We often talk about gut health as if it starts and ends with what we eat. But what if it starts long before that, deep beneath our feet?
The soil beneath us is alive with trillions of microorganisms that quietly orchestrate the fertility of our fields, the nutrient density of our crops, and even the microbes that eventually inhabit our own guts. In many ways, soil is the planet’s gut microbiome, and when it’s unwell, we feel it too!
The State of the Soil: How the UK Measures Up
The UK’s soils are in trouble. Around 40% of British agricultural soils are degraded, largely due to decades of intensive farming, monocultures, and overuse of fertilisers and pesticides (1). Compared to other European nations, the UK ranks mid-to-low for soil organic carbon and biodiversity, with southern England and East Anglia among the most depleted regions.2
By contrast, countries investing in regenerative and organic practices, such as Austria, Finland, and parts of France, maintain higher soil microbial diversity and better nutrient cycling. The result? Healthier soils, greater carbon storage, and more resilient food systems.3
Do We Really Need Everything to Be Organic?
“Organic” isn’t just a buzzword, it’s a signal of how a food was produced. Organic farming avoids most synthetic pesticides and fertilisers, instead focusing on soil health through composting, crop rotation, and biological pest management. But does that automatically mean “healthier” food?
Evidence shows that organic produce often contains higher levels of polyphenols and antioxidants, and that organic soils harbour more diverse microbial communities.4 However, experts caution that not everything needs to be organic. Prioritising the “Dirty Dozen” - the fruits and vegetables most likely to carry pesticide residues (like strawberries, spinach, and grapes) - can make the biggest difference.
The “Clean Fifteen”, such as avocados, onions, and sweetcorn, tend to be lower risk, meaning you can safely buy non-organic versions. This selective approach supports health without straining budgets or accessibility.5
To read more about "The Dirty Dozen" and "The Clean 15" head to our article here.
Pesticides, Soil Health, and the Ripple Effect
Pesticides are designed to kill. And while they target pests, they often hit non-target species too, including the microbes that keep soil ecosystems thriving. Repeated pesticide use has been shown to reduce soil microbial biomass and diversity, impair nitrogen cycling, and weaken plant-microbe symbioses.6
Over time, this microbial decline reduces soil fertility and structure, making crops more dependent on synthetic inputs. A vicious cycle that ultimately diminishes food quality. Fewer soil microbes mean weaker nutrient exchange between roots and soil, potentially leading to lower levels of minerals, vitamins, and phytochemicals in our food.7
Soil, Biodiversity, and the Human Microbiome
Here’s where things get fascinating: the health of the soil beneath us appears to mirror - and even influence - the health of our gut microbiome!
Emerging research describes a soil–plant–food–gut axis, where soil microbes seed plant surfaces and influence the microbial diversity of foods we consume. Humans have co-evolved with soil microbes through contact with food, water, and the environment. Therefore, loss of soil biodiversity may be reducing the diversity of our own internal ecosystems.8
When we move or travel, this connection becomes visible. A groundbreaking longitudinal study found that immigrants from Southeast Asia to the U.S. experienced a rapid “Westernisation” of their gut microbiome, losing native bacterial strains within months and continuing to lose diversity over time.9
While the study didn’t directly measure soil quality, it underscores how environmental microbial exposure - including food and soil microbes - reshapes our internal ecosystems. Reviews now suggest that soil acts as a key microbial reservoir, meaning changes in soil biodiversity across countries could influence the microbial exposures that shape our gut health.10,11
In short: your gut microbiome isn’t just shaped by your diet; it’s shaped by the land your food grows in. The microbes beneath our feet are, quite literally, part of who we are.
The Bigger Picture: Why This Matters
Healthy soil supports more nutrient-dense crops, stores more carbon, resists drought, and sustains pollinators. But it also connects us biologically to the ecosystems we inhabit. The global decline in soil biodiversity may be silently shaping the rise of immune and inflammatory disorders linked to loss of microbial diversity in humans.
5 Ways to Boost Biodiversity: In Soil, Gut, and Life
- Go Organic (When It Matters) - Prioritise organic versions of the “Dirty Dozen” to reduce pesticide exposure and support microbial diversity in soils.
- Eat the Rainbow, and Eat Local - A diverse, plant-rich diet feeds both you and your microbes. Local produce often carries beneficial microbes adapted to your environment.
- Get Dirty - Spend time outdoors, garden without gloves occasionally, and connect with natural environments, exposure to soil microbes can support immune tolerance.
- Support Regenerative Farms - Look for produce or meat from farms practising cover cropping, composting, and low-till agriculture. These methods actively rebuild soil microbial life.
- Feed Your Gut Microbiome - Fermented foods, polyphenol-rich plants, and prebiotic fibres fuel beneficial gut bacteria, creating a mirror effect between your gut and the earth. (Get 20% off Microbz Revive, plus a free shot glass here!)
The Gutology Podcast
Watch this clip from our latest episode, where Katie, MD of Microbz, discusses soil health and how pesticides and herbicides affect the microbial communities living beneath our feet.
