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Let Nature Nurture Your Microbiome

Spending time in nature exposes you to a diversity of microbes. Photo by Robyn Rosenfeldt

We use and value diversity in our gardens, farms, national parks and nature reserves. Yet do we use and value the diversity in our bodies, in that vast collection of unseen communities we call our microbiome?

When there are trillions of microbes involved that can directly affect your mood, immune system, weight and health, then diversity is definitely what you want to consider ‘culturing’, growing, farming and valuing in your own body.

If you are what you eat, then you are definitely what your microbes eat. Everything you grow and eat from your own and others’ gardens and farms, plus the way you eat food (eating a variety of colourful vegetables, eating your own homemade ferments, etc.) and your lifestyle choices (such as avoiding unnecessary use of antibiotics and reducing stress) will affect the diversity of your microbiome. And it is affected not just by what you put in your mouth, your environment and your stress levels, but also by the diversity that exists in nature. We are inherently connected to nature. Diversity matters to nature, and therefore to our own health and happiness as well.

Gut Microbiota Is One Community In Our Microbiome

Just as there are living ecosystems in nature, there are living ecosystems on and within our body. The human microbiome is made up of many communities of organisms, forming diverse and complex ecosystems. There are whole ecosystems living on our skin, within our organs, and even a community of microbes that live on the end of our eyelashes. More than 35,000 microbial species have been identified living on and within our bodies, and they make up about 10% of our total body weight.

The gut microbiota (just one of the communities in our microbiome) has received much attention of late. It has famously been said the gut is the seat of all health or all disease. Why is the gut thought to be ‘in charge’ of your health?

The gut, or gastrointestinal tract, is technically outside our body—from the moment we ingest something to the moment we excrete it. The gut acts as a physical barrier to the outside world, keeping foreign molecules out and allowing only select molecules in.

The gut is the juncture between your nervous system, your immune system and your endocrine (hormonal) system. At this intersection the body receives signals from the outside world, information in the form of foods, chemicals and microbes. The gut sorts through this information, sending signals to the other systems based on its findings. The conduit used to transmit this information is the gut microbiota.

The microbes create chemical messages that influence immune system response, modulate hormones and communicate with our genes. Gut microbes aid in digestion and absorption of nutrients, as well as creating additional nutrients, notably B vitamins and vitamin K2. Gut microbes assist in the detoxification process, taking pressure off our liver and kidneys. The gut microbiota is an organ in its own right.

What Affects Diversity

Colonisation of your gut microbiota begins at birth. The microbes you are exposed to in the first 20 days of life will have a huge impact on your lifelong immunity. What your mother ate, her environment and genetics play a large part, as does the place of your birth and geography. Less microbial diversity in the environment means less microbial diversity in the mother and, subsequently, less diversity in the child. This phenomenon has been termed the ‘intergenerational transfer of disease’.

The interconnectedness of our physical body and the microbes living on and within it has evolved over thousands of years. Our survival depends on this symbiotic relationship. Increased urbanisation has led to increased sanitation and antibiotic use, a separation from nature and poor land management practices (such as using weed killers on roadsides), all leading to a decrease in biodiversity. It has been shown that people living in urban areas are more prone to inflammatory disorders (e.g. type 1 diabetes) and allergic disorders (e.g. asthma) during infancy and adulthood. As we chip away at environmental diversity, we chip away at our own diversity, the consequence of which is poor health.

What Creates An Unhealthy Gut

Four broad factors can reduce diversity of our gut microbes:

  1. Chronic stress, so common in our modern lifestyle, is the number one factor affecting our gut microbiota. It increases cortisol, decreases nutrient absorption and immune response, and increases gut permeability and inflammation.
  2. Exposure to environmental chemicals, heavy metals, refined sugar, chlorine and antibiotics will kill or alter our microbes.
  3. Eating foods lacking in the nutrients (most notably fibre and phytonutrients) needed to feed our microbes. Phytonutrients provide the colours in fruit, vegetables, legumes and other wholefoods and act as antioxidants. They combat free radicals and help modulate the immune system.
  4. Lack of exposure to a diverse range of bacteria, yeast, viruses and other microbes via the skin, digestive tract and respiratory tract. This means not enough variety of whole and probiotic (fermented) food. Not enough getting outside our four walls and getting back to nature.

When this happens, the barrier between the outside world and the inside world is compromised, causing what we refer to as ‘leaky gut’ or intestinal permeability. This allows foreign materials, mostly proteins, to make their way into our bloodstream. Once there, the immune system gets involved, mounting an inflammatory response against the foreign molecules. Inflammation is necessary to manage acute invasion, but if the permeability continues long-term, inflammation is left ‘on’ and becomes chronic. We are not meant to stay in this state for long periods of time. A heightened immune system response can lead to the immune cells reacting to ‘self’, damaging the body’s own tissues inadvertently and causing chronic illness.


