5 Ways to Re-Wild Your Gut Garden: Transforming an Unhealthy Gut Microbiome

 An unhealthy gut microbiome can make you feel & look bleh. Your gut microbiome is the amazing garden of microbes that live in your digestive tract. Although they call your gut home, these microscopic critters influence your skin, brain, mood, detoxification, metabolism, antioxidant and immune systems.

With the silly season over for another year, you’re probably left wondering which 2 week cleanse | detox | reset will help with the wobbly bits, bloating, gas & reflux from too much of a jolly good time.

And what about your skin? 

Anyone with sensitive or reactive skin is probably experiencing redness, blotchiness, rashes, itchiness and breakouts right now, from a month or more of celebrations. Over indulgence in rich food, sugar and alcohol can take a real toll on your skin.   

And your gut garden.

Dietary indiscretions combined with stress, late nights and couch potato life can turn your gut microbiome from an old growth forest into a stinky swamp. These changes to your gut garden can have a huge flow-on effect upon your skin, metabolism and mood.

Your gut garden is heavily influenced by diet, sleep, exercise, hydration and stress levels. 

The best detox for a healthy microbiome?

A 2-week Influencer approved detox might make you feel virtuous, albeit with a lighter purse, but the reality is that it doesn’t really change anything long term. 

Type “detox” into your browser and you'll be met with some version of “detoxification is a process that happens 24/7”, and this is true. However, the many different enzymatic reactions and functions that occur in your liver, gut and other cells of your body, collectively called ‘detoxification’, require nutrient resources in the form of vitamins and minerals. 

In the same way that your kitchen garbage doesn’t empty itself – someone must take the full bag out to the bin and then wheel the bin out for curb side garbage collection. The garbage truck comes along next morning to pick up all the stinky garbage - it requires fuel and people to drive the truck.  Each step involved in the removal of your kitchen garbage is the equivalent of an enzyme reaction during detoxification. There are several detoxification pathways that deal with different kinds of toxins, chemicals, hormones and other substances. Each pathway requires specific nutrients to work optimally.

An out of balance gut microbiome can impair the absorption and supply of these essential nutrient resources (vitamins and minerals). A swampy gut garden can also be a source of toxins and chemicals that place an extra strain upon these detoxification pathways.

5 ways to transform an unhealthy gut microbiome

  1. Hydration
  2. Sleep
  3. Prebiotics 
  4. Exercise
  5. Sugar 
Hydration is important for a healthy gut microbiome


There is a wonderfully protective layer of mucous that coats all the cells of your gut, keeping them hydrated and nourished.  When you don’t drink enough water, this protective mucous coating dries out and doesn’t function properly. 

There are many competing theories on how much water you should drink.  In my role as a nutritionist/naturopath, I recommend adding in a minimum of 1 litre of filtered drinking water to your daily schedule. 

  • Drink two pint glasses each day of filtered water.
  • Drink one pint of water with breakfast and one with your evening meal or mid-afternoon.

Filtered water is best. If your water filter doesn’t re-mineralise your water, add the smidgiest pinch of sea salt to your drinking water. This adds some dissolved solids into your water and improves cellular hydration. If the water tastes salty then you’ve added way too much, you shouldn’t be ablet to taste any salt but the mouth feel of the water will be different.  It will feel ‘wetter’ in your mouth.

Why filtered water? There are many reasons, but from a gut microbiome perspective, chlorine is added to drinking water to kill microbes.  Which is a great thing when you’re talking about critters like Giardia and E coli but not so good for a diverse, abundant and healthy gut microbiome. It makes sense to remove it before you drink it.

Shop Water Filters

Zazen Alkaline Water Filter System: Australian made alkaline water system made for Australian water.
Sleep is important for a healthy gut microbiome and beautiful skin


There are more and more exciting glimpses emerging on the relationship between your gut microbiome and sleep.  The current data is a little bit chicken and egg, but what is clear is that sleep and the health of your gut garden are linked. Insufficient sleep is associated with less healthy changes to gut microbiome and an out of balance microbiome is associated with poorer sleep quality. 

