Soil And Human Health

Soil And Human Health

Soil And Human Health

From early childhood, we are in contact with soil; we taste it, inhale it, and we drink water which has passed through it. We eat plants grown on and in it, and eat animals who have done the same.

But our relationship with soil is an ancient one.

Our ancestors, who practised agriculture and animal husbandry were in even closer contact with soil. And we we are starting to understand how soil and human health are intimately connected.

We can take it one step further though! Since prehistory. we have used certain soils as detoxifying agents needed for making certain food items edible, as well as for medicinal purposes. We have also willingly consumed soils as a supplement. (source)

What Is Geophagy?

Geophagy is the habit of consuming clay soil such as chalk or kaolin. 

Though it is globally practised, the safety of this practice is yet to be fully established. It is thought to be highly prevalent in pregnant women because of its anti-nausea or therapeutic effects. It is also thought to be provoked by some nutritional needs. (source)

Interestingly dietary treatment has been observed to stop the habit – the latter strongly supports the theory that the behaviour stems from nutritional deficiencies. (source)

The Medical University of Vienna found that 30–80% of Africans eat clayey soil on a regular basis consuming between 100 and 400 g per day. But there are also reports of the habit being practiced in South America, Asia and Australia. (source)

Can Eating Dirt Help The Gut Microbiome?

Diarrhoea and parasitic infections have been treated by ingesting clay or soils (source). 

Are The Soil And Gut Microbiome Similar?

“In view of the functional similarities between the intestinal microbial community and the soil microbial ecosystem, a relationship between both appears possible. Looking at the entire ecological system, the human body and its microbes can be regarded as an extended genome” (source)

Soil and the human gut contain approximately the same number of active microorganisms, while human gut microbiome diversity is only 10% that of soil biodiversity and has decreased dramatically with modern lifestyles. 

Researchers have tracked relationships between the soil microbiome and the human gut microbiome and proposed a novel environmental microbiome hypothesis, which implies that a close linkage between the soil microbiome and the human gut microbiome has evolved during evolution, and is still developing. 

Compared to soil, the number of species in human faeces is approximately a factor of 10 lower. However, in soils, a large proportion of cells (~80%) is inactive compared to the human gut, where only approximately ~20% of cells are dormant. Considering the dormancy of cells, the total number of active species in the human gut and soil may be comparable. (source)

Read my article, What Does A Healthy Gut Microbiome Look Like to learn more about the gut microbiome.

We Are In The Midst Of A Microbial Extinction

“The rapidly urbanising world is facing serious biodiversity loss with global warming, which are interconnected.”

From hunter-gatherers to an urbanised society, the human gut has lost alpha diversity (the number of species of bacteria in the large intestine). 

What has caused this loss in diversity? It is thought several factors have contributed including: little contact with soil and faeces, hygienic measures, antibiotics and a low fiber diet of processed food.

At the same time, we are seeing a loss of soil biodiversity in many rural areas.

The increasing use of agrochemicals, low plant biodiversity and rigorous soil management practices have a negative effect on the biodiversity of plants.

“In order to correct these interferences, it may be useful to adopt a different perspective and to consider the human intestinal microbiome as well as the soil/root microbiome as ‘superorganisms’ which, by close contact, replenish each other with inoculants, genes and growth-sustaining molecules”. (source)

The result of these changes and practices is the loss of adaptive immuno-regulatory circuits and dynamic homeostasis. In practical terms this means in increase is autoimmune disorders and allergies.

Exploring the determinants of immunotolerance is the key for prevention and more effective treatment. Loss of immunoprotective factors, derived from nature, is a new kind of health risk poorly acknowledged until recently. 

The paradigm change, which emphasised tolerance instead of avoidance, has been implemented in the Finnish allergy programme. The first results show that allergy prevalence has started to decline. 

Healthy Soil, Healthy Food, Healthy Humans

As silly as it may sound, we frequently overlook the complete food life cycle. We focus on the quality of the last processing phases and ignore the soil’s health, which is essential to sustain the 95% of food derived from the soil. 

