A well-functioning gut with healthy gut flora holds the roots of our health.
Dr. Natasha Campbell-McBride

Lincoln Stoller, PhD, 2021. This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International license (CC BY-NC-ND 4.0)


Things to know about Covid-19:

  • Few people had immunity to it before it recently appeared.
  • It’s quite contagious and spreads quickly.
  • It poses little danger to young, healthy people.
  • Mortality occurs predominantly in the old and infirm.

Here is a graph of the mortality of people suffering from covid-19 taken from the Korean population (Cho, 2021) plotted against a patient’s incidence of comorbidity. The horizontal scale is the CCI, the Charlson comorbidity index, which counts the number of major ailments that a person has. The vertical axis is the percent of patients who died. The graph is based on the 7,890 people who were admitted to hospital with confirmed cases of covid-19.

covid-19 sarscov2 pandemic food gut biota agriculture big-ag nutrition immunity

Healthy patients who have no comorbities have a roughly 0.5% chance of dying. This number comes from that group of otherwise healthy people who are sufficiently ill with covid-19 to have been admitted to hospital. We assume roughly ten times this many people were ill with covid-19 at this time and in this population who did not go to the hospital. Consequently, the mortality rate for the whole, young, otherwise healthy population drops into the neighborhood of 0.1%, which is equivalent to that of the seasonal flu (Armitage, 2020).

For the older population with preexisting illness the mortality rates are huge. Remember the 0.1% mortality rate for the seasonal flu is for the whole population, including the ill and elderly. The mortality rate due to covid-19 for the whole population, young and old, is between 3 and 5% which is 30 to 50 times higher. The point is that these mortalities are coming from the older, infirm population. The covid-19 pandemic in its most virulent form predominates in this group.

Most healthy human immune systems can defend themselves from covid-19. The real pandemic, then, relates to the high number of people with unhealthy immune systems. Why are so many people unhealthy?

The Gut

The health of your immune system is linked to the health of your gut (Fields, 2015). It is in your gut, for the most part, where your body makes contact with the beneficial, innocuous, and infectious life forms of the outside world.

“A huge proportion of your immune system is actually in your GI tract,” says Dan Peterson, assistant professor of pathology at the Johns Hopkins University School of Medicine. ‘The immune system is inside your body, and the bacteria are outside your body.’ And yet they interact. For example, certain cells in the lining of the gut spend their lives excreting massive quantities of antibodies into the gut. ‘That’s what we’re trying to understand—what are the types of antibodies being made, and how is the body trying to control the interaction between ourselves and bacteria on the outside?’ (Fields, 2015)”

Insights into the crucial role of your gut are new, and this field of study is receiving a tremendous amount of attention. Thirty years ago little was understood, and 80 years ago, when the first pesticides, herbicides, and antibiotics were being introduced, the role of the gut was largely unknown.

“In the last few decades, there has been a huge shift in our comprehension of human-microbe connections… We now understand how human cells and microbial units have coevolved together in symbiosis, through the introduction of prokaryotic cells (bacteria) into eukaryotic cells (human and animal)… The immune system is particularly interconnected with gut bacteria (golbertlab, 2021).”

Our digestive system operates in three parts. The small intestine performs chemical reduction using enzymes. These chemical reactions lead to the production of some of the substances our body needs. The small intestine supports relatively few bacteria or other external organisms.

Most of our gut biota live in our large intestine where they digest our food by a process of fermentation. We don’t benefit from what our biota digest, we benefit from what they excrete. Our nutrition occurs downstream from that of the bacteria, viruses, and fungi that we host.

Many of the chemicals we absorb from our food we cannot use directly. They need further reduction and reconstruction and this is done in the liver.

The liver stores vitamins and minerals and metabolizes the fats, proteins, and carbohydrates absorbed in the intestines. Complex sugars like fructose are reduced to glucose in the liver. Disturbances in our sugar, carbohydrate, and protein intake impact both our gut and liver.