Not getting enough sleep tends to increase stress levels and also makes you crave sugar and processed foods - both of which lead to unhealthy changes in your gut garden.

Another clear link is the one that exists between sleep and skin.

  • DNA repair in your skin is dependent upon optimal sleep
  • Your skin makes collagen while you’re sleeping
  • Skin hydration suffers as a result of not enough sleep
  • Quality sleep is associated with a “more luminous complexion”
  • Poor sleep can worsen or trigger inflammatory and immune mediated skin conditions including atopic dermatitis (eczema), contact dermatitis, vitiligo and psoriasis.

If you needed more reasons to put your phone down and turn out the lights earlier, glowing skin and a healthier gut can be added to the list.

Improve your sleep, improve your gut

Aim not to eat for at least 3 hours before bed. This is one of the simplest things you can do to improve your quality of sleep and your gut garden.  If you feel hungry at night time, it means you’re tired and your brain is craving fuel.  Put the snack back in the fridge and go to bed instead.

Prebiotic rich foods are important for a healthy gut microbiome.


Prebiotic simply means ‘gut garden food’.  Think of prebiotics as a bit like compost in your vege garden, they feed up all the beneficial microbes in your large intestine.

Prebiotics are specialised types of fibre that are fermented by bacteria in your colon. They ferment fibre and create a wonderful array of fatty acids and nutrients that benefit the cells of your gut and your brain.

These specialised fatty acids do wonderful things for your metabolism too, and can help to curb cravings for sweets between meals. Craving sugar, sweets and carbs is often a sign that your brain is low on fuel. Fatty acids produced when bacteria in your gut ferment prebiotics can be used by your brain as a fuel source between meals. They also act as fuel for the cells of your intestine, helping to reduce inflammation in the gut.

In some people, fermenting bacteria from the colon migrate up higher to live where they shouldn't,  taking up residence in the small intestine.  The most well known name for this condition is SIBO (small intestinal bacterial overgrowth).  If you have SIBO, prebiotic foods and supplements will make you terribly bloated and gassy.

The general rule with prebiotic foods or supplements is to start low and go slow.  Starting with too much will tend to make you a bit gassy and bloated for a week or two as your gut garden adjusts to the sudden influx of prebiotic food.  

Types of prebiotic foods:

  • Blueberries
  • Oats and oatmeal (organic)
  • Garlic and onions
  • Apples (try some grated green apple mixed with a little sprinkle of cinnamon and some activated pepitas, almonds and a squeeze of lemon juice).
  • Asparagus
  • Jerusaleum artichokes (pay special attention to the start low and increase slow with these powerful prebiotics, or you’ll quickly learn why they have earned the nickname fartichokes)
  • Unripe bananas
  • Seaweed
  • White beans
  • Konjak root/shirataki noodles (remember to start low and increase slow)

Shop Prebiotic Supplements

ImmunoGenex: A delicious tasting Prebiotic + Probiotic supplement made from Pomegranate juice, Larch Arabinogalactans and an immune enhancing probiotic.


Exercise is important for a healthy gut microbiomeExercise

Exercise and higher levels of physical activity are associated with more diverse gut microbiomes. Diversity is a good thing for a gut microbiome.  Lots of different microbes producing lots of different chemicals and nutrients, all keep each other in balance.  Problems tend to arrive when one or more different species of bacteria, fungus or other microbe gets an upper hand and dominates the real estate opportunities in your gut.

How does exercise improve your gut microbiome? The research still can’t clearly explain why exercise makes your gut microbiome healthier and more diverse. One factor is likely to be that exercise helps you poop better.

Better pooping

Even low intensity exercise has a highly beneficial effect upon gut transit time – the amount of time it takes for food to travel from your mouth to the toilet. Sluggish digestion allows for an environment that favours the growth of microbes associated with higher levels of inflammation. Regular movement helps speed up and normalise sluggish digestion.

How long does it take for exercise to improve gut microbiome? Around 6 weeks is generally how long it takes to see improvements in your gut microbiome from exercise.

