Healthy Gut: Is Healthy Soil Linked to a Healthy Gut?
By Carrie Dennett, MPH, RDN
Today’s Dietitian
Vol. 25 No. 4 P. 16

Here’s what the research says about the connection between the microbiome of soil and the human microbiota.

It’s no secret that a healthy gut microbiome—the community of roughly 100 trillion bacteria and other microorganisms, in addition to their 3 million-plus genes that reside in the intestines—is important for overall human health. But just as the gut microbiota is only one part of the human microbiome, the human microbiome is just one small part of an environmental microbiome that also includes the soil microbiome. But other than being two parts of a whole, the question is, “Are the gut and soil microbiomes linked?” A growing body of research is finding that the soil microbiome may affect the human gut microbiome both directly and indirectly.

Broadly defined, a microbiome encompasses “the entire habitat, including the microorganisms, their genes, and the surrounding environmental conditions.”1 Just as the human gut isn’t a sterile tube, soil isn’t a sterile medium devoid of life. It’s home to billions of bacteria, fungi, and other microbes that are “the foundation of an elegant symbiotic ecosystem,” according to the National Resources Conservation Service.2 Soil depth determines the density of the microbial community, with the highest density in the top foot of soil. Forest soil has two to five times greater microbial density than organic agricultural soil,3 which in turn has greater microbial density than conventionally farmed soil.

Plant roots are immersed in a soil microbiome that, when healthy, provides the plants with important nutrients, protects them from disease, and helps them adapt to environmental changes. Similar to fecal transplants in humans, soil transplants can drastically affect plant health and growth.4 Researchers who look at the connections between soil health and human health have described roots as the equivalent of the gut, and the rhizosphere—the area of the soil around a plant root inhabited by a unique population of tens of thousands of microbial species—as the equivalent of the gut microbiome.5 If you were to examine the rhizospheres of different plant species grown in the same soil, you’d find different microbial communities in each one. As the gut microbiome acts as humans’ second genome, the microbial community of the rhizosphere has this function for plants, and so is crucial for plant health.6

The Soil-Human Health Connection
The National Resources Conservation Service defines soil health as “the continued capacity of soil to function as a vital living ecosystem that sustains plants, animals, and humans.”2 Soils existed globally for a long time before mammals and early humans came into existence and are by far the most extensive and diverse natural microbial habitats—and gene reservoirs—on Earth.7 A committee appointed by the National Academies of Sciences, Engineering, and Medicine is currently reviewing what’s known about the linkage between soil health and human health. What’s clear is that the soil microbiome connects to human health in two primary, albeit indirect, ways.

One is that a healthy soil microbiome improves the productivity and nutrient density of crops.8 Soils rich in biodiversity not only produce more nutritious foods but also control the proliferation of pathogenic microorganisms that could affect plant and human health. The Food and Agriculture Organization of the United Nations says soil biodiversity is a result of highly functioning, high-quality soil with a good balance of nutrients, good aeration, and water infiltration.9

The other is that the soil microbiome is a source of compounds that may treat human diseases.8 Soil-dwelling microorganisms are the source of most naturally occurring antibiotics—including many of the current clinically relevant antibiotics—used in human medicine.9,10 Maintaining the vast diversity of microorganisms in soil is important for preserving the potential for future discoveries important to human health.9

It’s important to note that the use of herbicides, excessive mineral fertilization, and improper land management have serious effects on microbial communities. A good example is the widely used herbicide glyphosate, which inhibits an enzyme in a pathway that bacteria and fungi rely on to produce certain amino acids. Several reports show negative effects on beneficial microbes in the soil—especially in the rhizosphere—including arbuscular mycorrhizal fungi, a microbe that can significantly improve plant nutrient uptake.4

What’s less understood is how the soil microbiome may directly influence the gut microbiome. While much of human food comes from soil, we’re also in contact with soil from early childhood, as the gut microbiota is developing. We inhale soil, drink water that has passed through soil, and often recreate in direct contact with soil—gardening, camping, hiking, swimming in natural bodies of water.11 The gut and soil microbiomes are connected in that they share similar bacterial phyla (Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria), and we ingest microbes from fruits and vegetables grown in soil.4 Could the health effects of eating or not eating adequate amounts of fruits and vegetables be partially due to the microbes we do or don’t ingest?

