The Microbiome


Healthy Soils Healthy Guts

Modern science has revealed the wonders of microbes that exist all around us. Ever since Anton Von Leeuwenhoek invented some of the first microscopes to reveal the hidden world of single celled organisms that are both around us and in us, humans have been fascinated by the world of microbes. After many centuries of being afraid of "germs" the notion of probiotics has taken hold in a valid fashion. While fermentation has been an ancient and ancestral practice for millennia, the mechanisms behind it's efficacy are still being revealed.  Now the current comprehension behind bacterial and fungal interactions has shown us that we are outnumbered cellularly in our own bodies by ten times the number of single celled organisms essentially making us colonies.

Which brings us to the word Microbiome, from the latin roots of micro=small and bio=life. Millions of years of mutation and adaptation evolutionarily has imbued every creature with a  unique symbiotic amalgam of fungi, bacteria, archae and viruses. Many facets of digestion are stimulated by friendly bacteria such as Lacto-Bacillii, which we inherit from our mother's birth canal and breast milk as our first inoculation against pathogens in the outside world. Unfortunately in our world today, many health problems are arising from overuse of anti-biotics and more sterile soils from industrial chemicals being applied agriculturally. While the goal of feeding the planet was an altruistic one it has contributed to more soil erosion in the last one hundred years than the ten thousand years before that. Agriculture has become the single most destructive force on the planet, creating dead zones at the mouth of every major river in the world in what was once beautiful ecosystems and habitats that flourished for eons.

Serendipitously, there has been trends emerging to restore biomes worldwide, by building soil organic matter, and restoring vitality in our guts through fermented foods. By utilizing biomimicry, we can follow the lead of virgin prairie and old growth forests to restore the soil food web that we depend on for our very existence. Research by folks like Paul Stamets has shown that every species of plant and tree(excepting a few exceptions like brassicas) has endo and ecto mycorhizzal symbiotes that bond to the surface of roots , increasing nutrient extraction from the surrounding soil. In one teaspoon of soil from  healthy ecosystem, there can be literally miles of hyphal connections. Fungus are an integral part of the microbiome of plants and the soil food web, acting in symphony with various bacteria and archae and providing food for higher life forms such as arthorpods and nematodes and worms while cycling nutrients and organic matter, solubilizing  minerals for bioavailability for plants roots and building humus. As the soil is the buffet for plants, and the roots are their stomach we should briefly discuss Cation Exchange Capacity(CEC). CEC is the balance of positively charged elements in a soil, found in highest proportions in a soil rich with organic humus. While the anions are the elements more stable, the cations are more prone to washing and leaching away, unless bundled up in the soil food web. Rocks and clay, broken down by fungi, which are fed sugars by plants roots in exchange for raw minerals, all the while with bacteria interweaving.

Each particular microbiome is termed a holobiont, coined by Lynn Margulis, famed discoverer of the fact that mitochondria and chloroplasts were eaten and became symbiotes with early prokaryotes to form the first eukaryotes. And just as the holobiont is the microbiome relative to each "organism", terroir is a french term denoting the effect each particular valley has on the palate of the food and drinks grown there. You can take genetically identical grape cuttings, grow them in nearby valleys side by side, and get different minerals, flavonoids, sugar contents, etc... affecting the whole flavor. The microbiome of the terroir has been shown to change the way plants take in nutrients, thus changing the total outcome of our sustenance at the end. Biodynamic principles have been shown to increase both carbon in the soil and sugar content in the grape. Using the idea of a farm as a self sustaining entity is integral to all regenerative agriculture, whether permacuture, biodynamics, biological farming, natural farming or whatever popular rebranding of old peasant wisdom with science to provide "evidence" of it's value.

Biomimicry has influenced many great minds such as Fukuoka and Master Cho, who have sought to replicate nature's processes in the farm setting, in which soil builds organic matter similar to an old growth forest. Similarly, some bacteria have been found only in virgin prairie, and disappear once tillage and traditional cultivation starts. No-till systems of agriculture help support the soil food web, and a mulch layer or living cover crop provides many benefits against erosion, all the while cycling nutrients. Just as humans eat yogurt or kimchi for the probiotic benefits, bioaugmentation of the earth is possible using aerated compost or anaerobic ferments. Korean Natural Farming in particular makes wonderful use of the indigenous microorganisms(IMO) in our bioregions to help heal the soil and ourselves through growing more nutrient dense food. Popular as well is using the preparation called EM-1(effective microorganisms), which is a proprietary strain of lactic acid bacteria(LAB), bread/beer yeast and photosynthetic purple non-sulfur bacteria.

Over the course of an ecological history, there is a process called terrestrial succession. In the Cascades for instance, alders are the first to come into an ecosystem, followed by Douglas firs, cedars, maple and ending with spruce and hemlock before forest fires or other natural events restart the process. Grasslands are interesting in being bacterially dominated while forests are fungally dominated.

Sadly, pesticides like glyphosate, besides being chelators of minerals leading to depletion in the soil, are antagonistic at the micro-level where lessened populations of LAB lead to greater fusarium outbreaks in wheatcrops. However since industrialization has spread around the planet there are far less undisturbed pockets of nature, and where humans have done damage it is not inhabitable even at the micro level. Bioremediation is possible to help heal and repair the damage done. Work has shown that the oyster mushroom can break down hydrocarbons and turn it into carbohydrates, and fungi and bacteria are being discovered more frequently with the alchemical abilities to turn our waste into their food source.

At this time though there are no large scale projects that are reversing dead zones at the mouth of rivers through managing runoff of agrichemicals through mycofiltration and competitive exclusion. But just as the macro and micro are present in our bodies, we too, as a species, are part of the global ecological synergy, a macrobiome. We are acting more pathogenic than beneficial at this time, a cultural monotony leading to a glorification of consumerism which makes the world around us as dead as our insides. This trend can be reversed, and just as LAB can be used in human therapy for PTSD, anxiety and depression, helping lift our serotonin levels, a less neurotic human is more likely to have empathy and biophilia. Studies have shown antidepressant effects from getting our fingers in the dirt, which makes one wonder just what "I" am.

I am a holobiont, a unique microbiome, colony organism created through millions of years or symbiosis, epigenetically passing down inherited information relative to survival and reproduction. At this time I live in a state of affairs where the spinach commercially available has 20% of the calcium that was present two generations back. While we will never have the bone density of a Neanderthal, we can at least work towards doing our part to help remineralize and bioaugment this beautiful Gaiome, planet Earth.