What type of exercise? Any type of exercise, outdoors is best.  It could be something as simple as a 20 minute walk around the block. A walk on the beach or doing some stretches or light weights in the back yard or under a tree in the park. Gardening counts as physical activity too.

We've never had such easy access to a range of fun and diverse exercise classes thanks with the recent explosion in online yoga, pilates, dance, belly dancing - pretty much whatever takes your fancy. The most important thing is to just get up and get moving.

A diet high in sugar and refined foods leads to unhealthy changes in your gut microbiome


Your gut microbiome reflects the foods that you eat. A diet high in sugar and refined carbohydrates leads to adaptations and changes in your gut microbiome that do not favour health. Sugar leads to a decrease in beneficial gut microbes and an increase in those which promote inflammation AND serotonin depletion.

The link between increased inflammation and skin is pretty obvious – inflammation creates redness, reactivity and sensitivity in skin. Inflammation drives skin conditions like acne, psoriasis, eczema and rosacea. But the link between serotonin and skin health is not as widely known.  We tend to typically associate serotonin, a neurotransmitter [brain chemical] with regulation of mood and sleep.  However, there’s more serotonin found outside your brain than within it. It plays a very important role in regulating digestion and there’s more and more data emerging of serotonins role in skin, especially skin conditions dominated by itching such as eczema and pruritis (pruritis simply means itchy skin).

This depletion of serotonin is also partly responsible for sugar cravings. A sugar binge leads to a short boost of serotonin - you feel calm, content and happy. No wonder sugar is so addictive. Unfortunately this sugar high doesn’t last long and is followed by the inevitable sugar crash, during which you feel pretty lousy and crave more sugar – a classic negative feedback cycle.

A more mindful relationship with sugar is important for a healthier gut microbiome and skin.

Should you quit sugar?
I’m going to be controversial here and recommend NOT focusing on cutting sugar out of your diet, at least to start with. Sugar cravings are a symptom of a body that is out of balance. A tired, stressed and depleted brain and body craves sugar. It signals a need to increase your nutritional resources and improve your digestion and absorption. Do this first and then you’ll find quitting sugar easy.

Instead of putting your focus onto eliminating sugar, direct it towards increasing delicious and healthy real foods.  Eat more salads, steamed and baked vegetables. Widen your palette and start including some fermented foods in your diet

  • Add miso to salad dressings
  • Use raw apple cider vinegar
  • Add fermented vegetables to your meal

If you want to quit sugar, make sure you’re getting enough protein

Eating more protein in the morning will help you to get off the crazy blood sugar roller coaster and really help to reduce those afternoon sugar cravings. Don’t be afraid to use a high-quality protein powder, especially in the morning for breakfast. Protein powders are ideal for breakfast skippers.  

Many people often ask if protein powders count as real food - the answer is that it depends on the product. There are many 'junk food' protein powders on the market filled with artificial sweeteners and flavours but there are also some very clean and high quality products too. 

Whey protein is a traditional European 'convalescent food', used to help nourish and re-build health after illness or stress. Today, protein powders have been co-opted by the weight loss and body building industry. Protein is used by your body for construction, repair and for producing enzymes - you need extra during times of stress or when you're working on improving your health.

Protein powders are convenient, easy to digest and can be used to create a healthy breakfast that ticks all the nutritional boxes. Starting your day with extra protein keeps your metabolism on a more even keel and reduces sugar cravings - helping your gut microbiome and skin to stay balanced.

Choose from grass fed whey protein, or, for a vegan/vegetarian option look for pea, hemp or brown rice protein. There are also products that use protein from pumpkin seeds/pepitas and even watermelon seeds. 

Breakfast Protein Smoothie
  • One serve of your favourite protein powder (providing 15-20 grams of protein
  • Organic milk of choice (dairy, goat, almond, coconut or soy milk)
  • Frozen organic berries
  • A spoonful of yoghurt – dairy, sheep or coconut
  • A tablespoon of LSA (linseed, sunflower seed  and almond meal) OR organic oatmeal
  • ¼ banana (optional)

 Blend and drink

How does sugar influence your gut microbiome?

