Soil biodiversity
Did you know some plants like grape, rice and lotus, have more genes than humans? This is contrary to the fundamental thought that humans, being the “most” evolved, should be biologically more complex and therefore possess more genes. How can this be you ask? The current hypothesis is that we come equipped with a significant amount of genetic material from the organisms growing inside our gut. These various bacteria, fungi, parasites and viruses provide signaling for the inner workings of our entire body. They support immune function, moderate inflammatory responses, generate vitamins that we are not capable of making, produce hormones from some of the foods we eat, help us to absorb minerals, and regulate the production of neurotransmitters. Most importantly, they allow our immune system to remain competitive with the rate of evolution of pathogens. Average bacteria have 500,000 generations for each human generation. Humans have only had 350-400,000 generations since the appearance of the earliest hominids in Africa. A team of researchers followed the changes of a genetically similar population of E. Coli for 50,000 generations. At 10,000 generations, a short time from an evolutionary perspective, “…the evolving genomes became increasingly different from their ancestors. Moreover, tremendous diversity accumulated within each population, such that almost every individual had a different genetic fingerprint” (Papadapoulus PNAS 1998)
Some surprises emerged at the 50,000-generation mark. One population had evolved to be able to utilize a completely different energy (food) source. Others changed in size, shape and antibiotic resistance. The successive generations were generally more resilient than the previous generations.
The human microbiome is passed on from generation to generation as an infant passes through the birth canal. The mixing of the mother’s secretions, including feces, provides the inoculation of these beneficial bacteria and fungi. The genetic material that we are carrying inside us today has evolved since the beginning of time and has been passed down through thousands of generations. Most animals on the planet, including many (and possibly all) born through eggs , receive this life-giving inoculation from their mother.
Over the past few years, we have observed a significant increase in autoimmune conditions, exaggerated immune responses, Celiac disease, allergy and asthma. Various factors have been attributed including lack of vitamin D, lack of sufficient parasites, an excessively sterile environment and deficiency of multiple bacteria, some of which are considered pathogenic. As I mention in my previous article, a lack of H. pylori, the bacteria that can cause stomach ulcers, can manifest as asthma. We are seeing startling changes to the human microbiome. Many individuals now require fecal transplants to replenish some of these missing organisms or face chronic illness. This is replacing what should have been passed down through the birth canal. Simply replacing these bacteria with fermented foods or probiotics is not always adequate. There are two reasons for this. First, like the soil, we have only been able to culture and identify only 1% of the organisms growing in the human digestive system. We don’t yet have enough information to re-create such a diverse system. Second, there is a hierarchy to the establishment of bacteria in the gut. E. coli, are like top soil on bedrock. They create a matrix for all the other single-celled creatures to grow and thrive. You can drink a gallon of yogurt daily but if E. Coli is not present, other beneficial species cannot establish themselves. So why not simply replace the E. Coli? Here’s the catch. Most E. Coli strains from other people and animal’s are rejected by our body’s immune system. This is likely why fecal transplants, which can work miracles, but must be obtained from the mother or siblings to avoid complications.
There are hundreds of studies linking cesarean sections (c-sections) and chronic antibiotic use with various autoimmune conditions and other health problems. Here are a few.
- A large study demonstrated a 52% increased risk of asthma in children delivered via cesarean section.
- Another study demonstrated a 2 fold increase in allergic reactions, asthma and sinus issues (J Allergy Clin Immunol 2008;122:274-9.)
- A meta-analysis (a study that looks at all studies on the same subject) revealed 19% increase in type 1 diabetes in children who were delivered via c-section.
- A study demonstrated significant reduction of TNF-alpha inflammatory response in piglets infected by Mycoplasma hyopneumoniae if they were inoculated with commensal bacteria. ***The fact that bacteria moderate inflammatory responses during infection could easily explain the increased incidence of severe allergic reactions.
