Key Factors for a Healthy Microbiome

I believe good gut health is foundational to overall wellbeing. In clinic, I see time and again that people feel so much better once we sort out what’s going on in their gut. And I know I’m not alone in thinking this! Gut health has become a major focus in the wellness world—and for good reason.

Your gut microbiome—made up of trillions of bacteria, fungi, viruses, and other microbes—is essential for everything from digestion and detoxification to immune function, hormone balance, and mood. Understanding what shapes this complex internal ecosystem can offer a powerful, holistic approach to feeling your best.

Here are some of the key factors that influence your gut health—and how a naturopathic lens can support a balanced microbiome.

1. Birth and Early Life: How Microbiomes Begin

The way we enter the world has a lasting impact on our gut. Babies born vaginally receive beneficial microbes from their mother’s vaginal microbiome—a process called vaginal seeding. This plays a crucial role in kickstarting a healthy microbiome and immune system.

In contrast, babies born via C-section may acquire more hospital-associated bacteria, such as Klebsiella and Pseudomonas, which are linked to higher risks of asthma, allergies, and type 1 diabetes. Research is currently exploring the use of specific probiotics for C-section babies to support more beneficial microbial colonisation—watch this space!

2. Genetics: The Influence of Ancestry

Our genes influence how our immune system functions—and by extension, our gut health. Certain inherited conditions, such as Crohn’s disease and ulcerative colitis, highlight the strong link between immune dysregulation and gut issues.

Interestingly, our microbiome is shaped even before birth. The womb was once thought to be sterile, but research now shows that the uterus has its own microbiome. Non-pathogenic microbes in the amniotic fluid may help prime the baby’s immune system, laying an early foundation for gut health.

3. Breastfeeding: Feeding the Gut from Day One

Breast milk is rich in beneficial bacteria, nutrients, and immune factors that support a baby’s developing gut and immune system. It helps establish a healthy microbial balance that protects against infections, allergies, and gut-related conditions.

Breastfeeding also supports the mother’s health—helping the uterus contract, conserving iron, releasing oxytocin, and reducing the risk of breast cancer, heart disease, and type 2 diabetes.

4. Environment: Exposure to Microbial Diversity

Our immune systems need to meet microbes to become resilient. Over-sanitised environments can reduce the variety of beneficial microbial exposures, which may contribute to immune issues later in life.

Let kids play in the dirt. Let them pat the dog, walk barefoot, or help in the garden. Nature is one of the best ways to support microbial diversity.

5. Diet: Fuel for a Thriving Microbiome

Your gut bugs thrive on variety. A diverse diet—especially one rich in plant-based foods—helps feed different beneficial bacteria. Think of your gut like a garden: you need many types of plants to create a healthy ecosystem.

Try to eat at least 40 different types of plant foods per week. This includes fruits, vegetables, nuts, seeds, legumes, and whole grains. Tracking your plant diversity for a week can be a fun and eye-opening exercise!

6. Stress: The Gut-Brain Connection

Stress affects gut health in profound ways. It can reduce the diversity of beneficial bacteria, trigger inflammation, and contribute to conditions like IBS, IBD, anxiety, and hormonal imbalance.

Supporting your nervous system is a powerful way to support your gut. Gentle movement, deep belly breathing, meditation, journaling, and quality sleep all play a role in calming your nervous system and nourishing your microbiome.

7. Medications: Antibiotics and More

Antibiotics are sometimes necessary, but they also disrupt the balance of gut microbes. Many people report gut symptoms after a course of antibiotics—sometimes for months or even years. If you do need antibiotics, taking high-quality probiotics during and after treatment (spaced at least two hours apart) can help support microbial recovery.

Other medications can affect gut health too. These include proton pump inhibitors (PPIs), metformin, oral contraceptives, antacids, and laxatives. As research continues, we’re learning more about how to counteract these effects through food, lifestyle, and targeted supplements.

Are you struggling with your gut health?

You’re not alone—and there’s so much we can do to help. Gut health is one of my favourite things to support in clinic. I use tools like the Co-Biome test to gain insights into your unique microbial makeup, and then tailor a plan using probiotics, prebiotics, nutritional strategies, herbs, and lifestyle shifts to fast-track healing.

If you’re dealing with bloating, irregular bowels, food reactions, or just a “gut feeling” that something’s off, let’s get to the root of it. Because gut health really is the foundation of everything.

AUTHOR: TALITHA

I specialise in gut health (IBS, IBD, microbiome testing), women's health (preconception, fertility, hormone balance), and mental health (depression, stress, anxiety). I am a degree- qualified naturopath who LOVES helping people transform their health stories!!