Soil and human gut dysbiosis

I’m sort of a soil nerd. Well, not sort of…I’m a HUGE soil nerd. Most of my environmental and food perspective is based upon what improves or degrades the health of soil ecosystems. Why? Because soil health largely determines planetary and human health. Thus I’m almost equally intrigued by nutritional science especially nutritional science related to the human gut microbiome. In nature soil and the microbiome biomes of various species (including homo sapiens) are all interconnected ecosystems. Though modern industrial germaphobic societies, to a degree in a variety of ways, have disconnected these ecosystems and this has resulted in a lot more chronic disease.

So what’s encouraging to me is that more and more doctors are not only recognizing that food is medicine, but also that the quality of this medicine is contingent upon how food is grown or raised. That quality is highly contingent upon the health of the soil microbiome as well as the health of microbiomes of livestock and humans.

To that end, I loved a recent blog by Dr. Casey Means I read on her Levels website. This blog was entitled, Why the way our food is grown matters for metabolic health. She’s a Stanford trained medical doctor, not a soil scientist, so she got some of the soil particulars wrong. But overall, the recognition of issues and the thoughts she shared were very worthwhile and inspiring. However being the huge soil nerd that I am, I sent her an email pointing out a few soil science things for her further edification. Hopefully, she didn’t take what I wrote the wrong way. What follows is the email I sent her.

Great blog! Here’s a blog I wrote two years ago that you might also find interesting: Restoring the plant’s soil microbiome.

Plus just a few soil science things to note and adjust. To start, there are different types of mycorrhizal networks. The two most prevalent kinds are ecto-mycorrhizal fungi [EMF] and arbuscular mycorrhizal networks [AMF]. EMF is with trees and AMF is with approx. 90% of other plants including most crops. Brassica like broccoli and rape seed don’t form AMF associations. EMF and AMF networks can interconnect.

Glyphosate kills AMF, but it doesn’t kill all soil life life. Gly is registered as both a chelator and antibiotic. So like other antibiotics, it instead shifts bacteria to an unbalanced unhealthy mix of bacteria. Think of it as soil dysbiosis. As a strong chelator, gly binds minerals making those minerals unavailable for plants to obtain from the soil. AMF attach to roots and expand root zones of plants. They also exude a sticky substance called glomalin that helps to create and improve soil structure (which is especially important for water infiltration). Without AMF associations, plants can’t mine minerals from sub-soil or exchange minerals between plants. With healthy AMF networks, AMF exude acids that can even break down rocks in sub-soil for minerals.

Others industrial and traditional practices destroy or weaken AMF especially application of synthetic nitrogen, tillage and bare fallows. Syn N makes plants lazy. Because they get this macro-nutrient via cation ion exchange with a lot of irrigation, plants stop exuding other carbon metabolites for other micro-nutrients. Tillage also shreds AMF networks, so it should be done as infrequently and as shallow as possible. Bare fallows are when ground is left bare between cash crops. Without roots in the grounds, plants aren’t exuding any carbon metabolites (sugars, fats, acids) so there’s no food for any of the microbiology (bacteria and fungi). A lot of the microbiology is primarily fed via these exuded carbon metabolites. The exuded carbon metabolites from roots are known as the microbial carbon pump [MCP]. The bacteria and fungi are fed by the MCP…they form and die, form and die. After these microbes die, they become the necromass that forms most soil organic matter. This is known as the MCP pathway.

There’s also saprophytic fungi. These are decomposers that break down organic matter into soil organic matter [SOM]. They work as part of a different pathway to form soil organic matter than the MCP pathway. Decomposers are part of the decomposition pathway. Though when saprophytic fungi die, they also become necromass. The outside cell walls of fungi are made of chitin, a fairly durable long lasting carbon molecule (a fibrous polysaccharide). Pesticides especially fungicides kill beneficial forms of saprophytic fungi.

Soil organic matter [SOM] is about 50 to 60% soil organic carbon [carbon]. When soil is tilled, it releases soil carbon into the atmosphere that’s oxidized and becomes CO2. So minimizing ground disturbance is one of the keys to regenerative Ag…not minimizing tillage. When soils are oxidized by disturbance, minerals are also oxidized and made less plant available for root/soil ion exchanges.

