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Steps To Improve Your Microbiome

Dec 01, 2020

By Naturopath Kasey Willson

 Mentioned throughout:

>> My DIY All Natural Hand Wash Recipe

>> Join The Waitlist For My Upcoming Pregnancy, Birth & Fourth Trimester Digital Course

It's likely you've heard about your microbiome. You know, the good bugs that live on your skin, in your gut, lungs and yes, even in your vagina.

We're made up of 90% bacteria- they out number us by 10:1! Yep, there's more of them than cells in your body.  So it makes sense that we take good care of them and create an environment where these healthy bugs want to hang out in.

Besides, these microbes are the ones needed in strength to provide us with immune health, anti-inflammatory and antimicrobial functions. The beneficial bacteria on your skin also promote a balanced, healthy complexion.

In your gut, your microbes specifically allow you to digest your foods, absorb your nutrients and allow adequate detoxification from toxins and wastes. Yes, they help move your poo through your colon and promote a regular and complete toilet stop.  They even play a role in the way you think, feel and sleep, through the influence they have on the production of your neurotransmitters, serotonin and melatonin. 

The balance of your microbes can also impact your baby, unborn baby and/or your one-day-baby's health. The health of your future generation begins with your preconception wellbeing and continues with the maternal nourishment you provide throughout pregnancy- and a big factor is the health of your microbiome. 

Great emphasis should be placed on the health of your microbiome throughout your preconception, pregnancy and postpartum stages of life. These are times when you particularly want to focus on good gut health, plus encourage a beautiful balance of bacteria throughout your body. 

Supporting Your Baby's Microbiome

Your baby's microbiome (which is passed on by you and continues to rapidly develop throughout your baby's first 2-3 years of life) and intestinal integrity, becomes the foundation for her long-term health. By encouraging the growth and maturity of her good gut bacteria throughout this critical period, you will be positively impacting important stages of her growth and development, function of her immune system, metabolic programming and healthy gene expression heading into adulthood. This has the power to reduce the risk of disease1 and promote thriving health for years to come.

The factors influencing your baby’s microbiome development in these early years has shown through research to impact early brain development and mental health outcomes2 and can also influence her mood, cognitive programming and development later in life.

Although this area of research is only in its early stages, one study of 250 infant stool samples showed attention and language improvement in babies with healthy levels of the bacteria Bifidobacterium longum and Bifidobacterium pseudocatenulatum,3 further highlighting the strong gut- brain connection.

Supporting your baby’s beneficial bacteria and her overall gut health also plays a role in promoting immune tolerance.4 A short chain fatty acid called Butyrate acts as fuel and protection for the gut lining and therefore is a major player in the overall gut health of your baby.

Research suggests butyrate, which is produced when specific gut bacteria break down undigested plant fibre in the colon, plays a role in preventing atopy in infants. Deficient genes responsible for breaking down breastmilk, lower levels of butyrate producing good bacteria and lower levels of butyrate itself, were evident through stool samples of infants who later developed atopy.5 Atopy is linked with heightened immune responses and includes the development of hay fever, asthma and/or eczema.

Your baby’s microbiome can also be a predictor for the development of the autoimmune condition of Coeliac Disease in later life,6 where an allergy to the protein gluten exists and there is initially (and long term if unmanaged) damage present to the small intestinal lining, leading to difficulty digesting foods and absorbing nutrients.

What You Can Do

While there's many contributing factors to your baby's microbiome development such as the mode of baby’s birth, milk feeding, introduction of solids, medications, supplementation and environmental factors (which I discuss within my baby book, Thriving Bubba), your maternal microbiome is a major factor.

Aside from limited transfer of bacteria into the amniotic fluid throughout pregnancy, baby is mostly sterile before birth. The mode of birth is one of the first significant ways to impact the development of your baby’s microbiome.

During a vaginal birth, your baby will pick up your maternal microbiota as she enters through the birth canal, or is swabbed post c-section and this will begin to lay the foundation of her immune system. This transfer will continue through skin-to-skin and breastfeeding throughout your baby's first days, weeks, months and years. 

So now you know how important it is to have healthy microbiome, let's go back to the beginning, with ways you can support your beneficial bacteria right from pre-conception and throughout pregnancy, so you can encourage healthy transfer when the time comes to meeting, cuddling and playing with your bubba.