Healthy soil generates a healthy society. 

Soil microbes play a key role in determining the nutrient content of our food through the mineralisation of degradable organic compounds to inorganic forms that are readily available to crops. (source) So another explanation for the link between soil and human health is related to how soil influences the health of our crops.

The Biodiversity Hypothesis

The biodiversity hypothesis states that contact with natural environments enriches the human microbiome, promotes immune balance and protects from allergy and inflammatory disorders. 

We are protected by two interconnected layers of biodiversity, the microbiome of the outer layer (soil, natural waters, plants, animals) and the microbiome of the inner layer (gut, skin, airways). 

The latter inhabits our body and is colonised from the outer layer

This hypothesis has societal impact, for example, on city planning, food and energy production and nature conservation. It also has a message for individuals for health and well-being: bring nature close. 

Biodiverse natural environments are dependent on planetary health, which should be a priority also among health professionals. (source)

We are increasingly disconnected from our evolutionary home, soil, natural waters, and air we used to breathe. The ecosystem of human body and mind has been tested, survived, and evolved closely in relation with other ecosystems. 

Does Soil Contribute To The Gut Microbiome?

Extending the “biodiversity hypothesis” to include soil biodiversity has the potential to provide more insight into the role of the environment and gut mediated immune health. Soils contain a dynamic reservoir of biodiversity and this diversity is essential for maintaining biogeochemical processes and ecosystem functioning. 

In this way, soil biodiversity provides benefits to human health indirectly through suppression of soil-borne pathogens, provision of clean air, water and food, and exposure to bacteria that have immune regulating properties. 

There is further evidence that soil biodiversity is interrelated with the gut microbiome. In particular, the gut microbial diversity in mice was increased by exposure to soil microbes. Gut microbial diversity could increase in mice that are in contact with non-sterile soil on a normal diet, while it was unaffected by sterile soil. While the addition of environmental microbes, increased gut biodiversity, a limited effect on the most abundant bacteria was described. 

It seems then that organisms primarily contribute to the diversity of the microbiome, while soil can change the community composition, and seems to affect it to a similar degree as diet

In conclusion, results from animal studies suggest that soil and human health are connected as soil is beneficial for a healthy gut microbiome. (source)

Does Soil Support Human Health?

Although much about microbial functions remains unknown, increasing evidence suggests that beneficial soil microbes are vital for enhancing human tolerance to diseases and pathogens. (source)

How Does Soil Benefit Human Health?

There is some indirect evidence that soil biodiversity and human health are interrelated. The current thought it that  (source):

  • Soil provides “natural immunity”.
  • Soil microbes may increase gut microbiota diversity.
  • There is also some evidence to suggest that exposure to possible soil pathogens could contribute to immune tolerance.

However, little is known about the impact of soil exposure on gut microbiota transmission and colonisation patterns in humans (source).

It is for these reasons that young children who encounter early contact with less hygienic environments, such as outdoor settings and farms, are less susceptible to develop autoimmune diseases. This aligns with the ’hygiene hypotheses’, which theorises that environments with high microbial diversity protect against allergies and autoimmune conditions.

Soil and human health are clearly intertwined.

A rich environment during this phase is important to human health for immunomodulatory development in early life. (source)

Microbial Dispersal – Why Community Matters

In one paper the researchers proposed that both environmental exposure and horizontal transmission of symbionts (collectively called microbial dispersal) are likely to drive the gut microbiome in rural populations, while the urban lifestyle results in the limited dispersal of microbes. This low dispersal can explain the high inter-individual variation of the human gut microbiome of urban citizens (beta diversity). 