As per the attachment, the other five principles of regenerative Ag (as they pertain to plant production) are know your context, keep ground covered, diversity, keep roots in the ground as long as possible (for reasons noted above to feed microbes), and animal integration. Animal integration particularly in mixed systems provides numerous benefits including a way to terminate cover crops (by grazing), cycling nutrients and adding more microbes to the soil ecosystem. However, in market gardens, livestock integration is a bit problematic due to food safety concerns and laws. So in these situations, compost, compost teas and extracts plus vermi-compost and extracts (from worms), often make more sense.

Compost can be a tool to keep ground covered and feed decomposters, but it’s not essential. Compost teas and extracts (derived from compost) though can be useful tools to expedite and establish microbial life as well as reactivate latent soil microbiology. Extracts can be applied as seed coats that greatly reduce the amount of compost material required.

So regenerative practices aren’t the same thing necessarily as organic practices. People often equate the two. As practiced in the United States, organic practices, especially larger scale commercial organic, are far from any sort of gold standard. Cover crops aren’t widely used yet so there are a lot of bare fallows.. There are numerous other issues (see below attachment) with organic farming as it’s practice in the US including most organic farms use organic pesticides that kill soil microbiology. Regenerative organic is what should be aspired to, but there aren’t that many regenerative produce or specialty produce farms yet.

Currently, it’s actually much easier to source regenerative meat than regenerative produce. Though it’s a spectrum, and many farms are slowly improving. And down here in California, with drought, building soil organic matter is especially important. Why? Drought resilience, since with every 1% increase in soil organic matter per acre of land, up to 27,000 gallons of water can be retained. Improved soil structure with AMF (see glomalin above) increases water infiltration and retention. Drought isn’t only a function of how much rain falls from the sky, drought is also a function of how much water infiltrates and is retained by soil.

As for nutrients, oxidized and chelated soils both bind nutrients and destroy the necessarily soil biology required to make macro and micro-nutrients plant available. So, soils aren’t so much depleted as much as they have the wrong soil microbial mix due to poor agricultural practices. Again think of it more like soil gut dysbiosis. Poor plant nutrition then, in turn, results in the need for even more chemical inputs to deal with disease and insect pressures. Poor plant nutrition makes plants more susceptible to disease and pathogens. For example, syn N increases nitrate levels in plant tissue, and nitrates attract insects. Poor uptake of micro-nutrients leads to less phytonutrients in plants, so plants aren’t as well equipped with their natural defense immune systems. So this isn’t dissimilar as to what occurs with humans who have poor “terrains” due to poor nutrient deficient diets and environmental toxins (including pesticide residues).

David & Anne discuss this in the paper you cited as well as their new book, What Your Food Ate, which I highly recommend. Another paper worth reading on phytonutrient diversity in meats is this one by my friends Dr. Stephan van Vliet and Dr. Fred Provenza: Health-promoting phytonutrients are higher in grass-fed meat and milk.

One final note, “sustainable” is not the same as regenerative. Currently around the world,most soil is very degraded. So soil ecosystems have to be regenerated first before any thought of sustainability factors into the equation, since right now, there’s really no point in sustaining a degraded resource.


4 thoughts on “Soil and human gut dysbiosis

  1. Hi there. I’m very interested in all of your briefings, and especially support your emphasis on the role of methane sinks in removing enteric emissions from livestock at source. Something else that you may wish to incorporate into this analysis is the fact that species-rich pastures, containing a mix of forbs have been found to generate lower levels of enteric emissions, as shown in this paper. It also shows evidence for a lot of soil health benefits, which you may wish to know about.

    with best wishes Bill


  2. We went on holiday and after 3 weeks away our newish and automatically watered lawn was waist high in different grasses and dense ground cover. The soil underneath, once grey, hard and cracked, was a luscious black and massive slugs and other creepy crawlies slimed their way through this mini forest while butterflies and pollinators buzzed happily. Mushrooms bloomed on the more kempt part where the dog lies down.

    My wife ripped up the “weeds” by hand (ooh lots of worms, she said) and threw them away. I see the now bare soil drying and reverting to its previous state. She plans to plant more attractive grass. What should I say to her?


  3. I live in northern ca. our ground is dry from April to November is it hard on the soils to work them dry? I plant winter cover and graze it in the spring I leave the residue till fall when I plant the cover I have tried notill in the fall but it hasn’t been successful so now I work the soil lightly and drill in the cover is there a better way thank you Keith


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