Eight Strategies for Microbiome Restoration - www.clarabailey.com

Eight Strategies for Microbiome Restoration

The old saying “you are what you eat” is very true in many regards, however, “you are what you absorb” is truer still. If our digestive system is not functioning properly, many of the healthy nutrients that we consume cannot be broken down and absorbed into our bodies.

Modern living involves many factors that can disrupt the optimal functioning of the digestive system and our microbiomes. These include:

  • antibiotic use
  • physical, mental or emotional stress
  • eating a diet that lacks whole-grains, fruits and -vegetables
  • food intolerances
  • high sugar intake
  • the oral contraceptive pill
  • regular consumption of alcohol

Over time these factors can contribute to an array of digestive discomforts that ultimately impacts our general sense of well being and energy. The good news is, through simple dietary and lifestyle modification it is simple to create an environment for the digestive system to return to proper functioning.

Understanding Your Microbiome

The human gut microbiome contains 10^14 living microorganisms (In other words, 100,000,000,000,000) from over 1000 different species that weigh between 1-2kg. This is x10 the number of cells in the human body, or in other words, we’re composed of 90% microbial & 10% non-microbial cells!  So technically us humans are super-organisms (or ecosystems) as opposed to a single entity.

The microbiome is responsible for so many processes essential for our health that many scientists consider it to be a vital human organ.  In fact, it exceeds the liver in the number of metabolic processes it’s apart of. So it’s very important that we take good care of them.

What does our Microbiome Organ do for us?

We have a mutually beneficial relationship with our microbiome, each of us requiring the other to preserve our health.

  • Protects against allergy development
  • Gut motility (how fast food transits through our digestive systems)
  • Improves nutritional status: B vitamins, Vitamin K and mineral absorption – Calcium, Magnesium, Zinc.
  • Energy salvaging & weight management
  • Metabolism of estrogen (including Xenoestrogens in environment & plant phytoestrogens)
  • Blood glucose balance & insulin sensitivity
  • Mood management
  • It represents 70% of our immune function and is responsible for our 1st line immune defence, which means it prevents other microbes from colonising.

Nourishing & Restoring Your Microbiome

These are the basic guidelines I use in my naturopathic practice to help my patients’ guts and microbiomes return to a happy place.

1. Remove Triggering Foods

Avoiding harmful foods is the most important place to start. In my practice, I recommend a particular hypoallergenic diet or an elimination diet to follow, which will identify any foods that your body is adversely reacting to. For some people who don’t have the time or patience to do an elimination diet, a food intolerance test can be in clinic and tests over 46 different foods.  It’s a nifty tool that provides a lot of information in 40 mins.

The most common food triggers are wheat, gluten, dairy products and soy. An accessible version of a digestion healing protocol can simply be to eliminate these.  It is important to stick to your dietary plan while healing the digestive tract to give the tissues, bacteria and enzymes the best chance at repairing. Most commonly, once the digestive tract has healed, foods that were once not tolerated well in the past will no longer cause discomfort.

2. Prepare foods that has easily absorbable nutrients.

While your digestive system is healing, it is important to make it as easy as possible for your body to access nutrients.

Get out your favourite recipes for soups and slow cooked stews.  Be sure to include orange coloured vegetables such as carrots, sweet potatoes and squash which are rich in beta-carotene which converts to vitamin A in the body. These nutrients support the repair and function of the mucous membranes of the digestive tract.

For stews, choose meats that are on the bone, such as lamb shanks and necks, whole chickens, chicken Marylands, rabbit etc. and cook slowly (crock pots are your best friend in this area). Not only are bones a rich source of minerals, but the cartilage and collagen collectively help to heal, repair and rebuild damaged connective tissue within our digestive tract.  Bone broths and stocks are also extremely beneficial.

Vegetable juices containing carrot, beetroot, celery, ginger, silverbeet/spinach and a little apple for sweetness are an excellent way of boosting your nutrient levels for the day.

3.  Increase probiotic foods.

Probiotic foods boost our internal beneficial bacteria. These bacteria repair the gut while preventing the invasion of opportunistic organisms (a.k.a belly bugs). They also prevent food sensitivities and prevent inflammation.

Probiotic foods include:

  • natural, unsweetened yoghurt (organic, vaalia or activia brands are best)
  • kefir
  • sauerkraut (fermented cabbage)
  • kimchi

Probiotic supplements are also useful. There are many out there, and all have slightly different actions. It’s an art form and science in itself to prescribe the right probiotic.

4. Increase fibre.

A diet rich in fibre regulates bowel function, feeds the beneficial bacteria in the gut and regulates energy throughout the day. A pretty impressive array of virtues!