Clockwise from top: Fermented
drinks; kombucha, milk kefir, jun and water kefir; Get your ferment on: kimchi, milk kefir, water kefir and sourdough; Playing in nature; Spending time in nature benefits your microbial diversity. Photos by Robyn Rosenfeldt


Healing The Microbiome


Healing the gut starts with removing obstacles to health, primarily reducing our exposure to damaging substances and reducing stress. Exposure to harmful substances may not be something you have much control over (for example, weed spraying in your area), but you can address your home, office and car. If this seems like an overwhelming task, take it one step at a time. The Environmental Working Group (EWG) can help; visit their website and have a browse.

Reducing the burden of stress is something we can all benefit from. Stressors will always be present in our lives; it is our response to the stress that needs to shift. Integrating a daily practice that focuses on a deep connection between mind and body, such as meditation, mindfulness or yoga, is essential.


The second phase of gut healing is replacing missing nutrients. Dietary fibre and phytonutrients support microbial diversity in a few different ways. Dietary fiber feeds your gut microbes so they can multiply. The greater the number of friendly bacteria in your gut the better. The bacteria produce by-products called short-chain fatty acids, which are chemical messengers used by the gut to balance the immune system.

Plant pigments (phytonutrients) combat what we commonly call ‘ageing’. Cells generate negatively charged molecules (free radicals) that can be damaging, but phytonutrients go around cleaning them up. Eat a variety of different coloured vegies, from white to dark blue (such as mushrooms to blueberries) each week. The more phytonutrients you consume, the more your friendly bacteria will proliferate.

Something to keep in mind is the breeding of food nowadays. Phytonutrients are being bred out of carrots, cabbage and potatoes, and diverse heirloom varieties with their bright and varied colours have all but disappeared. Also up to 80% of phytonutrients are lost when fruit and vegetables are transported and stored in supermarkets. Eat as local and fresh as possible.


Re-inoculation of the gut microbiota is the final step. Here are three ways to build microbial diversity:

  1. Eating fermented (sometimes called cultured) foods are the best way to repopulate your gut with a variety of friendly bacteria and yeasts. There are so many to choose from: sauerkraut, kimchi, olives, yogurt, kefir, kvass, kombucha, and the list goes on. Start by incorporating a teaspoon into each meal and increase the amount over time.
  2. Visit as many natural landscapes as you can, breath in the air, swim in the waters, feel sun on your skin, dig in the dirt, bathe in the biodiversity. Not only will you increase your microbial diversity by being outdoors, but it has been shown immune cells multiply after a walk in the bush and the effects last up to a month. Walking in a forest can expose you to useful chemicals undetected by your eyes and nose. Areas rich in biodiversity can change the microbes on your skin. The Japanese have a term ‘shinrin-yoku’, meaning forest air-breathing and walking. The documented effects of this practice include reducing stress and improving mood, plus the negative ions in the air outside can influence the growth of beneficial microbes in the intestinal tract.
  3. Fasting might seem out of place here, so let me explain what occurs in your gut when it is freed of digesting and assimilating food. Fasting allows the gut to get on with all its other jobs—communicating with your central nervous system, modulating the immune system and balancing hormones. Another interesting thing happens when the gut is empty—a bacterium called Akkermansia proliferates on the mucosal lining, and we know people with more Akkermansia are healthier. When I say fasting, I mean just skipping a meal. Eat a solid breakfast and lunch, then eat nothing until the next morning. Start once a week, then try two days, but make sure you stay hydrated.

Get Back To Nature

Ultimately, this is a cultural shift; a shift away from a sedentary, poorly nourished, isolated life high in toxins and stress for one that is built on biodiversity, connection and purpose. Not only do we need to replenish our microbial diversity, but on a deeper level we need to recognise our place within nature. We are part of the interconnectedness of everything on Earth. We are of the Earth and consequently, as we do to the Earth, we do to ourselves. If we destroy the biodiversity of the environment through poor land management, loss of local habitats, depletion of resources and decreased biodiversity, the same will be reflected in our health. Conversely, by nurturing nature, she nurtures us.


Yoghurt. Photo by Robyn Rosenfeldt


3 1/4 cups fresh milk

3 tablespoons yoghurt


  1. Heat milk on gentle until it reaches 85 °C (use a kitchen thermometer) in a heavy bottom saucepan. It is best to stir the milk often with a balloon whisk. Once the milk reaches temperature turn off the heat.
  2. Let the milk cool to 43 °C, again using a thermometer. Stir often as the milk cools. Once cool add the yoghurt and mix well.
  3. Pour into a glass jar. Place jar in a styrofoam box with a good fitting lid or in a good esky – the idea is to keep the temperature stable the whole time. You may need to keep a thermometer in the box and check periodically that the temp is around body temperature. Place the box/esky in a warm area of your house for 8 to 24 hours. The longer you leave the yoghurt mixture the more lactose is used by the bacteria and the more tangy the flavour will be (and the more microbes you will have).
  4. Put your jar in the fridge to cool. The yogurt should last 1-2 weeks, but remember to keep enough yoghurt to inoculate your next batch. The recipe can easily be doubled.

Nikki Wagner is a nutritionist living and practising in the Bega Valley, NSW.

For more info: The Secret Life of Your Microbiome: Why Nature and Biodiversity are Essential to Health and Happiness by Susan L. Prescott and Alan C. Logan (New Society Publishers 2018). It’s available in the Pip shop.


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