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Orthomolecular Medicine News Service, June 18, 2023

Orthomolecular plus Microbiome Science
Restoring the Immune System of a Farm Community

Commentary by Theo Farmer

OMNS (June 18, 2023) By combining Orthomolecular science and Microbiome science we find information necessary for the restoration and optimization, over multiple generations, of the health of widespread living systems, such as a local farm community. In our view, the living system called "farm community" consists of the soil, water, air, microbes, plants, insects, wildlife, and livestock of a farm plus the local community of people that receive food and information from the farm.

If we also take the view that the "immune system" of animals and humans extends beyond the body into the microbiome of the surrounding environment, then the prevention of disease and optimal health in animals and humans is achieved over several generations by tuning the microbiome, both internally and environmentally, to restore balance and resilience to this broader immune system.

Restoration of the microbiome first requires removal of nearly all inventions and interventions that disrupt the balance of the microbiome, which includes virtually all agricultural chemicals and pharmaceutical products developed in the last two centuries. Once this is achieved, then tuning the microbiome to restore balance favorable to humans and livestock can be accelerated using methods described below.

The Orthomolecular Advantage

During the years it takes to restore microbiome balance, it is critical to abstain from the use of chemicals that disrupt the microbiome. Orthomolecular methods are critical to relieving disease conditions caused by past damage to the microbiome. Orthomolecular methods alone, such as adopting a practice of high-dosing vitamin C to bowel-tolerance regularly, can be corrective to gut microbiome damage. But more importantly, because only nutrients are used, orthomolecular methods, unlike pharmaceutical chemicals, are interventions that resolve disease conditions without causing further disruption to the microbiome balance. The microbiome has built-in natural tendencies and strategies to restore itself to a healthy balance over time, so relying strictly on nutrient-based treatments of disease conditions allows for progress to a natural restoration of balance.

For example, in a pen of bottle-fed calves, an individual calf may develop symptoms of calf diphtheria (swollen cheeks caused by a bacterial infection). Treating the calf with antibiotics disrupts the microbiome balance inside the calf and in the environment around the calf and may expose the other calves to an unhealthy microbiome balance at a vulnerable stage in their development. In contrast, feeding the individual calf high-dose vitamin C and niacinamide in a bottle several times a day fortifies the individual calf to resolve the disease without disturbing its microbiome balance and affecting the other asymptomatic calves. [1]

The Human Microbiome Project

The human microbiome project was launched in 2007. Not 1907, but 2007 [2]. The results, by 2016, were a major revision of human biology that, in a world that favored optimal health for humanity, would have quickly obsoleted or severely restricted the use of damaging chemicals and interventions developed in the previous centuries. [3]

The results of the human microbiome project were profound. Microbiome science tells us that besides our collection of human mammal cells with mammal genetics, we are also a symbiosis, with microbial cells and microbial genetics working as a complex, balanced system. Humans, in fact, have fewer unique genes than a rice plant. Our bodies can be viewed as microbial gardens, and restoring and cultivating a healthy balance in our microbial gardens is critical to preventing disease and optimizing health.

Profiting from Multigenerational Microbiome Disruption

Orthomolecular methods are highly-effective remedies for disease conditions in both humans and animals, and they can help to maintain the microbiome balance. Nevertheless, orthomolecular science for use with humans and animals is ignored, obfuscated, and suppressed by the medical science mainstream. Apparently, the viability of entire highly-profitable industries depends on ignorance of orthomolecular methods. To the orthomolecular-aware person, the mainstream medical industry, ignoring high-dose nutrients as remedies, looks like a form of mass murder for profit and control. [4]

Similarly, modern microbiome science illuminates internal and external microbial relationships that, properly cultivated, optimize the health of living systems and eliminate many types of disease. However, paying attention to the information coming from microbiome science does little or nothing for industrial medicine or industrial agriculture profits, so it is also at risk of being shoved aside by the same dominant forces that suppress orthomolecular treatments for disease.

The profitable pattern for the disease-dependent industries can be viewed as follows:

  1. Introduce a product (i.e., a chemical, invention, or intervention) that disrupts the microbiome of a living system. Control the narrative (marketing/propaganda) to create a need for the new product.
  2. Control the research and mainstream narrative of disease conditions caused by the damage that the product inflicts to the microbiome and living systems over time.
  3. Produce and sell additional products that treat the symptoms of diseases that emerge from the first product, and that inflict further damage to the microbiome.