“Microbiome refers to the collective genomes of the micro-organisms in a particular environment, and microbiota is the community of micro-organisms themselves. Approximately 100 trillion micro-organisms (most of them bacteria, but also viruses, fungi, and protozoa) exist in the human gastrointestinal tract—the microbiome is now best thought of as a virtual organ of the body. The human genome consists of about 23,000 genes, whereas the microbiome encodes over three million genes producing thousands of metabolites, which replace many of the functions of the host, consequently influencing the host’s fitness, phenotype, and health (Valdes, 2018).”

Our health is determined by the diversity and the balance of the micro-organisms in our gut and by the food we eat. Over the past 100 years that diversity has been negatively impacted by our ingestion of processed foods, pesticides, antibiotics, and a nutritionally denuded diet. This has also changed the chemicals that we’re processing in our liver.

“Whole grain consumption is consistently linked with improved health—including decreased risk of type 2 diabetes, cardiovascular disease, and weight gain—and it is likely that many of the benefits of whole grain consumption are mediated through their effects on gut microbes.

“… high consumption of fibrous plant foods, [is] strongly correlated with [non-Western society’s] freedom from typical Western diseases including obesity, diabetes, and colorectal cancer (Valdes, 2018).”

Modern Agriculture

Modern agriculture depends on pesticides, herbicides, and artificial fertilizers. The pesticides reduce the biological diversity of soil bacteria which, in turn, reduce plants’ ability to nourish themselves making them more reliant on artificial fertilizers. The herbicides threaten both the weeds and the crops leading to the development of genetically modified crops resistant to the herbicides.

The herbicides are incorporated in the surface, the structure, or the water that the food product absorbs which we then ingest. The genetic modifications are linked to the application of the environmental poisons used to increase the yield.

“Factory farmers discovered that low dose antibiotics help livestock to gain weight more quickly than normal. Meat is usually sold by the pound and cheap pharmaceuticals can add a lot to the old profit margin… More than 80% of the antibiotics sold in the United States are used in the agriculture industry. Millions of pounds of drugs are added to our food supply every year. Drugs that never appear on ingredients labels…

“Herbicides were invented to take care of the weeds. But to be effective, the seed companies needed to get the crop plants to survive the weed killer. Enter genetically modified seeds, resistant to glyphosate, commercially known as Roundup®. Having Roundup-Ready crops in the field means that more and more glyphosate is being used on our food. Glyphosate doesn’t just kill weeds. When we eat food that has been treated with this herbicide, it acts very similarly to antibiotics in our digestive tract. (Golden-Tevald, 2021)”

The increasing use of agrochemicals, low plant biodiversity and rigorous soil management practices have a negative effect on the community of supporting plants that the food crop depends on, and on the supportive fungi and bacteria that grow on and within the food crop plant. Modern factory agriculture reduces bioactive soil to dust so that our food, which is one of our main sources of bacterial diversity, becomes biologically inert.

“Over 50% of the world’s population lives in cities, which is expected to increase to approximately two-thirds by 2050. The reduced contact with microbes in the living environment, increased sanitation, and use of antibiotics pesticides and hormones deplete the richness of gut microbiota…

“Our diet has also changed within the last decennia. In order to preserve food for long transport, storage and distribution, it is often sterilized. In addition to more processed nutrition, the intake of more energy-rich food, abundant in sugars and fat, decreases the biodiversity of the intestine…

“Modern changes in farming and nutrition also include plant breeding efforts, e.g., to reduce the bitterness of Brassicacae, such as broccoli, cauliflower, and cabbage. The bitterness is due to glucosinolates, which help the plant to resist pathogens and is assumed to be an anti-cancer metabolite. The digestive function of glucosinolates is mostly depleted in the human gut…

“On top of antibiotic medication, the elimination of microbes from food via processing has direct impacts on the human gut microbiome. The intake of diverse food rich in fibers and secondary plant metabolites, with living microbiota, from a diverse soil environment may positively influence the gut (Blum, 2019).”

