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Dishing the dirt on the gut microbiome 🧠

Dishing the dirt on the gut microbiome 🧠

Why soil might be the secret to happier guts and healthier minds

Dr Emily Leeming PhD's avatar
Dr Emily Leeming PhD
Apr 09, 2025
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Dishing the dirt on the gut microbiome 🧠
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When was the last time you got your hands dirty - literally?

Soil, the often-overlooked ground beneath our feet, might just hold some important clues for our health and well-being.

There's plenty to dig into (pun absolutely intended), from questioning our ultra-clean lifestyles to exploring why gardening or even a simple walk outdoors could be the key to a healthier gut and a happier mind.

What we’ll cover today:

  • The clean hypothesis: Is being too clean hurting our health?

  • What is the soil microbiome? And why does it matter

  • How spending time in nature helps your mental well-being

  • Actionable tips for your gut microbiome and health

Are we too clean?

We often think being clean is good for us, but there could be a catch.

The “hygiene hypothesis” suggests that by making our homes too clean (and living in urban areas) we’re missing out on important microbes from nature, and in particular, the soil.

These microbes help train our immune system and keep our gut healthy.

Limiting exposure to these microbes may potentially lead to an underdeveloped immune system, making us more susceptible to autoimmune diseases and gut issues.

So, being too clean might, in theory, actually harm us in the long run.

Soil is the most diverse habitat on earth

Soil is home to about 59% of all life on Earth, which makes it the most biodiverse habitat.

It’s estimated (extrapolated from bacterial counts) that a teaspoon of healthy soil could contain over 8 billion microbes, more microbes than there are humans on the planet.

Anywhere from 22% to 89% of bacteria types (called species) can be found living in soil.

And it’s not just bacteria either, like the gut microbiome, soil also contains a wide variety of other tiny living organisms, called microbes, like fungi and viruses.

Do you like gardening?

Spending time outdoors and interacting with soil could actually improve your gut health.

Gardening temporarily changes the microbes on your skin by transferring some from the soil, though these changes usually disappear within 12 hours.

With regular gardening, this exposure to soil microbes may also have an impact on the microbes in your gut over time - transferred to your mouth when you touch your face or eat.

Gardening families usually have a more diverse gut microbiome. Soil-derived bacteria in their guts increased across the gardening season by an average of 3.2% in adults and 7.6% in children - reaching 23% in one child.

People who have a wider variety of plants in their garden, like shrubs and flowers, tend to have healthier gut bacteria.

Nature boosts mental-wellbeing

A study found that preschool children who spent time in nature-based daycares, where they played outside and interacted with nature, had healthier gut microbiomes and felt less stressed compared to kids in cities.

People who spent at least two hours a week in nature* (like parks, beaches, or woodlands) were nearly 60% more likely to say they felt healthy, and about 20% more likely to say they had good mental well-being.

These benefits were similar in size to the positive effects you'd get from meeting weekly exercise recommendations compared to doing no exercise at all.

*These two hours can be spread out over the week, you don't need to do it all at once.

3 unexpected ways to pick-up new microbes

  1. Move over fermented foods, they’re not the only food sources of live microbes.

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