- Another study demonstrated a significantly increased incidence of Celiac disease in children born via C-section
- Here is a wonderful article summarizing many of this information http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3110651/#R47
- Here is a book that goes into detail about some of these findings and their implications: An Epidemic of Absence – New Ways of Understanding Allergies and Autoimmune Diseases by Moises Velasquez-Manoff
These facts have sparked interest in the scientific and medical communities regarding the practice of cesarean section and antibiotic use. Less well recognized is the detrimental influence of seemingly harmless chemicals upon the microbiomes of various species. In 1974 the miracle herbicide, glyphosate or Roundup ™ was introduced to different agricultural markets in Malaysia, the U.K. and the U.S. Back then, techniques for evaluating the safety of chemicals was primarily based on two aspects. First, was the chemical’s ability to create disease. Second, the dose of the chemical that caused death in 50% of the recipients. (the LD50). Until recently, all studies on glyphosate suggested that most animals could literally drink the stuff without ill effects. However, as our knowledge and research techniques have evolved, we are discovering that we may have made committed irrevocable and possibly unprecedented mistakes in introducing this chemical into our environment.
A study performed on the bacteria populations in the digestive systems of poultry demonstrated that glyphosate caused significant reductions in the populations of various species of beneficial bacteria including Enterococcus faecium, Bacillus badius, Bifidobacterium adolescentis and Lactobacillus spp. (As I referenced above, we now know that beneficial bacteria are passed from the mother hen to her offspring and are inside the developing embryo within the egg). The reduction of these beneficial bacteria allowed overgrowth of bacteria that cause disease in humans like typhoid and botulism along with various other strains of salmonella.
As these pathogens have become more and more prevalent, we have had to use more and more antibiotics to protect ourselves from foods that have been part of the human diet for generations. Of course, the increased antibiotic use has further reduced the populations of the bacteria that prevented the pathogens to begin with. As time passes the pathogens develop more and more resistance to the antibiotics. We’ve replaced a system that worked for thousands of years with a scenario where we must innovate or die. I predict that in five to ten years we will come full circle and use bacteria and fungi as a replacement for antibiotics and to replenish what has been lost.
All of the beneficial bacteria mentioned in the study above are the same ones that exist in the human digestive system. As I have discussed in previous articles, the bacteria residing in our digestive system are reflective of the bacteria growing in the soil. Similar species of Enterobacter, Pseudomonas, Bacillus and Enterococcus are found both in the soil and in the human GI tract.
The world’s grasslands contain within them the highest level of microbial biodiversity of any other soil or ecosystem on the planet. Over millions of years this biodiversity created the dark, deep rich soil that made the Midwest of the United States one of richest resources for food production on the planet. The introduction of glyphosate allowed humanity to produce more food than has ever been possible. However, it is possible that it has already altered our evolutionary path. Dr. Don Huber, Professor Emeritus of Plant Pathology, Purdue University has studied various aspects of soil microbiology and plant pathology for decades. Here is the perspective he offered regarding glyphosate in an interview a few years ago.
“All it does is make it possible for that plant to survive and to accumulate more glyphosate. We still change the soil ecology, microbial ecology, and… our intestinal microbiology.”
Daily discoveries demonstrate that human health is inextricably linked with the health of the tiniest aspects our environment. Through innovation we have overcome many of Nature’s obstacles to create abundance and, for now, have become one of the most successful species on the planet. Through our knowledge we are finding new crossroads where it is obvious our actions are interfering with our own ability to adapt and evolve. It is becoming imperative that we use this knowledge to restore balance to correct the mistakes we have made. Otherwise, we will back ourselves into a corner where innovation is no longer about advancement but obligatory for our own survival.
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A few weeks ago I published an article about Traditional Chinese Medicine and the Origin of Scientific Thought. Part of its emphasis was discussing Five Element Theory which marked the beginning of scientific medicine and a departure from Shamanism. The following is a discussion of the interconnected systems of soil biodiversity, plant ecology, gut microbiology, and human health and evolution.