Limited dispersal combined with sanitation, medication and dietary changes reduces the successful colonisation and hence gut microbiome richness. (source)

Hygienic measures reduce the risk for transmission of pathogens, but also of gut symbionts. This limitation in dispersal via the modern lifestyle reduces the possibility for homogenization among individuals too, and leads to high beta diversity in Western populations, thus successfully linking the colonisation of species by dispersion, reducing richness. (source)


Although much progress was made in understanding links between soil and human health over the last century, there is still much that we do not know about the complex interactions between them. Therefore, there is still a considerable need for research in this important area. (source)

We know there are both structural and functional similarities between the soil microbiome and the human gut microbiome, and researchers have concluded that both can be viewed as functional ecosystems, which interact with each other. The diversity of these two ecosystems have been declining in recent years, and as a result so has the interaction between them, potentially reinforcing losses of biodiversity. (source)

Soil and human health are inextricably connected.

What To Do To Improve The Gut Microbiome

Pick Local and In Season

The intake of mostly unprocessed organically grown regional products is one way towards this goal. Further, wild relatives of the currently used high-yielding crop varieties could increase aboveground and belowground biodiversity, and hence provide benefits to soil and human health, e.g., through reintroducing lost beneficial microbes.

Spend time with people

Remember we discussed bacterial dispersal. Research has shown that our social network is a determining factor on our gut microbiome diversity.

Visit Your Local Farms

Studies show that growing up in microbe-rich environments, such as traditional farms, can have protective health effects on children. (source)

if early-life exposure to environmental microbes increases gut microbiota diversity….then soil biodiversity loss due to land-use changes such as urbanisation could be a public health threat” (source).

Gardening Contributes To The Gut Microbiome

A fascinating study revealed that the gut microbiome of gardening families differs from non-gardening families, and that there are detectable changes in the gut microbiome community of gardeners and their family members over the course of the gardening season.  (source)

Consistent contact with soil over a growing season may result in transmission of soil microbes, which results in a more diverse gut microbiome structure and a different composition in gardeners. (source)

The most fascinating thing about this study is that, even though there was just one gardener in each family, the sharing of soil-sourced bacteria was detected in most (20 of 23) gardening individuals. (source)

Spend Time In Natural Environments

Access to more biodiverse areas in urban environments, such as green spaces and parks, is related to health benefits regardless of socioeconomic status, which can be associated with the exposure to rich environmental microbiota. Hence, recent studies on urban re-wildering to improve the urban biodiversity of our living environments can be protective against immune disease by greater contact with a diverse set of environmental microbiota and consequently improve human health. (source)

Eat A Diet Rich In Plant Fiber 

A diet with a high intake of fiber is associated with a more diverse gut microbiome. In fact, it was a stronger predictor for gut microbiome diversity in the less developed areas of Papua New Guinea than antibiotics, although this is a locally common medication. (source) What this shows us is that the impact of a course of antibiotics is partly dependent on your gut microbiome diversity, and this is partly dependent on your fibre intake. 

Limit Medications When Safe To Do So

Medication mainly drives the gut microbiome of Western populations and explains the greatest total variance of the fecal microbiome as shown by a large size Danish study. 

Increased medical antibiotic intake as well as increased meat consumption (of animals given antibiotics) has led to an increasing number of antibiotic-resistant bacteria and genes. Antibiotic resistance can be spread between bacterial populations via the horizontal transfer of antibiotic resistant genes. Studies have shown that surfers have a higher likelihood of antibiotic resistant bacteria in their gut. 

Not only that but antibiotics may impact the soil microbiome, yet another connection between soil and human health.

Read my article How To Restore The Microbiome After Antibiotics to learn more.

Avid GMO Food

The consumption of genetically modified plants should also be considered with caution, because the modified genes could be transferred via bacteria into the rhizosphere or the gut.


In summary there is a clear connection between soil and human health and if we are to improve our health we must consider the health of the soil our food is grown in.

Alex Manos Profile 2015 AM Logo scaled

Alex is a certified Functional Medicine Practitioner (IFMCP) and has a MSc in Personalised Nutrition. He is also a breathwork facilitator with a background in personal training and massage therapy. He also runs The Resiliency Program - a 24 week program aimed at building physical, mental, emotional, and spiritual resilience.

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