1. Avoid Wiping Out Your Good Bugs

Your skin has a delicate microbiome that is needed to remain healthy and provide biological protection to your body. It helps to keep your "bad" bugs in check, acting as an immune first line of defence, along with promoting balanced skin health, preventing dryness, oiliness and breakouts.

So if your skin is an ecosystem that requires good bacteria to thrive, what happens when you apply products to your skin? This is a question I'm posing to get you to think about the effects of constant sanitising may have in throwing out this crucial skin microbiome balance. Let alone, the impacts the toxic ingredients found in conventional hand sanitiser, are having on you and your baby's health.

Take the antibacterial agent Triclosan for example, which is found in all products labelled as "antibacterial" and commonly seen in conventional soaps, shampoos, toothpastes, chopping boards and antimicrobial sponges.  Firstly regular use of products containing Triclosan will impact your delicate microbiome on your skin and can lead to antibiotic resistance. When you meet, touch and continually have skin to skin contact with your baby, what effect may this be having on their skin microbes?

It has been shown to penetrate your skin, enter your bloodstream7 and has also disturbingly shown up in human breastmilk in high levels.8 So you can just imagine what impact this may be having on babies gut health once you begin your breastfeeding journey.

Animal studies indicate Triclosan is also linked to disturbed hormone activity (including thyroid function),9 and impacts normal muscle function10 and cardiac function. 

As Dr Josh Axe sums up across at

"Allowing ourselves to come into contact with new types of bacteria is essentially like a workout for the immune system that eventually pays off, even if it means dealing with some unwanted symptoms along the way (like being sick a few times when you’re a kid)."

While we're on the topic of wiping out our good bugs, it's important to note that just one course of oral antibiotics is enough to disturb the delicate balance of your beneficial gut bacteria.10 The oral contraceptive pill also acts as an antibiotic in your gut and can throw out the delicate vaginal microbiome balance, contributing to a case of thrush.

When I was on the pill years ago, this (along with the binge drinking antics of my late teens) was a contributing factor for ongoing thrush. As many times as I went to the GP, their only answer were anti fungal creams, but never any talk of the contributing factors and how to support my beneficial gut and vaginal bacteria.

As I discuss in my Glowing Mumma preconception guide, I recommend women stop the use of the OCP, other synthetic hormone contraceptives, as well as the copper IUD, at least 6 months prior to conception. You can learn more about the topic of contraceptive options in this blog post.  

Other safe alternatives?

In place of antibacterial products which contain Triclosan, or other toxic ingredients for that matter, aim for these natural alternatives:

>> Wash hands with warm water and natural soap (download my go-to no-tox hand wash here)

>> Use a Triclosan-free dishwashing liquid and other products around your home (you'll find most products claiming "antibacterial", "fights bacteria", "protects against mould" contain this toxic ingredient). 

>> If you want extra protection in times such as using public toilets and before eating (when a sink and soap isn't handy), opt for a natural hand sanitiser using the natural antibacterial action of essential oils and that doesn't contain Triclosan. But this should be limited, as the alcohol needed in these products will still impact your skins microbe balance. 

>> Also use as little products on your skin as possible, to avoid disrupting the delicate skin bacteria balance and be sure they are free of all the nasties for your overall health. You can download my "ingredients to avoid" list here.

2. Be Mindful Of Foods That Disrupt Your Gut Microbiome

As I've mentioned in previous episodes, conventionally farmed produce that has been sprayed with glyphosate, can also impact your gut health.

"Foods grown using glyphosate can disrupt your significant microbiome balance (and our good bacterias ability to produce essential amino acids through the shikimate pathway), contribute to intestinal permeability (leaky gut lining) and impact your ability to safely detoxify from hormones and toxins.11 Glyphosate easily permeates through your gut and is stored within your body, where it contributes to health issues." I explained back in episode  5.

You also want to minimise your intake of refined sugar, which will encourage an overgrowth of your pathogenic bacteria and the yeast Candida albicans. When these microbes take over, this crowds out your beneficial bacteria strains and impacts their important functions, especially for your gut and immune system health. 

All processed foods will have a similar negative effect on your gut microbiota balance.

