soil and health connection

Eat That Bacteria - Soil and Health Connection

“We live in a microbial world. The earth is covered in microorganisms, or microbes, and has for billions of years.”

Justin and Erica Sonnenburg, PHDs, “The Good Gut” Human health is directly tied to soil health and to the billions of microbes that keep it healthy.

Healthy soil is teaming with bacteria, fungi, protozoa, nematodes, and many other micro and macro-organisms, making up the soil microbiome. Those organisms work together, living - dying, eating - being eaten, in cooperation with plants and the roots that supply many of the nutrients microorganisms need to thrive.

A healthy human, or any mammal, gut is also teaming with bacteria, fungi, and other microorganisms. There are 30,000 species of bacteria in the human body, according to Dr. Zach Bush. (1) A majority of those bacteria are in our gut but the signals they create between one another and the rest of the body are critical and are passed from the gut to the brain via the vagus nerve. This video explains in more detail the gut-brain connection and how soil health is integral to human health.

Our entire parasympathetic system including heart, lungs, and reflex actions such as sneezing or swallowing are connected to our digestive system. A healthy human microbiome is necessary for brain and body health and to keep our immune system strong. We acquire that health through the food we eat and the air we breathe.*

What Is a Healthy Gut?

How do we define a healthy gut? It used to be simple, there were certain bacteria that were necessary components of a ‘core’ gut microbiota. But as technology has allowed researchers to do more refined studies of gut microbial populations and their interactions the ‘core’ has given way to the idea of a ‘functioning core’ microbiome. Researchers have discovered “in industrialized societies as few as 10% of microbial strains may be shared among healthy individuals.” (2)

healthy gut bacteria

A healthy gut is dependent on the naturally available microorganisms, it’s site specific as well as an outcome of socioeconomic and cultural conditions. The ingredients used and the recipes passed down through generations, especially herbs and spices, have a profound impact on the gut microbiome.

Is a healthy soil as complex as a healthy human gut? Yes and no.

Healthy Soil – the Definition

A healthy soil has a large amount of organic material which leads to a diverse community of microbes, arthropods, and other larger wildlife. With a high organic matter content, a soil has good water infiltration, a structure that allows for air pockets, and that soil structure is aggregated. The soil biology, especially fungi, plays a key role in soil aggregation using their hyphae to create a tight net between the micro aggregates in the soil to create larger soil macro aggregates.

Soil microbes make up only about one-half of one percent of the total soil mass. Yet you can fit 40 million of them on the end of a pin. (3) Without soil biology organic matter wouldn’t decompose and plants wouldn’t have allies in the plant root’s hunt for essential nutrients. In fact, plants couldn’t survive without microorganisms.

Humans couldn’t survive without microorganisms either. Those essential nutrients soil biology supplies to plant roots are necessary for healthy human gut. The microbiome of the human gut is remarkably similar to the microbiome of healthy soil. Which only makes sense because the soil biology is in and on the food we eat.

With modern agriculture we have decreased the diversity of crops and therefore microbial diversity. The health of soil is diminished. How does that affect your health? If you’re not eating organic or regenerative food then your food is grown using conventional agricultural practices.

Modern Industrial Agriculture – Conventional Ag Practices And Their Impact On Soil Health

Modern conventional agricultural practices use tillage to create a smooth field, or seedbed, and then sow seeds coated with a synthetic fertilizer or add synthetic fertilizer. Both are high in nitrogen for what is believed is a good start to crop growth.

After the crops get a good bit of growth many conventional farmers go through their fields and proactively spray a fungicide if that crop happens to be susceptible to any type of fungal diseases. Synthetic fertilizers with different combinations of nitrogen, phosphorus, and potassium are sprayed on fields close to the seedlings. These fertilizers may, or may not contain micronutrients and will contain salts. If it rains at the right times and in the right amounts, or is irrigated, and remains dry for harvest the farmer will get a high yield.

Tillage, fertilizers, and fungicides may appear to make farming easier and create good yields but… are they economically profitable in the long-term? And how do conventional agricultural practices impact the farm ecosystem as a whole?

What happens to the microbes that are considered necessary for soil health and the nutrition needed by both plants grown and the humans who eat them? Plants are like every other organism; they take the path of least resistance. If the farmer is going to give them the nutrients they need, in plant available form, then they don’t look to create symbiotic relationships with the soil microbes. Nitrogen, and other synthetic fertilizers, applied close to the plant roots, in the rhizosphere, are taken up by the plant. Over time, the beneficial microbial life goes dormant as it is no longer able to receive those important nutrients from the plant.

