What if I told you that there’s an entire world inside you — a living, breathing ecosystem that influences your digestion, immunity, energy, mood, hormones, skin, and more? Well, there is and it’s called the gut microbiome!

As a naturopath, I see the gut as a foundational system. It’s often the starting point in my treatment plans because when the gut is healthy and balanced, the whole body has a chance to thrive.

What Is the Gut Microbiome?

The gut microbiome refers to the trillions of microorganisms — mostly bacteria, but also fungi, viruses and archaea — that live in your digestive tract, particularly the large intestine. These microbes weigh about 1–2 kilograms in total and collectively contain 100 times more genes than your own human genome.

It’s not just about numbers — these microbes are metabolically active and constantly interacting with your body. Some of their vital roles include:

Digesting food that your body can’t break down on its own (like certain fibres)
Producing vitamins such as vitamin K2 and some B vitamins
Regulating the immune system
Assisting with detoxification
Helping to balance hormones
Supporting mental health by producing neurotransmitters like serotonin and GABA

how does the microbiome affect the body: Gut-Brain, Gut-Immune, Gut-Hormone Connections

Here’s where it gets really interesting!

Gut-Brain Axis

Roughly 90–95% of your body’s serotonin (a neurotransmitter linked to mood, sleep and wellbeing) is produced in the gut, not the brain. The gut and brain communicate via the vagus nerve and through chemical messengers like cytokines and metabolites. This is why an imbalanced microbiome can contribute to anxiety, low mood, and brain fog.

Gut-Immune Connection

Approximately 70% of your immune system is located in the gut lining. The microbiome plays a key role in training the immune system to distinguish between friend and foe — reducing the risk of autoimmune reactions, chronic inflammation and food sensitivities.

Gut-Hormone Connection

There’s even a special group of gut bacteria called the estrobolome that helps metabolise estrogen. If these bacteria are out of balance, estrogen can recirculate in the body instead of being excreted, potentially contributing to hormonal symptoms such as PMS, bloating, and period pain.

What Happens When the Microbiome Is Out of Balance?

Modern life doesn’t always support microbial diversity. Antibiotics, stress, processed food, alcohol, low-fibre diets, and environmental toxins can disrupt the balance of bacteria — leading to a state called dysbiosis.

You might experience:

Bloating, reflux, irregular bowel movements
Low energy and frequent colds
Anxiety, mood swings or difficulty concentrating
Skin issues like acne, eczema or rosacea
Hormonal imbalances or stubborn weight gain
Food intolerances and sensitivities

How to Support Your Microbiome Naturally

The good news? Your microbiome is incredibly adaptable. It responds quickly to dietary and lifestyle changes — often within **3–5 days**. Here are some naturopathic ways to nurture your inner ecosystem:

1. Eat More Plants

Diverse plant foods = diverse microbes. Aim for 30+ plant varieties per week. This includes vegetables, fruits, legumes, whole grains, nuts, seeds, and culinary herbs. The fibres they contain feed the beneficial bacteria.

2. Include Prebiotic-Rich Foods

Prebiotics are specific types of fibre that fuel friendly microbes. Examples include:

Garlic
Onions
Leeks
Asparagus
Jerusalem artichokes
Green bananas
Oats
Flaxseeds

3. Add Fermented Foods (If Tolerated)

Foods like sauerkraut, kimchi, kefir, miso, tempeh and plain yoghurt contain live probiotics — strains of beneficial bacteria that help reseed the gut and promote balance.

4. Minimise Microbiome Disruptors

These include:

Ultra-processed foods
Excess refined sugar
Artificial sweeteners (e.g. sucralose, aspartame)
Alcohol (especially in excess)
Frequent antibiotic or NSAID use
Household and personal products - use low tox only!

5. Prioritise Stress Reduction

Chronic stress can alter gut flora, increase intestinal permeability ("leaky gut") and impact digestion. Incorporate:

Breathwork
Meditation
Vagus nerve toning
Nature time
Gentle movement like yoga or walking

6. Herbal & Nutritional Support

Depending on your symptoms, herbs like slippery elm, chamomile, marshmallow root, licorice, and turmeric can help calm and heal the gut lining. Antimicrobial herbs such as berberine or oregano may be used short-term under practitioner guidance for dysbiosis or SIBO.
Nutrients like zinc, glutamine and B vitamins also support gut repair.

Gut Healing Is a Journey, Not a Quick Fix

One of the things I love most about gut work is that it’s foundational and transformational. When we support the gut, we often see shifts in energy, skin clarity, hormone balance, immune resilience and emotional wellbeing.

But it’s not about band-aid solutions. It’s about gently rebuilding your inner terrain — with whole foods, herbal wisdom, and compassionate guidance.

Ready to Heal Your Gut?

Whether you’re dealing with digestive discomfort, fatigue, skin issues, or you're simply wanting to improve your overall health — tending to your gut microbiome is a powerful first step.

At BG Naturopathy, I create individualised plans using herbal medicine, nutrition, lifestyle therapy, and functional testing — always tailored to you.

🌿 Book your appointment here
📧 Or reach out at bgnaturopathy@gmail.com
📍 Clinic based in Kensington, VIC

The Gut Microbiome: The Hidden Ecosystem That Shapes Your Health