Use in place:

>> Foods that have been grown and raised without the use of the herbicide glyphosate and best, source or grow foods without the use of any sprays or are certified organic. This type of produce will be beaming with natural sources of beneficial bacteria.

An example is when you use a homegrown or organic cabbage to make the fermented veggie dish of sauerkraut, you actually don't need a probiotic starter, as the leaves will contain the bacteria to begin fermenting naturally. 

If you don't have room to grow your own, having a relationship with your farmers through seeing them at markets or contacting them through their websites, is an empowering step to ensure you and your family are supporting farmers who care for you and the environment. You can see my list of favourite organic (or spray free) produce here. If you're eager to see more organic options,  start by voting with your dollar. 

>> If you are desiring something sweet, embrace fresh fruit (which also contains fibre) or some natural sweeteners such as raw honey. Raw local honey is a great source of beneficial organisms or enzymes native to your environment and can actually help to prevent allergies. 

>> In place of processed and refined foods (including wheat, industrial seed oils, transfats and sugar), prepare your own meals from scratch, using whole (spray free) foods. Eg. in place of a wheat based sandwich, opt for a salad with loads of colourful vegetables (some starchy) and a source of protein. 

3. Encourage Gut Microbiome

Along with avoiding any damage to your microbiome through the products you use on your skin and the foods you eat, there are also some ways of encouraging your good bugs.

Skin bugs

As I previously mentioned, reach for low-tox products for anything that comes into contact with your skin and minimising the amount of products you apply to your skin. There are also benefits for your skin microbes when you get out in nature. The extra benefit of-course is the de-stressing benefits nature time brings and you'll also be scoring some sun to skin exposure to maintain healthy vitamin D levels. More on that in episode 4.

Start by get your hands and feet dirty in the dirt and at the beach. This is a source of natural bacteria to expose your skin to and if you have little ones, playing in the dirt and with pets,12 is a powerful way to build their adaptive immune system in these younger years of life. A regular gardening practise has also shown to lower stress levels and improved brain health, plus it's a wonderful exercise.13

Just a couple of notes- firstly make sure you are playing in dirt that is free from glyphosate and other chemical sprays- often public parks and areas are regularly sprayed.

We were rudely shocked the other week when visiting the ocean across at the Coorong with family and we stopped to have a cup of tea at a public picnic area. We all jumped out and started walking over to the area but were luckily stopped by another family. They explained a council worker had just  sprayed all around the picnic area (on a Saturday mind you when there were families, including young kids playing and camping within metres). We thanked the family and moved swiftly on. 

So keep your digging and barefoot time for the beach and  if you're lucky enough to have a front or backyard, enjoy regular gardening to get exposed to the beneficial bugs. I aim to plant something each week with my daughter, wether it's a veggie seed, moving a seedling we've grown from a small pot and into the ground or an established pretty flower from our local nursery. I love teaching her the benefits of getting out in nature time and how this supports our good bugs at the same time.

The second caution is if you have cats outdoors (or you neighbours do), it is best to avoid playing in the soil. Cats faces in the garden can spread the toxoplasmosis organism which can in pregnancy cause mental disabilities and blindness in your unborn child. If you do own or have cats around, gardening gloves are recommended and if you're growing your own produce to eat, cover with a netting to keep the cat/s away.

Thirdly, in all cases when using potting mix in the garden, use gloves and open the bag slowly and wet it before use, to avoid breathing it in. The same goes for handling compost. This is to avoid exposure to the Legionella bacteria, which thrive in a moist, warm environment.  

Gut & Vaginal Microbiota

Along with eating organic, or spray free produce, there are ways to encourage and nourish your beneficial bacteria within your gut, through your diet.

Firstly, consuming probiotics through your foods, drinks and supplements can play a role at delivering the live microorganisms to inoculate your gut and support your immune system (among much more). Beneficial bacteria have also shown through research to specifically reduce inflammation within the gut.14

Examples of probiotic rich foods are fermented coconut cream and milk into yoghurt and kefir; coconut water into coconut water kefir; fermented vegetables into sauerkraut, beet kvass and kim chi and fermented tea into kombucha.  If you're new to fermented foods, go slow as they can cause a die off effect initially when they start to crowd out the pathogenic microbes.

