbes to support a wide range of gut species. Plants also contain polyphenols – the chemical compounds with powerful antioxidant and anti-inflammatory properties known to positively impact gut health and general wellbeing. Include a wide variety of fruits, vegetables, nuts and seeds, legumes, herbs and spices as well as wholegrains.

  • Eat probiotic foods – Probiotic foods contain live microorganisms which are beneficial bacteria that will displace harmful pathogens and restore balance to the gut. Eat fermented foods like kimchi, sourdough, Greek yoghurt, kefir, apple cider vinegar, tempeh, miso, kombucha. It’s important to introduce these foods slowly into your diet.

  • Eat prebiotic foods – prebiotic foods are indigestible fibres and natural sugars which act as fuel for gut bacteria, promoting the growth of beneficial microbes. When gut bacteria metabolise prebiotics, they produce beneficial by-products like short chain fatty acids (SCFA) which strongly influence overall health. High fibre, natural prebiotic foods include garlic, onions, leeks, asparagus, Jerusalem artichokes, bananas, berries, apples, chickpeas, lentils, almonds, flaxseeds, oats, wholegrain cereals.

  • Reduce stress – stress negatively influences the gut microbiome by altering the function of the gut, gut motility, increasing harmful bacteria and triggering “leaky gut”. Reduce stress with walking, spending time in nature, practicing deep breathing and meditation, connecting with people, taking a holiday, getting a hobby, laughing out loud often, listening to music, journaling.

  • Exercise – 20-30 minutes of moderate to vigorous activity three times a week has been shown to reduce inflammation, increase diversity and beneficial gut bacteria and improve gut function.

  • Sleep well – gut microbiome and sleep have a bi-directional relationship. Poor sleep quality can lead to an imbalance in the gut microbiome. Unhealthy gut microbiota can influence the regulation of sleep and contribute to poor sleep patterns. Maintain a regular sleep schedule, try to have 7-8 hours a night, stop screens and other stimulants three hours before sleep, meditate, do not drink or eat close to bed time, stop caffeine intake by lunchtime.

  • Drink green tea – whose powerful polyphenols – epigallocatechin gallate (EGCG) exhibit direct effects on the stimulation on specific beneficial gut microbes. It also contains L-theanine which promotes relaxation and improves sleep quality.2-3 cups of green tea a day is shown to be health promoting.

  • Reduce unnecessary antibiotic use – which contributes to the depletion of both diversity and abundance of healthy gut bacteria. Always follow antibiotic use with a course of probiotics.

  • Reduce your toxic load – toxic load is the cumulative burden of harmful environmental substances known to disrupt the composition and integrity of the microbiome. Common environmental toxins: Persistent Organic Pollutants (POPs) like PFAS, dioxins, pesticides and industrial chemicals like PCBs. Heavy metals, phthalates and parabens. Emulsifiers, nitrates, artificial colours and artificial sweeteners in our food. Rethink your dishwashing and laundry detergents, cosmetics and personal hygiene products. Choose non-toxic, organic, fragrance-free products. Use natural clean house cleaning products like white vinegar, lemon, baking soda and essential oils. Avoid excessive food additives and processed foods. Eat organic when possible. Drink filtered tap water. Use glass or stainless-steel food storage products. Cook with stainless steel, ceramic or cast iron cookware.

  • Stay well hydrated – have 35ml of water each day per kilogram of body weight to support the removal of waste, aid digestion and balance the microbiome. A 70kg person should drink at least two litres of water a day.

Article authored by our Bowel Care Clinical Nutritionist, Jo.

Published: October 13, 2025

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