Plants look healthy and produce from them is found on our grocery shelves. Those fruits and vegetables might as well have been grown without any soil at all because all the food nutrients have come from synthetic additives to the soil.

A study published in the British Journal of Nutrition found organic and conventional vegetables had similar levels of nutrients...but the human body needs more than just nutrients for health. The study found a significant difference in antioxidant levels. Organic vegetables had much higher compounds such as flavonoids and carotenoids. These compounds have been linked to a reduced risk of chronic diseases. The higher antioxidant levels are related to farming practices, according to Charles Benbrook, co-author of the study. (4)

A conventional farm field has a very low level of microbial health so very few microbes are passed on to us in our food. In fact, a long-term study conducted by Ali Y Srour et al found “ecological guilds featuring arbuscular mycorrhizae, mycoparasites, and hematophagous fungi favored in no-till soils. While fungal saprotrophs and plant pathogens dominated in tilled fields.” (5)

If plant pathogens dominate in tilled fields, then a conventional farmer has to use a fungicide to have any crop. The other alternative is to plant crop varieties that are resistant to pathogens commonly found in the area. How long before those varieties are no longer resistant?

GMOs and Glyphosate

Farmers encounter numerous problems in any growing season including pests and weeds. The invention of Genetically Modified Organisms (GMOs) in 1973 has led to a majority of GMO crops. Side note: the first use of a GMO was as human insulin to treat diabetes. Perhaps that’s why we accept the idea of genetic modification so easily.

Everything from tomatoes, soybeans, cotton, corn, potatoes, canola, and papayas have GMO varieties. The FDA supports GMO research and has found no measurable difference to human health from a GMO to a non-GMO food. (6)

But there is a larger story here. GMO corn, for example, resists insect pests and has a greater herbicide tolerance. According to the FDA, “GMO corn produces proteins that are toxic to certain pests but not to humans, pets, livestock, or other animals.” (7) And if you eat meat or processed foods that aren’t organic chances are very good, you’re eating GMO food.

The ability of crops to tolerate more herbicides means farmers who have weed issues in their fields can spray glyphosate to kill the weeds and not hurt their crops. Glyphosate is a strong antibiotic and it not only kills the weeds but all the microbial life in the soil. This leaves dead soil but it has a much farther-reaching effect.

The way glyphosate stops growth is by blocking an enzyme pathway, the shikimate pathway, that produces some of the critical amino acids needed for plant health. All weeds die, almost all, some weeds are now expressing resistance to glyphosate. (8) Scientists are doing further studies on all the interconnections between amino acids and plant metabolism.

Those interconnections are important because the food we eat affects our gut microbiome. Humans have 9 essential amino acids. Glyphosate contaminated food will kill 3 of the nine essential amino acids in the human gut.Consequently, we are left compromised and poisoned. (9)

Is there a better way to farm so that GMOs and glyphosate aren’t needed?

Organic and Regenerative Agriculture and Your Health

Organic and regenerative farmers have been following distinctly different agricultural methods. The way an organic farmer sees the field depends on his metrics. Organic farmers look at four metrics:

  • Productivity
  • Environmental impact
  • Economic viability
  • Social well-being

The metric an organic farmer chooses as dominant determines farming practices. If productivity or economic viability, for example, are the dominant metrics a farmer may choose to mono-crop with tillage and natural fertilizers and pesticides. An organic farm that focuses on environmental impact and biodiversity will look radically different from a farm based on productivity.

A regenerative farmer sees his field much differently than an organic farmer. An organic farm is not necessarily a holistic farm but a regenerative farm, by definition, is. There is no hard and fast definition of regenerative agriculture at this time. But the Rodale Institute and Patagonia with a group of other supporting companies have developed the Regenerative Organic Certification or ROC, overseen by the Regenerative Organic Alliance.

The three pillars of the regenerative agriculture certification are soil health, animal welfare, and social fairness. It’s organic with the inclusion of the entire community, from soil microorganisms to community potluck and everything in between.