Include sources of fibre from:

  • unpeeled fruits (apples, pears, kiwis, peaches, pomegranates and citrus in particular)
  • vegetables (especially chicory root, garlic, Jerusalem artichoke, leek, onion, dandelion greens, asparagus, banana, fennel bulbs).
  • legumes
  • flax and chia seeds
  • whole grains (grains such as oats, rye, barley, brown rice, buckwheat and whole grain bread).

You can boost your fibre intake by sprinkling oat bran, psyllium husks, chia or flax seeds on your morning porridge or added to smoothies.

5. Quality protein at every meal.

Proteins provide the building blocks for tissue repair. When the digestive tract has been under stress from low-grade inflammation (as a result of food intolerance, long term antibiotic use or parasitic infection) it is important it has all these building blocks at the ready to rebuild the tissue.

Fatty fish such as tuna, salmon, mackerel, herring and sardines are rich sources of both protein and omega-three fatty acids. Omega 3s are highly anti-inflammatory compounds that further promote the healing process.  Other good sources of protein include lean meats, eggs, legumes, tofu and tempeh.

6. Eat good quality anti-inflammatory oils.

Use only cold-pressed oils that are high in omega three fatty acids. For cooking, these include extra virgin olive, macadamia and coconut oil.

For salad dressings or when you are not heating the oil; walnut, almond, pumpkin seed, chia and flax (linseed) seed oils.

Avoid all rancid oils (vegetable oil, peanut, soy, canola), hydrogenated, shortenings and other synthetic fats (this includes all kinds of margarine).

7. Morning gut healing smoothie

This smoothie recipe is truly food as medicine! If you are serious about healing your digestive system, making this smoothie your beginning to the day is putting your best foot forward. The smoothie is a complete package of probiotics, prebiotics, anti-inflammatory compounds and gastrointestinal repair nutrients. I’ve prescribed this smoothie many a time, and find my patients love not only the effects but also the taste.  It is inspired by Dr Jason Hawrelak’s original recipe (Jason is a naturopath in Hobart, guru on all things bowels and bacteria and is a really wonderful human to boot).

Therapeutic Gut Healing Smoothie

1 cup milk: preferably soy, rice, almond or oat or apple juice

1/2 cup vaalia yoghurt or activia yoghurts (no added sugar variety) or probiotic supplement

1 tablespoon flax seed or hemp oil

1 tablespoon of oat-bran (or 2 teaspoons of flax or chia seeds)

1 teaspoon slippery elm powder

2 teaspoons glutamine powder

1-2 teaspoons lactulose (an excellent prebiotic and can be purchased at your local pharmacy)

1/2 cup berries – strawberry, raspberry, blueberry (frozen ones are fine)

1 unripe banana

a little honey and cinnamon to taste

extra water to achieve desired consistency

Blend and drink up!

Microbiome by Clara Bitcon Bailey Naturopath

8. Drink stomach soothing herbal teas.

Herbal teas such as chamomile, peppermint, fennel and liquorice are all calming to the digestive system. Drink after meals.

For a tasty digestive tea place 1 teaspoon each of lemon balm, meadowsweet, chamomile, spearmint, fennel or anise seeds and orange peel in a teapot.  Pour 2 cups of boiling water over the herbs, cover the pot, and let it steep for 15 minutes. Strain and sweeten with honey, and drink warm.

To listen to this blog, press play:

With love,


Healing Wise

November 8, 2019

  1. Hilde says:

    Hi! Can I serve the guy healing smoothie to my children?

    • Clara Bitcon says:

      Hi Hilde, yes it’s absolutely safe for kids 2 and above. They may experience a bit of gas a bloating in the beginning, if so, just lower the amount of lactulose and glutamine, and gently increase from there.

  2. […] The number one thing to do to get on top of poor digestive function is to identify the foods that are harming and alarming your system. And from there working out which foods are going to heal and calm your system. I’ve written more in-depth about healing your gut in previous posts. […]

  3. […] The number one thing to do to get on top of poor digestive function is to identify the foods that are harming and alarming your system. And from there, working out which foods will heal and calm your system. I’ve written more in-depth about healing your gut in previous posts. […]

  4. […] The best place to begin is by doing an elimination diet guided by a practitioner to uncover your unique triggers. These are going to be different from person to person. Following a gut-healing protocol for a minimum of 3 months will allow your body to rebuild its resil… […]

Leave a Reply

Your email address will not be published. Required fields are marked *

Free Menstrual Cycle Masterclass eBook

download the ebook

Understand the five dimensions of your cycle and how to create deeper alignment in your life in this 27 page ebook


free resources


download chart


Uncover your cycle's unique pattern with the free chart.