A diet high in sugary foods and drinks promotes the growth of gut microbes that increase inflammation and immune system dysregulation. Inflammation decreases numbers of beneficial microbes in the gut. High sugar food are usually low in prebiotics which feed and nourish good bacteria.

The link between your gut microbiome and your skin

From your body’s point of view, your gut is actually located on the outside, the same as your skin.  Imagine yourself as a doughnut, your gut is simply the hole in the middle. Gut and skin are all about defending your internal body and organs from attack by invading bacteria, viruses and other microbes. They both interact and work in a symbiotic relationship with microbes that live upon their surface. Skin and gut also both play important roles in temperature and fluid regulation, and helping internal body functions to adapt to environmental changes.

A gut microbiome that is out of balance and predisposes towards inflammation and immune dysregulation will upset your skin.

  • The immune system in your skin becomes more cranky, reactive and less tolerant
  • A reduction in fatty acids produced by gut bacteria fermenting prebiotics can influence the bacteria that make up your skin microbiome
  • The inflammation and chemicals generated by unhealthy gut microbes can affect the skin regeneration cycle and skin’s ability to heal

There are clearly established links between an unhealthy gut microbiome and a range of skin conditions including acne, eczema, psoriasis and rosacea. If you’re struggling with any of these chronic skin conditions, you may need to take a more inside-out approach to skin health.

Is an unhealthy gut microbiome holding you back from achieving your best skin?  Get in touch with us today for inside-out advice on making this year your best skin year ever.


Sarah Luck, naturopath, nutritionist and herbalist. Specialising in wholistic beauty and skincare. About Sarah

Sarah has been in private practice since 1999 as a naturopath, nutritionist and herbalist. She has worked in wholistic beauty clinics and Integrative Medical centres in Sydney's Eastern suburbs. She now specialises in wholistic beauty and skincare, having a special interest in the relationship between gut and skin microbiome. Her guiding motto when formulating skincare is Beautiful, Simple and Safe.

Shop Microbiome Friendly Skincare

Healthy Skin[care]: Microbiome friendly skincare, made in the Noosa Hinterland, Sunshine Coast

Shop Probiotic Skincare

Honey Probiotic Cleanser: A raw honey cleanser with probiotics from radishes and coconut. Skin balancing treatment and gentle exfoliant. 

Probiotic Toners + 2% Niacinamide (vitamin B3): Organic Rose or Lavender hydrosol blended with probiotics from radishes and coconuts plus niacinamide (vitamin B3). Niacinamide helps to regulate oil production and may help to reduce skin redness. 

Shop Essential Skin Nutrition

DefenceCell: Broccoli sprout powder + essential B vitamins and minerals. Assists in maintaining the livers natural detoxification processes and reducing free radicals formed in the body.

Shop Detox Drinks for Gut Health

ImmunoGenex: A delicious tasting Prebiotic + Probiotic supplement made from Pomegranate juice, Larch Arabinogalactans and an immune enhancing probiotic. Australian made. 

EnduraCell PomGenex: Freeze dried pomegranate juice + broccoli sprout powder. Australian made. 

Further Reading

Getting to Know Your Skin Microbiome

Gut microbiome diversity is associated with sleep physiology in humans - PMC (nih.gov)

Circadian Rhythm and the Skin: A Review of the Literature - PMC (nih.gov)

0221 Acute Sleep Deprivation: Consequences On Healthy Face Skin. A Non-invasive Instrumental Investigation | SLEEP | Oxford Academic (oup.com)

Sleep, Immunological Memory, and Inflammatory Skin Disease - FullText - Dermatology 2021, Vol. 237, No. 6 - Karger Publishers

Frontiers | The Gut Microbiome as a Major Regulator of the Gut-Skin Axis | Microbiology (frontiersin.org)

Exercise Modifies the Gut Microbiota with Positive Health Effects - PMC (nih.gov)

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