The Connection Between Soil Health & Gut Health

The Connection Between Soil Health & Gut Health


We participate in an on-going soil to gut microbial exchange every day. To make this exchange the most robust, there has to be strong microbial diversity in the soil and in the gut.

Getting nutrients into our bodies is very simple – we eat. It is the processes involved with getting the nutrients into the foods that are complex. Processes that are the result of a symbiotic relationship of soil microorganisms and plant roots. So, to get the most nutritional value into food there needs to be a microbial community to break down organic matter into molecular forms of nutrients that are plant available.

The human gut microbiome, responsible for digesting those nutrients, must also be diverse to be the most efficient. Each individual has a signature microbial community, unique as a fingerprint. The microbes on (and in) our food contribute to our gut microbiota, even if they are only there for a short time. The human and soil microbiomes have similar bacteria phyla; Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. (1) Which only makes sense because our food is grown in soil.

Both root and gut microbes synthesize essential amino acids. Beneficial soil microbes in and on both the roots and shoots of plants increase plant resistance from herbivores, pest insects, and pathogens. They also increase nutrient use efficiency in the fruits and seeds, creating higher nutrient profiles.

Human gut microbes break down our food into constituent nutritional molecules which are used for myriad purposes, including a stronger immune system. But our gut microbiome has only 10% of the diversity of the soil, (2) and is getting less diverse over time as our modern diet leans toward processed and fatty foods.

Agriculture also plays a role in human gut microbiome decline. High yielding crop varieties have lost many secondary metabolites that protect human and plant health. (3) Even crops grown through organic farming have less nutritional value than they did ten years ago because we are breeding for shelf life and shipping ease, not nutrition. As a result, we are losing a number of immunosuppressants, anti-cancer, and anti-inflammatory properties of foods.

While non-processed food is still full of nutrients, sometimes even fresh produce can contain substances that are detrimental to our health.

How Conventional Farming Impacts Our Gut

When herbicides, pesticides, and fungicides are sprayed on crops - pests and disease organisms are destroyed. Unfortunately, this means that the soil microbiome is also destroyed. Furthermore, the impact of chemical residue reaches much further than the soil and plants. It also impacts the gut microbiomes of those who eat the plants, both humans and animals alike.

Many farmers in the Midwestern US use a crop rotation of 2 crops, corn and soybeans. That means there are only 2 types of plant roots in those fields, which is not enough to create the microbial diversity necessary for healthy food. Often these two crops are grown conventionally and numerous passes are made over the field with fertilizers and synthetic pest and disease killers (pesticides, fungicides, and herbicides – called the “ides”). Those “ides” may take care of pests but they also weaken and eventually destroy the soil microbiome.

conventional farming pesticide

Synthetic pesticides are antibiotics, and they are sprayed onto crop fields multiple times throughout the growing season. No matter how much we scrub store bought fruits and vegetables they will retain residual pesticides.

Antibiotics are naturally found in the soil. (4) They are produced by bacteria, fungi, and as defense against other microorganisms. The amount of antibiotic produced by microorganisms is not even measurable against the amount of antibiotics sprayed on a field with conventional “ides.”

In an orchard, synthetics are sprayed in early spring before bud break, at fruit set, and in 14-day intervals. The residual chemicals on the exterior of a fruit may be washed off but what about the chemicals that are inside the fruit? Fruit does not have an impermeable skin and some synthetic pesticides are even formulated to be absorbed by the flesh for pest control. (5)

The USDA tests fruits and vegetables for pesticide residue. The Environmental Working Group publishes a list of the "Dirty Dozen." Fruits and vegetables with the most pesticide residue.

The impact of those residues on our gut microbiome is similar to their impact on the soil microbiome. The EPA sets tolerances for potential chemical residues on fruits and vegetables. According to the USDA the yearly report of fruit and vegetable testing showed…

“…that nearly 99 percent of almost 10,000 samples of fresh, frozen and processed foods had pesticide residues below levels set by the U.S. Environmental Protection Agency (EPA).” (6)

Although the amount of residue we ingest at any given time may be small, that amount of chemical was enough to kill the insect pest. How might it affect the microbes in our gut, which are microscopic?

How do we grow healthy food at a profit without “ides”? Organic farming is one answer. Another is regenerative farming.

Regenerative Farming Leads to Healthy Soil

Maintaining a diverse soil microbiome is necessary for growing healthy food.  Regenerative farming’s principles support what traditional farmers around the world have always known. Farming with nature, instead of against her, includes these practices:

  • Protect topsoil with cover crops 365 days a year
  • Disturb the soil as little as possible with conservation tillage or no-till
  • Rotate crops with at least 5 crops to create diversity above and below ground
  • Water wisely, this is becoming a precious commodity
  • Limit chemical use, both synthetic and natural
  • Recycle finished compost back to fields to complete the nutrient cycle
  • Incorporate livestock in crop rotations, include mixed grasses and forbs pasture in rotation for fodder and nitrogen fixation

There is a great deal of evidence that a diverse soil microbiome is responsible for foods with a high nutritional profile.  So, following regenerative agricultural practices makes sense for human gut health.

crop rotation regenerative farming

A rotation with many different plants, including cover crops between rows of cash crops, increases soil microorganisms. A diverse soil microbiome has a direct impact on plants. A strong microbial community deters pathogens in the soil and pests on leaves and fruit. Microbes are everywhere and either protect a plant by leaving no space for pathogens or signal the plant to activate its defenses against pathogens.

There is an ongoing battle between beneficial microorganisms and pathogens. In healthy soil the beneficials win. That same battle is taking place in the human gut microbiome.

From Soil to Food to Human Gut: A Nutritional Journey

Healthy soil leads to healthy food and healthy people. The nutrients in food are extracted by gut microbes. Humans need more than just the nutrients in food, we also need the microbes. Humans can only make 11 of the 20 essential nutrients, most of the rest we need to get from food.

In order to retain our health the food that we consume has to come from healthy soil. There is a direct correlation between the use of synthetics and a rise in chronic disease. (7) Our gut microbiome cannot operate efficiently when antibiotics and other pesticides are consumed. The microbes in our gut are compromised by “ides” and do not have the ability to support a strong immune system, which can result in us getting sick.

Most vitamins and nutrients come from the soil via plants and animals but there are some vitamins that are only made by microbes, Vitamin B12 for example. It is a vitamin only used for 2 enzymatic activities, but very important for human health. (8)

Vitamin B12 is not found everywhere. The meat and milk of ruminant animals (cattle) contains B12 because of the symbiotic relationship of the cow with bacteria and archaea. Vitamin B12 is also abundant in seafood because of the host – bacteria symbiotic relationship.

cows ruminating in farm field

The symbiotic relationship between cattle and microbes is a lesson in microbial diversity and the value of certain species of bacteria for human health. Healthy soil with the right community of microorganisms maintains animal health and eventually the health of the human body.

Keeping “ides” or antibiotics out of our gut microbiome leads to healthy humans. The “ides” have been linked to a number of serious chronic human diseases.

The quality and quantity of the soil microbial community can be increased through natural soil amendments such as Humic Land, respecting the soil, and choosing food sources wisely. Dr. Daphne Miller advises a simple way to source food wisely. Buy local and ask; “Does the farmer live on the farm?” If so, you will be choosing food that is grown with care. (9)




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