Farming Practices and Their Impact on Your Health

It depends who you’re talking to which farming practices are better. A conventional farmer will point to the fact that since 1940, corn yields have increased more than five-fold and commercial tomatoes have gone from less than 25 tons/H to 97 tons/H; that’s with the addition of synthetic fertilizers, irrigation, increased soil tillage, and improved crop varieties. (10)

The use of NPK fertilizers by conventional farmers gives macronutrients to crops and speeds plant growth. Those fertilizers have low, or no, micronutrients and soils that have micronutrient deficiencies yield low nutrient food. The lack of micronutrients and antioxidants in our food fuels chronic disease.

An organic farmer may talk about yield but he’ll also talk about nutritional content and biodiversity. He’ll say everyone should buy organic because organic farming makes up “less than 1% of the 911 million acres of total farmland nationwide” according to Pew Research. (11) Although that’s a 56% increase from 2011, when the USDA started keeping track, it’s a very small market share.

The crops on an organic farm may grow more slowly than a neighbor's conventional crops and that is actually good, nutritionally speaking. Crops that grow fast and are larger often have a dilution of the nutrient profile. Benbrook says “when you buy these great big juicy apples that are just as sweet as sin, it’s that extra moisture and carbohydrate that dilutes the vitamin C and the anthocyanins.”

A Regenerative farmer will talk about the cover crop mix, the number of earthworms in a shovel of soil, and that he doesn’t have any soil erosion. He may also tell you what he’s heard Gabe Brown say “I’ll take profit over yield any day of the week.” (12) The number of certified regenerative farmers is still too small for the USDA to count.

High nutritional profiles are one of the goals of a regenerative farmer or rancher. The complex connections between healthy soil and healthy humans are part of the overarching food web. Humans impact, and are impacted by, the soil web.

These three different farming practices have a direct impact on our health. We are what we eat. Food grown by organic and regenerative farmers has far less pesticide residues (pesticides are in the air and water so we can’t get away from them entirely) which have been linked to certain types of cancer, Alzheimers, and Parkinson’s. Regenerative farmers don’t use any synthetics, don’t till, and pasture raise all livestock. They often sell directly to the consumer, greater profit for them – fresher food for the consumer. The less time between picking a fruit and eating means more nutritional value.

Organic farmers only use natural fertilizers and pesticides. They have many different ways to sell their crops depending on the scale of the farm. Organic field corn farmers may sell their crop to a company that makes organic corn tortillas; a tomato farmer may sell at the local Farmers Market or to your local grocery store.

Conventional farmers have the largest market share. Almost all processed food has ingredients from a conventional farmer. The majority of the produce at your local grocery store is conventional. Most of the food most of us eat has synthetic chemicals in or on it.

The Health of the Planet = Your Health

An agricultural practice that emphasizes diversity is healthy for the planet.

Dr. Axe, a chiropractor, author, and co-founder of the supplement company Ancient Nutrition writes: “Having different crops grow within one location – called crop rotation – helps to not only ensure that crops are being continually produced, but it also supports healthy topsoil and helps to boost defenses against pathogens that may wind up harming some crops. Additionally, it aids in biodiversity in soil and plant species.” (13)

The greater the diversity of foods we eat the greater the diversity of our gut microbiome. But since the end of WW 2 we have decreased food diversity in our diets dramatically. Of the 250,000 plant species known today only 7,000 have been used for food. Today we cultivate about 120 different crops. Of those 9 provide more than 75% of human food…but only 3 provide more than 50% of our daily nutrition. (14)

We are starving our soil microbiome and malnourishing ourselves even though, as the western diet spreads across the world, so does diabetes, obesity, and …

Dr Zach Bush writes about how our human activities are affecting ourselves and the planet.

“This war against microorganisms is not saving us. It’s killing us. The microbes we are destroying are the direct link between our bodies and the Earth. The dramatic increase in human disease we are currently experiencing is a symptom of the failing health of our planet.” (15)

When you eat food that has had all the right bacteria and other microorganisms in the right place, the plant rhizosphere, at the right time you’re eating a food with a high nutrient profile. We’re dependent on an holistic ecosystem that begins in our soil system, translates into our food, which reinforces and inspires a complex microbiome in our gut that feeds us.

* Exercise and a healthy lifestyle is also very important to maintaining a healthy life. Sonnenburg, Justin, Erica Sonnenburg, PhDs, “What is the Microbiota and Why Should I Care?” The Good Gut, Penguin Books, pp 9

  2. Mayer, Emeran, “The Emerging View of a Healthy Gut Microbiome,” The Gut-Immune Connection, Harper Collins, 2021, pp 32-33

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