I had a patient who after recommending adding some sauerkraut to her meal, she went home very excited and confused a whole bowl full. She was very ill with flu like symptoms and diarrhea for a few days, as this big dose of probiotic rich food was such a shock to her gut bugs. This was a reminder however of just how powerful foods can be (when used in the right amounts) to heal your gut and boost your beneficial bacteria. 

Sometimes you do need to hold of on wild ferments such as sauerkraut and kombucha while you work on controlling pathogenic bacteria or an overgrowth of candida. My favourite coconut yoghurt and kefir are perfect right from the start however, as they have levels of the good yeast Saccharomyces boulardii which acts to mop up dysbiotic bacteria and control candida. 

I'd suggest starting with 1 tbsp of the coconut water kefir and yoghurt and working up to 1/2-1 cup daily. The kefir is refreshing, hydrating and is a healthy bevvie to reach for when you feel like some bubbles. The yoghurt is a gut friendly addition to smoothies and mixed into porridges (once cooled), used in chia sed puddings or alongside a (healthy) desert.  You can head here to find these cultures and use code BABY for a 10% off discount. 

Simply consuming probiotic rich fermented foods and taking probiotics isn't enough however. You do need to make sure you're feeding your good bugs, so they can thrive. 

Enter prebiotics. When you eat prebiotic rich foods, they withstand digestion (cant be broken down by stomach acid and enzymes) in both your stomach and small intestine of your gut. Once the prebiotic rich food reaches your large intestine, it is fermented by your bacteria, providing fuel for them called postbiotics, which stimulates the growth of your probiotics and your original gut microbes.

Having adequate prebiotics in your diet allows your beneficial bacteria to grow and multiply, so ideally, for a healthy gut bacteria balance, consuming both probiotics and prebiotic rich foods is beneficial. 

Research has also indicated that prebiotic rich foods play role in providing multiple benefits to the body, such as improved health of:15

  • heart 
  • digestion
  • stress
  • hormone
  • immunity (including autoimmunity)
  • weight
  • inflammation

The types of prebiotics fibres that can feed your beneficial gut bacteria, include vegetables such as...

  • Jeruselum artichokes: sliced very finely or grated and sprinkled through a salad, mixed into a dip, or added into a smoothie. Although the prebiotic properties are lower once cooked, jeruselum artichokes are delicious roasted too.
  • Raw asparagus: chop and add to salads added to a salad- and even yummier when you grow these fresh and eat them straight out of the garden. Another option is to try it fermented.
  • Raw dandelion greens: chopped and added through a salad.
  • Raw or cooked onions: they can go in all almost all savoury dishes for prebiotics and a flavour hit. and raw garlic (slice very finely and add to salad dressing or sauce like pesto).


  • Chicory root: often found in roasted dandelion tea and used as an alternative to coffee. 
  • Resistant starch found in green bananas and cooked and cooled rice is another source of prebiotics.
  • You can find the prebiotic acacia gum in gut health supplement powders, which is a beneficial addition to water or smoothies.
  • I love snacking on prebiotic rich tiger nuts and baking with tigernut flour. You can find recipe inso here.

As with probiotics, introduce these foods slowly to avoid symptoms such as abdominal cramping, flatulence, bloating and loose bowel movements. Drink plenty of water to avoid constipation and be mindful if you have issues with IBS, SIBO (small intestinal bacterial overgrowth) or FODMAP intolerance, you may not tolerate prebitiotics until this condition is under control. 

Consider Diet, Medication & Lifestyle Habits  

So there you have it, when you are aiming for tip top gut microbiome, for your preconception, pregnancy and mum life, consider the multiple factors which can be a positive or negative influence. 

Use natural products for your body care and cleaning, avoid over sanitising and using products containing Triclosan and reach for natural contraceptive methods.

Get and enjoy the benefits of natural microbes in nature and avoid the use of antibiotics when not absolutely necessary.

Base your diet around spray free produce and better still, get your hands dirty and grow your own food. Avoid sugar and processed foods and consume probiotic and prebiotic rich foods and supplements daily.

Further specific support for prepping your microbiome throughout your pregnancy, pre and post birth is found within my updated digital course, Path To Glowing Mumma. You can join the wait list here, so you're first to gain access when doors open early 2021.


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