Healthy Soil Boosts a Healthy Gut


The connections between the soil and human health run deep. Learn how to restore gut health with healthy soil microbiome. Choosing the best foods for gut health and supporting holistic agricultural methods can make a big impact.

Today, there is more and more emphasis on how eating a healthy diet can boost our gut microbiome. We’re often told to consume a wide variety of fruits and vegetables or, eat the rainbow, to nourish our bodies with the vitamins and minerals it needs to survive, as well as fiber and a diversity of phytochemicals that positively impact the gut microbiome. Our gut microbiome is composed of microorganisms that live in the gastrointestinal tract; they strengthen our immune system and protect us from harmful diseases. In addition to digesting vitamins, minerals, and other nutrients from the produce we consume, we’re also digesting microbes found in plants. And research shows that microbiota found in plant soil directly and indirectly benefits the human gut microbiome, too. It’s all connected! In fact, scientists are discovering that the microbiome of the human gut and microbiome of the soil are similar in many ways. 

California strawberry farm
The gut microbiota in humans and the soil exist under similar environmental conditions, EMBO, 2020

In the Gut 

Plants receive beneficial microbes from the soil they’re grown in, which means that it is important to include a vast array of fruits and vegetables in your diet and pay attention to where and how your produce is being grown for your own optimal health. Maintaining a healthy gut microbiota is critical for immune health, which helps protect us from diseases, such as cancer. They also help us digest our food, synthesize essential nutrients, and turn those phytochemicals in foods into powerful antioxidant compounds. The term gut microbiota simply refers to microorganisms living in the human gut—it’s estimated that the human body consists of ten times more bacterial cells than human cells, the majority of which reside in the gut. There are slight differences in gut microbiota composition by gender, but the biggest factor contributing to microbial composition is diet. In order to boost a healthy, diverse, plentiful gut microbiome it’s important to ensure your diet is packed with fiber, which feeds those hungry microbes in your digestive tract. Foods that contribute to gut health include whole grains, pulses, fruits, and vegetables that are high in fiber. While meat, highly processed foods contribute to poor gut health because they lack the nutrients your gut needs to flourish. 

A California farm getting ready for planting

In the Soil

Humans aren’t the only living creatures with microbiotas. Soil and plants also have their own microbiota. In fact, soil microbiota is extremely rich in microbes, including fungi, archaea, bacteria, and protists. A single teaspoon of productive soil contains 100 million to 1 billion bacteria. The microbes contained within soil contribute to plant growth which, in turn, provides humans with a food supply and beneficial bacteria. For example, vitamin B12 is produced by bacteria and archaea in the soil before being transferred to plants and animals via microbial interaction. The primary benefits from including vitamin B12 include DNA synthesis and red blood cell formation, which helps prevent anemia. 

It is estimated that 98.8% of our calories come from the soil. This is a fact that we often overlook. Unsustainable practices in food production place an emphasis on quantity over quality, which can lead to land degradation and strip soil of beneficial microbes. The use of pesticides, herbicides, fungicides, and fertilizers has been linked with reduced soil health. As we’ve learned, this results in a negative impact on the immune function of humans, and leaves plants susceptible to attacks from pests and pathogens

The direct and indirect effects of the plant microbiota on the human gut microbiome, EMBO, 2020.

Organic, Sustainable Agriculture and the Microbiome

Just like antibiotics can harm the human gut microbiome by destroying the diversity and volume of health-protective microbes, so can pesticides, herbicides, and fungicides destroy the diversity and colonies of microbes in the soil, as well as those found on the fruits and vegetables grown in that soil, and, ultimately, eaten by people. This in turn contributes to poor gut health in people, because plants lack the diverse microbes your gut needs to flourish. Organic, sustainable agricultural practices have been documented to boost soil microbial health, and promote greater nutrient content of the fruits and vegetables grown in that soil. Research has also linked the consumption of organic produce to reduced pesticide residues, as well as lower risks of cancer

Carrots from my organic vegetable garden in Ojai, California

The growing use of chemicals in industrial agriculture is of great concern to our health and the environment. To reap the benefits found in plant soils, aim to consume produce grown in soil that is rich in microbial diversity due to being treated with reduced amounts of pesticides and fertilizers. These types of plants are more likely to be organic and environmentally sustainable, which provide benefits well beyond the gut. Learn about how foods are grown in your own community by buying directly from farmers markets or CSAs, where you can discuss with the farmer how foods are cultivated and practices for soil health. You can also grow some of your own food and compost—an organic fertilizer practice that boosts soil microbial health immensely. 

For more information about the relationship between health and agriculture, check out these blogs:

Written by Cara Joseph, dietetic intern, with Sharon Palmer, MSFS, RDN

Photos by Sharon Palmer, MSFS, RDN


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