It’s likely that exposure to soilborne microorganisms plays a direct and important role in developing and regulating the human immune system. There has been an increased research focus on the linkages between contact with the natural environment, including soils and microbially driven immune system responses in humans that positively influence mental and physical well-being via the gut-brain axis. One of the strongest areas of study has been in relation to allergy prevalence and is known as the “biodiversity hypothesis.”10 This hypothesis states that contact with natural environments enriches the human microbiome, promotes immune balance, and protects us from allergy and inflammatory disorders.12

We’re protected by two nested layers of biodiversity. The outer layer is made up of microorganisms in the environment around us, including soil, natural waters, plants, and animals. The inner layer consists of microorganisms inhabiting our own bodies, including those that live in the gut and airways and on the skin. The inner layer is colonized from the outer layer. While this interplay, and the resulting diversity and stability of the gut microbiota, is strongest in early childhood, the interaction never stops and is necessary to maintain our innate immunity. Developing and maintaining tolerance to foreign proteins seems to depend on exposure to diverse bioparticles and microbes.12

Interactions Between the Soil and Gut Microbiomes
While research in this area is still limited, there are studies that lend support to the idea that the gut and environmental microbiomes are linked and that human contact with soil microbial communities plays an important role in human health.10

Results of an intervention study published in 2020 found that the diversity of gut and skin microbes among children in Finnish daycare centers greatly varied based on each child’s interaction with nature, including soil and plants. Gut microbial diversity increased among children at “intervention” daycare centers that were enriched by covering part of the play yard gravel with forest floor and sod, planters for growing annual plants, and peat blocks for climbing and digging. This corresponded with a positive stimulation of immunoregulatory pathways.13

A 2020 analysis of data from the Edmonton, Alberta, Canada, site of the CHILD (Canadian Healthy Infant Longitudinal Development) birth cohort study found that proximity to a natural environment plus pet ownership has the capacity to alter gut microbial diversity in formula-fed infants to more closely resemble that of breast-fed infants.14

Applying This Knowledge to Clients
Although more research is needed, a public health campaign in Finland offers some ideas on how dietitians can help clients nurture their gut microbiome through exposure to greater microbial diversity than what’s found in an indoor environment—essentially other humans, pets, and air.3,12 This may be especially important for clients who live in urban environments. Some ideas include the following:

• Strengthen connections to nature in everyday life. Visit parks, walk barefoot, or sit on a picnic blanket in grassy areas where herbicides aren’t a concern. Walk on nature trails and swim in lakes and rivers.

• Plant a garden. Digging in the soil, pulling weeds, planting seeds, and harvesting root vegetables all put us into direct contact with the soil.

• Increase use of fresh fruits and vegetables. While washing produce is important from a food safety standpoint, some gut microbiome researchers suggest being less thorough when the produce comes from one’s own garden.

• Wash hands less. Certainly, washing hands that may have been exposed to toxins, pesticides, or viruses is important but may require less vigilance after gardening or petting a dog.

Abundant evidence shows that spending time in nature is good for mental health, and the more dietitians learn about the microbial universe, the clearer it’s becoming that time in nature is good for physical health, too.

— Carrie Dennett, MPH, RDN, is the nutrition columnist for The Seattle Times, owner of Nutrition By Carrie, and author of Healthy For Your Life: A Holistic Guide to Optimal Wellness.

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8. Exploring linkages between soil health and human health. National Academies website.

9. Food and Agriculture Organization of the United Nations and Intergovernmental Technical Panel on Soils. Status of the World’s Soil Resources. Published 2015.

10. Brevik EC, Slaughter L, Singh BR, et al. Soil and human health: current status and future needs. Air, Soil and Water Research. 2020;13:1-23.

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12. Haahtela T. A biodiversity hypothesis. Allergy. 2019;74(8):1445-1456.

13. Roslund MI, Puhakka R, Mira Grönroos, et al. Biodiversity intervention enhances immune regulation and health-associated commensal microbiota among daycare children. Sci Adv. 2020;6(42):eaba2578.

14. Nielsen CC, Gascon M, Osornio-Vargas AR, et al. Natural environments in the urban context and gut microbiota in infants. Environ Int. 2020;142:105881.