As a result of modern agriculture, our bodies are less able to produce anti-cancer, anti-inflamatory, anti-biotic, and immune enhancing substances. As a result we are experiencing epidemics of obesity, diabetes, hypertension, auto-immune disease, and cancer. These are the diseases that constitute the comorbities associated with mortality from covid-19 and, in the case of obesity, diabetes, and hypertension, they are the main comorbities leading to mortality.

“Most of our daily food comes from industrial agriculture and has been exposed to herbicides, fertilizers and a large array of pesticides to obtain high yields. Pesticides are a large class of chemical compounds that include fungicides, bactericides, nematicides, molluscicides, avicides, rodenticides and animal repellents. A large literature is available to show the negative effects of many commonly used pesticides on human health… Many beneficial microbes are also among the targets of pesticides with direct and indirect implications on soil, plant, and food safety (Hirt, 2020).”

covid-19 sarscov2 pandemic food gut biota agriculture big-ag nutrition immunity


I was aware of the connection between food, the gut, and health from before the time last year when I wrote my book Covid-19, Illness and Opportunity. I found the references I’ve used to support his article within a few hours. This information is now widely known in research circles, the connections and implications are not. The media tells us what those who own the most assets direct them to tell us, and this is another aspect of the pervasive failure of the media such has preceded the media’s catastrophic failure with regard to providing information about covid-19.

“Many who study the microbiome suspect that we are experiencing an extinction spasm that parallels the extinction crisis gripping the planet… What the Sonnenburgs’ experiment suggests is that by failing to adequately nourish key microbes, the Western diet may also be starving them out of existence. They call this idea ‘starving the microbial self.’ (Velasquez-Manoff, 2015)”

Here are the things that you must do to improve your gut health and our food web:

  • Reject factory agriculture and support organic farming.
  • Avoid processed foods and food additives.
  • Prepare food from raw ingredients.
  • Eat high-fiber, biologically active foods.

Justin Sonnenburg is a microbiologist who’s written the 2016 book, The Good Gut: Taking Control of Your Weight, Your Mood, and Your Long-term Health. His work is reviewed in a short article that’s found online and is titled, A fermented-food diet increases microbiome diversity and lowers inflammation, Stanford study finds. (Weaver, 2021).

“Soluble fiber is an umbrella term for complex plant sugars—including some polysaccharides, oligosaccharides, and fructans. The molecules consist of simple sugars linked together in long, hard-to-dismantle chains. If you dump a load of fiber—or microbiota-accessible carbohydrates—onto a colonic community of microbes, those that specialize in fermenting it will bloom. And they’ll start churning out short-chain fatty acids, including butyrate, whose smell you might recognize from aged cheese, and acetate, which gives vinegar its sharpness.

“These acids, Sonnenburg thinks, are one of the long-sought mechanisms by which fiber prevents disease. Rodent studies suggest that as they diffuse into circulation, they stimulate the anti-inflammatory arm of the immune system—cells that help you not attack tree pollen and other harmless proteins—preventing allergies and other inflammatory diseases. The calming effect reaches as far as the bone marrow and lungs, where, as a recent Nature Medicine study showed, the acids reduced animals’ vulnerability to asthma (Velasquez-Manoff, 2015).”

Most of my book is devoted to explorations of the gut and the immune system. You can get free digital copies of Covid-19, Illness and Illumination from my Dropbox at this address:

COVID-19, Illness & Illumination


Armitage, M. (2020, Aug. 27). How Do COVID-19’s Annual Deaths and Mortality Rate Compare to the Flu’s?, GoodRx Health. https://www.goodrx.com/conditions/covid-19/flu-vs-coronavirus-mortality-and-death-rates-by-year

Blum, W. E. H., Zechmeister-Boltenstern, S., and Keiblinger, K. M. (2019, