Rewilding Your Gut: How to Restore Microbial Diversity in a Modern World

Modern habits have stripped away the microbial variety our bodies once relied on. In this piece, we explore simple, natural ways to rewild your gut and restore balance from the inside out.

Introduction: The Invisible Extinction

You don’t need to be sick to know something’s off.

You might feel it as low-level fatigue, a sluggish mind, or a growing list of foods you “can’t handle anymore.” You might notice skin that flares, mood swings that come out of nowhere, or a gut that never quite feels settled.

What’s often missing in these moments isn’t just a nutrient or supplement. It’s diversity.

Inside your gut lives a vast, invisible world—a living ecosystem of bacteria, fungi, and microbes that’s meant to be wild, abundant, and teeming with life. But for many of us, that inner wilderness has quietly faded.

Modern life—processed food, chlorinated water, antibiotics, indoor living—has unintentionally sterilised our internal terrain. We’ve lost species. We’ve lost variety. And as a result, our bodies are less resilient, less adaptable, and more prone to inflammation, intolerance, and imbalance.

Rewilding the gut is about remembering what we’ve lost—and gently inviting it back in.

The Over-Sanitised Life: How Modern Habits Deplete the Microbiome

In the pursuit of cleanliness and convenience, we’ve created an environment that’s increasingly hostile to microbial life. We filter our water, bleach our surfaces, sanitise our hands, and package our food in sterile wrappers. The result? A world where the microbes we need to thrive are barely getting through.

Our ancestors lived close to the land. They ate food pulled from soil, drank water from natural sources, and shared microbes with animals, plants, and one another. Their guts were constantly exposed to a rich and varied microbial landscape.

Today, that exposure is rare.

Tap water, treated with chlorine and fluoride, kills bacteria on contact—including the good kind. Antibiotics, while life-saving when truly needed, are prescribed far more than necessary. And the modern diet—often ultra-processed, low-fibre, and heat-sterilised—offers little to no support for microbial growth.

Even birth by Caesarean section or bottle feeding in infancy can reduce early microbial exposure, shaping gut health for years to come.

It’s not that hygiene is bad—it’s that over-sterilisation has swung the pendulum too far. We’ve cleansed away not just the bad, but the beneficial. And in doing so, we've starved the internal networks that help us digest, regulate, repair, and protect.

Why Microbial Diversity Matters

Your gut isn’t just home to bacteria—it’s home to balance. And that balance depends on diversity.

A healthy microbiome is like a well-functioning ecosystem. The more species it contains, the more stable, adaptable, and resilient it becomes. Each strain of bacteria has its own role: digesting fibres, regulating inflammation, producing vitamins, modulating hormones, defending against pathogens. When one species disappears, others can often step in. But when diversity drops below a certain threshold, the entire system becomes fragile.

Reduced microbial diversity has been linked to a growing list of chronic conditions—obesity, inflammatory bowel disease, allergies, autoimmune conditions, depression, even type 2 diabetes. It’s not that microbes cause these issues directly. It’s that low diversity reduces the body’s ability to adapt and repair.

Think of it like this: if your internal ecosystem is made up of only a few dominant strains, you’re more vulnerable to imbalance. A sudden diet change, a round of antibiotics, or a period of stress can tip the scales. But when your gut is populated by hundreds of species, it can bend without breaking.

Microbial diversity isn’t a “nice to have.” It’s a core requirement for long-term resilience.

How to Rewild Your Gut (Naturally)

You don’t need expensive supplements or strict elimination diets to begin restoring microbial diversity. What your gut often needs is a return to the basics—rhythms and exposures that reconnect you to real food, real environments, and natural variety.

Here are some of the most effective ways to rewild your gut, gently and sustainably:

1. Eat a Wider Range of Plants Different fibres feed different species of gut bacteria. The more variety you eat, the more species you support. Aim to include 30+ different plant foods each week—fruits, vegetables, herbs, nuts, seeds, legumes, grains. Even small amounts count.

2. Reintroduce Fermented Foods Fermented foods like sauerkraut, kefir, kimchi, miso, and live yoghurt introduce beneficial bacteria and help reinforce microbial diversity. Start small—1 to 2 tablespoons a day is often enough—and rotate your choices to keep things balanced.

3. Embrace the Outdoors Spending time in nature—gardening, walking barefoot, hiking, swimming in natural bodies of water—brings your body into contact with environmental microbes. These exposures help replenish your ecosystem and remind your immune system how to stay flexible.

4. Live with Animals (If You Can) Pets, especially dogs, have been shown to increase microbial diversity in the home. Households with animals tend to have more robust microbiomes—not just in pets, but in the humans who care for them.

5. Get Dirty (Within Reason) Over-sanitisation strips your environment—and your skin—of beneficial microbes. Letting kids play in the mud, eating unpeeled fruit from a farmer’s market, or using natural cleaning products are small ways to reintroduce contact without compromising hygiene.

6. Reduce Chemicals That Kill Microbes Chlorinated tap water, antibacterial soaps, chemical-laden cleaners, and overuse of sanitiser can disrupt your microbial environment. Use a water filter, choose natural body products, and clean with vinegar or essential oil-based alternatives when possible.

7. Vary Your Environment Modern living often means eating the same foods, in the same setting, day after day. But microbes love variety. Travelling, exploring new places, and changing your food routine—even slightly—can stimulate new microbial growth and diversity.

8. You don’t need to do everything at once. But every small shift towards natural living makes your inner ecosystem more robust.

A Slower, Wiser Way of Living

Rewilding your gut isn’t about chasing perfection. It’s about rewriting your relationship with your body—and the world it moves through.

Modern health advice often feels like a checklist: eat this, avoid that, take these supplements, follow that protocol. But beneath the noise, the body is asking for something simpler: consistency, nourishment, connection, and rhythm.

Supporting your microbiome is less about doing more, and more about living differently.

That might mean:

• Eating meals slowly, without screens

• Preparing food from scratch, even a few times a week

• Walking barefoot in your garden

• Getting sunlight first thing in the morning

• Taking moments of stillness during your day, without reaching for stimulation

It might also mean letting go—of obsessive food rules, rigid health routines, or the idea that you’re broken. Your body isn’t failing you. It’s responding to the environment it’s been given.

When you begin to change that environment—through food, movement, connection, and nature—your gut responds. Not instantly, but steadily. And from that response, health begins to rebuild.

Conclusion: You’re Not Broken. Your Terrain Is.

If your gut feels out of balance, it doesn’t mean you’re broken. It means your internal ecosystem is struggling to adapt to a world it was never designed for.

The loss of microbial diversity isn’t a personal failing—it’s a cultural one. It’s what happens when modern living separates us from soil, sunshine, fresh food, wild bacteria, and the messiness of life itself. Rewilding your gut is about returning to what was once normal: variety, exposure, connection, and rhythm.

This isn’t a detox. It’s a homecoming.

The good news is, your microbiome is incredibly responsive. Small shifts—eating more plants, spending time in nature, reducing chemical exposure—can have a profound impact over time. Every step you take to rewild your environment, your routine, your diet, is a step toward restoring what your body has always known how to do: heal.

So take the pressure off.

 Live slower. Eat closer to the earth.

 And trust that your gut—given the right environment—knows the way back.