Chemical pesticides put into widespread use during the 19th and 20th centuries are examples of products that never were tested for the disruption they cause to microbiome balance. Disease conditions are often traceable to microbial overgrowth, indicating that the microbiome balance has been disrupted. The chemical companies that produce pesticides are often the same companies that introduce pharmaceutical products for downstream diseases arising from the microbiome disruption caused by new chemicals.

A dramatic example is the agricultural chemical glyphosate, used initially as a descaling agent to remove mineral deposits from pipes and boilers, [5] then as a weed killer, and now applied to ripen certain hay and grain crops right before harvest (desiccation). Glyphosate is also patented as an antibiotic that targets a wide variety of microbes, and it is active as an antibiotic at 0.01 parts per billion. [6] The long-term disruption inflicted by glyphosate to the microbiome balance of the soil, livestock, and the human gut is shocking, and the disease conditions that arise from that microbial imbalance are only beginning to be uncovered. [7]

A Broader Definition of the Immune System

The National Cancer Institute (NCI) defines the immune system as a complex network of cells, tissues, organs, and the substances they make that helps the body fight infections and other diseases. The immune system includes white blood cells and organs and tissues of the lymph system, such as the thymus, spleen, tonsils, lymph nodes, lymph vessels, and bone marrow.

A broader, microbiome science definition of "immune system" could be a complex subsystem within a larger living system that prevents and fights disease in the larger system.

Let's apply this definition to one example where microbial disruption is the likely cause of increased disease on farms: Clostridial overgrowth causes various disease conditions in dairy cattle, and the incidence of these diseases is on the rise in some dairies. According to one patent owned by Monsanto, glyphosate at concentrations lower than the allowed residue amounts in feed acts as a broad-spectrum antibiotic. Some veterinarians are beginning to see a connection between dairy cattle fed "conventional" genetically-modified (GM) grains, many of which have glyphosate residues, and increased incidence of Clostridial disease.

One or more activities of glyphosate-tainted feed may be an increase of Clostridial disease conditions:

  • disruption of the microbiome balance caused by glyphosate targeting microbes that are antagonistic to the Clostridial organisms present in the gut.
  • disruption of the microbiome balance due to increased inflammation in the gut creating anaerobic pockets that favor bacteria not normally found in the healthy aerobic gut environment.
  • some other known or unknown activities of glyphosate or feed produced with the application of glyphosate that disrupt gut microbiome balance.

Although studies by employees of the manufacturer of glyphosate continue to attest to its safety, [8] veterinarians find that removing feed tainted with glyphosate quickly reduces the incidence of Clostridial disease in cattle. [9]

If it is true that the presence of glyphosate in the feed modifies the microbiome to favor increased Clostridial disease, then we can say that the "immune system of the farm" is weakened by the presence of glyphosate in the feed. Therefore, microbiome balance inside and outside the cow is critical to preventing disease, and all of the microbial life present on the farm is part of "the immune system of the farm."

Newborn Mammals have Self-Completion Periods

When a calf is born, ideally within minutes of birth, it is nursing on its mother's dirty udder. When it latches on, the calf is sampling the microbiome of the herd. Within days, calves can be observed licking walls and eating bits of manure. The colostrum and milk from the mother is designed to sort microbes from the environment and install beneficial microbes in the gut while the calf gut is developing and is open to receiving microbes. The period when the calf is nursing, exclusively being nourished by milk, is a time for "self-completion." A completed calf, like a completed human, has a symbiotic system of microbial life in its gut, and the milk from the calf's mother has components that are specific to nourishing beneficial microbes which will become the calf's lifelong partners for health. The milk is protective to grow and selectively cultivate the calf's internal microbial garden.

A human baby and all other mammals go through a similar self-completion process after being born. The human self-completion period is said to be 1000 days, or just under 3 years. The newborn gut is open to receiving microbes from the mother and the environment during the first months or years while the milk from its mother is helping select the correct microbes. After the self-completion period, the gut closes down to new microbes, the fully-developed digestive processes in the stomach kill incoming microbes, and, after that, it is far more difficult to "plant" the appropriate microbes in the correct places in the microbial garden inside the gut. [10]

Parents are often frustrated as their babies are driven to put everything into their mouths as soon as they can grasp objects. But microbiome science would interpret this as a normal and natural drive by the human baby mammal to sample the microbiome of the environment around them. Ideally the microbiome around the newborn is rich and balanced, favorable to healthy mammalian processes. Breast milk is protective and selective during this self-completion process. Disrupting this self-completion process (e.g. with antibiotic use) can result in an imbalanced gut microbiota, and the result can be lifelong, chronic health problems. [11,12]

Pharmaceutical chemicals or vaccines are not tested for the impact they have on microbiome balance, so avoiding all pharmaceutical interventions, and all untested chemicals in the environment, during the self-completion period of a baby is best practice to ensure a healthy and balanced internal microbial garden.

