The Human Gut and the Soil Microbiome: More in Common than You Might Think!

Tree roots, with their cylindrical passage ways, penetrate the subterranean ecosystem where they absorb nutrients and water, and stabilize the large trunk. 

Similarly, the intricate canals of the human digestive system exist deep within the base of our torso. 

The small and large intestines of humans absorb vitamins, minerals and water, and provides a barrier against pathogens. 

Both of these systems have a symbiotic relationship with tiny microorganisms. In fact, nearly all living things owe their vitality to microscopic networks of fungi, bacteria, protozoa and yeast. Regenerative agriculture is a practice of building soil health and boosting soil microbes. This leads to healthier plants with higher mineral content and increased productivity. However, a commonly overlooked aspect of soil health is how these microbes can benefit human health. 

layers of the digestive tract diagram
Layers of the GI tract
Layers of the root

Soil Microbiome + Human Gut Microbiome

The rhizosphere is the tenuous area surrounding plant roots bacterial colonies and fungus (aka mycorrhizae) like to hang out. This precious zone is crucial for plant health and nutrition. 

Microbes actively mine for minerals and transport nutrients to plants. In exchange, plants feed these tiny colonies by delivering glucose (aka sugar) to the rhizosphere, which is a product of photosynthesis. Some soil-based organisms produce, pest-fighting molecules, boost immunity and more. 

Similarly, the human gut microbiome often referred to as a ‘forgotten organ’ because it is so intricately involved with immunity, digestion, metabolism, mental health and much more.

Furthermore, some of the exact same species of soil-based organisms inhabit the GI tract of the human body. 

In fact, scientists believe we have co-evolved with these microbial species throughout our ancient history, developing a deeply rooted, synergistic relationship. 

Soil Probiotics and Human Health: A Beautiful Symbiosis

Humans are born with a nearly sterile GI tract. 

Infants receive beneficial bacteria from their mother, through vaginal birth and breast milk. 

As we grow, exposure to soil, other people, fermented foods and the outside world in general, bacteria begin to populate the distal ends of the GI tract. 

Here, they form colonies that aid the the development of the immune system. Approximately 80% of human immune cells reside within the large intestine. They communicate with gut microbiota, who have quorom sensing abilities. This means they can sense miniscule changes in their surroundings and subsequently modulate gene expression and immune response in the human host, accordingly. 

Quorum sensing means they also have an ominopresent awareness of the status of their colony. So fascinating!

petri dish

If pathogens or harmful molecules are detected in the gut, the microbes send signals to the immune cells and prompt the removal of these invaders. 

However, an imbalance of gut microbes (gut dysbiosis) confuses our immune system and leads to systemic inflammation and chronic disease. It is no doubt that gut related disorders are rapidly increasing in the modern age. Scientists theorize that gut dysbiosis is caused by antibiotics, poor diet and living in hypersanitized environments. But what if part of this problem is that soil health is also suffering worldwide?

What Went Wrong?

In ancient times, good bacteria hitchhiked into our gut from the foods we eat and through contact with nature. 

In the past few generations, contact with these vital microbes has sharply declined. Through the destruction of soil, loss of biodiversity and living in hypersanitized, unnatural environments, we have lost contact with these precious microbes. 

We have placed a barrier between us and nature, so to speak. 

According to numerous studies, chemical intensive farming has decimated many bacterial and fungal species. Not surprisingly, chemical insecticide exposure from conventional farming disrupts bacterial homeostasis and wreaks havoc on the human gut microbiome. 

Furthermore, people living in cities have higher rates of allergies. Yet, children who grow up on farms have lower rates of these immune-driven disorders. 

It all comes down to microbes and their vital importance in developing our immune system!

banana peel and sausage
Processed food has replaced whole food
women staring out window in a city
We are separated from nature
Kids aren't outside as much as they used to be
applying hand sanitizer
Hypersanitization has reduced our exposure to microbes

What Does the Science Say?

The concept of soil health impacting human isn’t new. Numerous studies show how diet and microbial exposure from our foods dramatically alters gut health and incidence of disease. Below, I outlined 3 studies that show how food, exposure to microbes and our connection with the natural world can alter our gut microbiome. 

Urban Europeans vs Rural Africans

A recent study examined the gut microbiomes of children living in Italy vs. the African village of Burkina Faso. 

Italian children represented the westernized model of diet and lifestyle. The African children, on the other hand, represent lifestyles of ancient peoples. 

Researchers found that the African children possessed microbes that were completely missing in the Italian children, such as certain species of Prevotella and Xylanibacter. 

These microbes help break down fiber-rich foods and produce short-chain fatty acids (SCFAs). SCFA’s, such as butyrate are liquid gold for our bodies. These molecules reduce inflammation and promote appropriate immune responses. This means they may reduce allergies and other disorders related to an over-active, hypersensitive immune system.  

In addition, African children had significantly lower abundance of Shigella and Escheria, despite living in ‘un-sanitized’ conditions. This indicates that the good bacteria out-competed pathogens for a niche in the human gut. Likewise, African children had lower rates of disease and allergies. 