In Traditional Chinese Medicine, each of the Five Elements, fire, Earth, metal, water, and wood “symbolize five different inherent qualities and states of natural phenomena” including five movements and five phases in the cycle of the seasons. People are often stumped by the fact that there are four seasons but five elements. Being the source of all life on this planet, Earth was the fifth, and viewed as the source of all the other elements.
The ancient Chinese scholars identified the digestive system to be an extension of and our connection to the Earth. After all, it is where the elements of Earth are taken in as food and are transformed into a living being.
The bacteria and fungi present in every square millimeter of soil ultimately act as the digestive system or Earth element for plants. They fix nitrogen and break down soil nutrients and minerals into forms that can be taken up by the plants’ roots. When we eat plants, we also take in some of the bacteria and fungi present in the soil. These become part of the incredibly complex ecosystem of the gut.
Each and every organism present in digestive system is a reflection of the organisms present in the soil. Each one creates its own unique signals and immune responses that literally determine our state of being on EVERY level.
We are already aware of the anti-inflammatory and immune boosting benefits of acidophilus and bifidus which are being marketed in several yogurt products. A more interesting example of this appeared in the journal, Neuroscience, in May of 2007. Researchers found that the presence of the bacteria Mycobacterium vaccae (which is common in soil and not pathogenic to humans) created an immune response that stimulated serotonin sensitivity in the certain parts of the brain. A couple of things to take note of here: First, not all immune responses are bad. They are simply signals. Secondly, this bacteria’s presence in the gut results in actual behavioral modifications via serotonin which has a happy, calming effect. Further investigation suggested that this is one reason gardening makes us happy.
Another example is the pathogenic fungus, Rhizopus arrhizus. This fungus is also common in the soil and in trace amounts in our digestive tract. Like an ecosystem, the richer and more diverse, the more resilient. As long as our digestive ecosystem is diverse and healthy this fungus remains at low, non-threatening levels and actually serves many beneficial biologic functions. For example, if you eat anything from the yam family this fungus converts some of the phytochemicals it into the hormone progesterone which is then taken up into the blood via the lymphatic system. It’s also used very effectively in German Biologic Medicine as a low-dose suppository to stimulate the body to break up its own blood clots and vascular congestion.
A broader example is the influence of Firmicutes and Bacteroidetes and weight gain in humans. An article that appeared in Nature demonstrated a strong correlation between a low level of Bacteroidetes and obesity. Conversely, thinner people had higher levels of Firmicutes. Further research showed that these bacteria directly alter carbohydrate metabolism in the digestive system.
Ultimately the bacteria in the soil determine what types plants can establish. However, after a plant establishes itself, it creates its own local pathogen controls by promoting rhizobacteria. When we eat plants and their roots the immunity from the rhizobacteria are passed on to our own digestive systems. From the soil, to the plant, to our own digestive system and back again. They are not separate. They are one system. The foods we eat have a direct impact on the preponderance of the various bacteria and fungi present in our gut. This, in turn, determines the signals and immune system responses. As a very simple example, too much sugar results in an overgrowth of some fungi like candida albicans. (more information on this in the future)
The emerging field of gut microbiology has incredible potential for treating disease. However, after all the research is done, I believe the ultimate conclusion will be that eating food grown in healthy soil with extensive biodiversity will manifest as a healthy, evolving human community. With our current technology we have only been able to culture between 0.1 and 1% of the soil fungi and bacteria. The rest is completely unknown to us.
It is important to consider the impact of microbial deprivation (via the use of bacteriocides, fungicides, irradiation, triple washing and chlorination of our food and water) on the human health and evolution. There is a growing body of evidence that suggests the immune system problems we are seeing in the younger generations are a result of insufficient bacterial and viral exposure. Furthermore, because plants determine the presence of specific bacteria, it’s important to consider the impact that monocultures have on soil biodiversity and how this affects human health.
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