Decades ago, studies showed that children raised on farms had fewer allergies, and attributed this to exposure to "animal dander". Microbiome science shows that modern cities are "microbial wastelands," -- they tend to lack the beneficial microbiome content found in nature. Farms, especially those with minimal damage from agricultural chemicals, offer a broader and more balanced microbiome, and that is one possible factor in improving the immune system development of the child to prevent allergies.

Niacin and the Microbiome

Nutrients and the microbiome have a tight relationship. Niacin, vitamin B3, is one example. The robust human gut microbiome includes more than 162 species of microbes identified that produce niacin. [13]

Lifelong niacin deficiency, and niacin deficiency diseases, are a plausible result of having a damaged gut microbiome: a gut microbiome that is missing a complete set of these niacin-producing species. Niacin deficiency is implicated in many chronic diseases and "mental illnesses." [14] A search of the peer-reviewed body of orthomolecular science at on "niacin" or "vitamin B3" reveals this connection. Lifelong supplementation with niacin or other forms of vitamin B3 may be necessary to resolve these deficiency diseases in individuals.

Microbiome damage is also passed from mother to child. Microbial imbalance is multi-generational. This means that mental illnesses that "run in families" may actually be caused by microbiome damage inflicted by some agent, like mercury medicines or pesticide exposure, in generations past. A great-great grandmother may have passed a niacin-deficient microbiome through her female descendants.

Many other essential nutrients besides niacin can be impacted by microbiome damage to the gut. Microbes generate and help with uptake and use of many minerals and nutrients. Microbial organisms are therefore orthomolecular engines for living systems. As we focus on optimizing health of the coming generations in a farm community, orthomolecular methods can be used to stop many prevalent diseases, and a focus on restoring microbial balance can move the farm system toward greatly reducing the overall incidence of disease.

A Farm Community as Living System

On our orthomolecular restorative farm, we view orthomolecular methods as critical to helping animals and humans overcome incidence of disease. But we view restoration of the microbiome balance as the key to optimizing the health of future generations, preventing and eliminating the incidence of disease over multiple generations. A human generation is on the order of 20-30 years, so this is a long-term challenge. However, a chicken generation is 1-2 years, hogs about 2 years, and cows 2-3 years. So, if livestock are employed to restore the microbiome balance of the soil and farm community, the entire farm community, including all the people involved and babies in their self-completion period, can expect to see significant health benefits in a matter of a few years.

Microbiome Tuning

In developing strategies for tuning the balance of the microbiome in the soil, water, air, plants, livestock, and humans that comprise farm community, reductionist science is a laborious pathway to answers. [15] Analyzing individual microbial functions and relationships in a laboratory can provide valuable insights to the workings of the overall system, but it is impossible to analyze all the protagonistic and antagonistic and synergistic relationships between the billions of microbes ("parasites", fungi, bacteria, and viruses) that make up the microbiome.

A systems approach is better, employing some fundamental understandings about how the mammalian microbiome system works and how it will respond over time.

Farmers and gardeners that work organically, without man-made chemicals, will consistently observe that nature, undisturbed over generations, will move toward restoring a healthy microbiome balance on its own. By adopting a few principles that we see acting in nature, we can accelerate the natural forces of microbiome restoration. During this tuning period, one of our assumptions is that by using only nutrients (i.e. orthomolecular methods) to treat diseases in livestock, we are not causing imbalances to the microbiome.