While this is not an intervention study, researchers speculate that a majority of these outcomes is due to a natural, fiber rich diet and microbial exposure in their environments. 


African Children Playing outside
Girl in school uniform

Nomadic vs. Westernized People of the Himalayas

Similar studies looked at the gut microbiomes of Himalayan people’s living in 4 different locations. Each group had varying degrees of separation from their traditional nomadic culture. This study is interesting because it examines people of genetically similar backgrounds instead of people from vastly different cultures and geographic regions. 

Results indicated that groups that still foraged had gut microbes similar to other foragers around the world. Groups that had developed agriculture had gut microbes similar to other farming cultures. The further towards a western lifestyle the cultures became, the more similar their gut composition was to a typical American – which is to say, more imbalanced. 

Fascinatingly, researchers found that significant changes happen in the gut microbiome within 1 generation!

Furthermore, this study indicated that gut microbes are impacted by industrialization, farming techniques, water source and food sources. While this is not an intervention study, it does indicate that changes in the gut microbiomes are related to environment, diet and lifestyle. 

Japanese Study: Genetic Material is Transferred from Microbes on our Food

According to a recent study in Japan, beneficial marine probiotics hitchhike into the gut of people who consume seafood. 

Bacteroides plebeius has genes which encode the production of enzymes that help breakdown the popular nori seaweed. B. plebeius is found in the GI tracts of many Japanese people, yet is missing in the North Americans. The enzymes found in this microbe help Japanese people digest and extract otherwise unattainable nutrients found in seaweed. 

Most appealing, it appears that this rare strain of bacteria received enzyme-encoding genes from a marine bacteria called Zobellia galactanivorans. The natural home of this bacteria is edible seaweed, such as nori. Both seaweed and seafood have long been part of traditional Japanese cuisine. Long enough for a rare horizontal gene transfer that would create a new strain of beneficial bacteria that would benefit the Japanese people.

Evidence suggests that the nori enzyme-encoding gene has been transferred from dietary seaweed to the human gut bacteria in a process known as horizontal gene transfer. This has substantial implications for how microbial genetic material and food production effects the human gut for generations to come. 

It is important to note that while there is a promising connection linking food sources to gut microbial populations, experimental studies have yet to fully explain this relationship. However, this research gives us a glimpse into how food + microbes traveling on that food effects our health. 

Chemical intensive farming practices have similar effects on the soil microbiome as antibiotics have on the human gut microbiome: they create dysbiosis. At times, this produces an environment where healthy microbes die off or become inactive. Without their natural defense mechanisms against pathogens, plus reducing competition for nutrient sources, disease-promoting microbes can proliferate. 

Of course, antibiotics and pesticides are impressive advancements in human biotechnology but their use must be mediated responsibly. 

Humans are mirrors of their environments, as the research has shown. This underscores the importance of eating food that comes from healthy, microbially rich soil such as found on regenerative, organic farms.

Woman holding a tray of soil

What We Know

What we do know is that food we eat dramatically impacts our gut microbiome. Fiber rich, whole foods like fruits and veggies boost abundance of bacteria such as lactobacillus, Bifidobacteria, Akkermansia muciniphila, Faecalibacteria prausnitzii and others. 

These strains gobble up the fiber and other nutrients found in food and produce anti-inflammatory molecules known as short chain fatty acids. In addition, these beneficial microbes train our immune system, help ward of disease, and support nearly every facet of human health.

Microbial exposure in our environment, water supply and even the air we breath can effect gut bacteria.

We also know that many soil-based probiotics form spores. These include species such as B. subtilis, B. clausii, B. coagulans and more. Several scientific studies how consuming these spores as supplements boosts concentration of other beneficial bacteria and increases microbial diversity in the human gut.

In addition, these soil probiotics produce anti-oxidants and anti-microbial molecules in the gut and direct the immune system. 

What We Need to Find Out

If a small sprinkle of marine based bacteria can hitchhike into the gut of Japanese people and transfer genetic material into gut bacteria cells, what can be said of soil probiotics eliciting similar responses?

Most health professionals would say, we don’t know yet. The research just isn’t quite there. 

We simply haven’t tried offering healthy soil as an intervention or what that would look like. However, there are multiple studies showing that soil based probiotics, which have been isolated and placed into supplements, have remarkable health benefits. 

Soil based probiotics are shown to reduce gut barrier dysfunction, improve skin health, improve rheumatoid arthritis, reduce symptoms of irritable bowel syndrome and MUCH more. 

How and What to Eat for Improved Gut Health

There are many soil based probiotics available on the market. 

However, spending more time in nature, starting a home garden with compost, getting your hands dirty in rich, microbially abundant soils and eating from local, organic farms may provide a natural amount of soil-based probiotics to your body. 

Bottom Line: Support farming practices which focus on soil health! 

As stated in a previous article, regenerative agriculture is a tool for environmental healing. However, as you can see here, it is also a tool for improving human health!

fresh radish with soil on it
couple stands in a field of organic crops