Here are some principles and educated assumptions we have employed to tune the microbiome of our farm community during the past decade:

  1. Humans are mammals, raised on raw milk from our mothers, and raw milk in the gut promotes balance with respect to the microbiome. It has antimicrobial, probiotic, and prebiotic characteristics. Through mother's milk, nursing mammals receive in their self-completion period a spectrum of beneficial microbes (probiotics). Milk also selectively nourishes beneficial microbes for the proper microbial balance (prebiotic). These characteristics make milk and fermented milk a natural force for tuning the microbiome to a healthy balance, that is a balance favorable to mammals.
  2. When infectious diseases are experienced and overcome, the individual that overcomes the disease condition, and the environment around the individual, has an immune system tuned to better overcome the disease. A well-balanced microbiome passes from mother to child, and immunity information from a mother that experienced a disease condition is passed to the child through one or more channels (some known and others likely unknown [16]), arming the immune system of the child to better resolve the disease condition.
  3. Lactofermentation, soaking animal feeds in fermented raw milk, favors selection of beneficial microbes and creates a microbial balance in animal feed that fortifies a healthy mammalian gut microbiome.
  4. "Herd immunity" is achieved when one generation of livestock or humans fully experiences and resolves infectious disease conditions, gains the immune-system information, and then passes that information to the next generation. Part of this immune system information is conveyed through the herd microbiome. When orthomolecular methods are employed to treat any and all disease symptoms on a farm, the farm immune system fully experiences the disease, without chemical disruption of the body or the microbiome. The immune system and microbiome are tuned through the complete disease process, while the individual experiences minimal suffering. Dr. Robert Cathcart coined the term "unsick" as a description of fully tuning the human's internal immune system while not suffering the full symptoms of the disease. [17] Orthomolecular methods eliminate the symptoms that cause pain and suffering, without disrupting immune system tuning or microbiome balance.

Orthomolecular Restorative Farming Examples

"Regenerative livestock farms" raise multiple species of livestock and move the animals on the land in a way that benefits soil fertility and the overall health of the farm. In our case, we call our methods "orthomolecular restorative farming" because we use only nutrients to address disease conditions. Our feeding and livestock rotation practices, farming methods, and food production processes focus on cultivating a healthy microbiome balance in the entire farm system.

Microbiome tuning requires tight controls of the products and methods that are allowed on the farm. In our case, we operate as a private association ministry providing food from our 160 acres for up to 1000 families, all members of our private association. We have an on-farm dairy and creamery and an on-farm butchery, controlling all methods used in food harvest and production. Operating in the private domain for the benefit of our private association members means that we can lawfully produce food following best practices according to orthomolecular and microbiome science rather than statutory practices required by often misguided regulatory and licensing agencies that control food commerce in the public domain.

In our private jurisdiction, we use dissolved ascorbic acid and niacinamide as the pre-milking teat wash in our raw dairy, and we use fermented raw milk as the post-milking teat dip for the cows. The ascorbic acid and niacinamide wash serves to clean the teats. Ascorbic acid and niacinamide, in combination, are antimicrobial and antitoxin. Twice a day topical application of these nutrients increases the overall health and flexibility of the skin that makes up the teat. Applying naturally fermented raw milk to the teat after milking bathes the teat in probiotics, lactic acid, and enzymes that promote a favorable microbiome balance on the teat and udder.

Bleach is never employed because it sterilizes in a way that favors imbalance in the microbiome. Instead we use pH shifts in the dairy for cleaning. All equipment is washed first in sodium bicarbonate, then in citric acid, and then rinsed with hot water. The sodium bicarbonate wash removes fats from surfaces and the citric acid wash exposes the surfaces to a major pH shift and rinses away mineral residues. These two cleaning agents are both beneficial molecules in the human and animal bodies and they react with each other in the drain water leaving sodium citrate, another beneficial molecule for humans and animals.

With a focus on microbiome balance, we rarely see mastitis in the dairy. If we do, it is usually associated with injury or birthing stress. We recognize mastitis in the udder as "localized scurvy" and we treat it simply using topical application of a lotion rich in ascorbic acid and niacinamide massaged into the affected quarter or entire udder. The lotion can be as simple as a handful of fermented raw milk (clabbered milk) mixed with a tablespoon of ascorbic acid and 1/8 tsp of niacinamide applied after milking twice a day. Generally this treatment clears the issue in a few days.

In the butchery, we use hot water primarily as the cleaning agent. We use wood cutting surfaces rather than plastic, as science shows that wood favors a beneficial microbiome balance. Plastic cutting surfaces that are washed with chlorine and other cleaning agents, as required in public domain butcheries, favor pathogenic microbial growth.

Excess skim milk from the creamery is fermented and used to soak the grains and legumes fed to chickens and hogs. The microbiome in the manures of the chickens and hogs is tuned by this lactic-acid-rich and probiotic-rich feed, and the nutrients in the grains are made more bioavailable by lactofermentation.

Chickens and hogs run on the land alternately with grazing cows, distributing manures that have a favorable microbiome balance. Cows grazing the lands in subsequent seasons then have their microbiomes further tuned toward a favorable balance by the manures distributed by the other species.


By employing the natural balance of raw milk and fermented raw milk throughout the farm, along with rotational grazing, we create a positive feedback loop, a microbiome tuning, that plays out over multiple seasons resulting in a microbiome balance in the "immune system of the farm" that reduces or eliminates disease conditions.

Banning any chemicals from the farm that disrupt the microbiome tuning process ensures that the tuning process moves forward to optimize human and animal health and toward the elimination of disease conditions on the farm.

Employing only orthomolecular methods to treat disease conditions ensures that microbiome balance is preserved as the restorative methods tune the microbiome balance of the living system called "farm community" over multiple seasons.


1. Farmer T (2020) C is for Cattle: How high-dose ascorbate therapy works on the farm. Orthomolecular Medicine News Service.

2. Integrative HMP (iHMP) Research Network Consortium (2019) The Integrative Human Microbiome Project. Nature, 569:641-648.

3. Microbiome and PTSD: Hemmings SMJ, Malan-Mülle S,van den Heuvel LL, et al. (2017) The Microbiome in Posttraumatic Stress Disorder and Trauma-Exposed Controls: An Exploratory Study. Psychosom Med. 79:936-946.

4. Gifford-Jones W (2020) Medical Ignorance and the Mass Murder of Coronavirus Patients. Orthomolecular Medicine News Service.

5. Glyphosate as a descaling agent: Jayasumana C, Gunatilake S, Senanayake P (2014) Glyphosate, hard water and nephrotoxic metals: are they the culprits behind the epidemic of chronic kidney disease of unknown etiology in Sri Lanka? Int J Environ Res Public Health. 11:2125-2147.

6. Glyphosate as antibiotic: Abraham W, Monsanto Tech LLC (2010) Glyphosate formulations and their use for the inhibition of 5-enolpyruvylshikimate-3-phosphate synthase. US Patent 7,771,736.

7. Samsel A, Seneff S (2013) Glyphosate, pathways to modern diseases II: Celiac sprue and gluten intolerance. Interdiscip Toxicol. 6:159-184.

8. Vicini J, Reeves W, Swarthout J, Karberg K (2019) Glyphosate in livestock: feed residues and animal health. J Anim Sci. 97: 4509-4518.

9. Dupmeier T. (2021) Children's Health Defense Video Interview (14:42). Glyphosate + The Severe Suffering of Animals.

10. Dietert R, Dietert J (2012) The Completed Self: An Immunological View of the Human-Microbiome Superorganism and Risk of Chronic Diseases. Entropy 14:2036-2065.

11. Mueller N, Bakacs E, Combellick, J, et al. (2015) The infant microbiome development: mom matters. Trends Mol Med. 21:109-117.

12. Mammals, milk, and the microbiome: Quigley L, O'Sullivan O, Stanton C, et al. (2013) The complex microbiota of raw milk. FEMS Microbiol Rev. 37:664-698.

13. Niacin and the Microbiome: Magnúsdótt S, Ravcheev D, de Crécy-Lagard V, Thiele I (2015) Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes. Front Genet. 6:148.

14. Gao K, Mu C-L, Farzi A, Zhu W-Y (2020) Tryptophan Metabolism: A Link Between the Gut Microbiota and Brain. Adv Nutr. 11:709-723.

15. Reductionist approach to the microbiome: Wolf-Jäckel GA, Strube ML, Schou KK, et al. (2021) Bovine Abortions Revisited-Enhancing Abortion Diagnostics by 16S rDNA Amplicon Sequencing and Fluorescence in situ Hybridization. Front Vet Sci. 8:623666.

16. Viza D, Fudenberg HH, Palareti A, et al (2013) Transfer factor: an overlooked potential for the prevention and treatment of infectious diseases. Folia Biol (Praha). 59:53-67.

17. Cathcart RF (1981) Vitamin C, titrating to bowel tolerance, anascorbemia, and acute induced scurvy. Med Hypotheses 7:1359-1376.

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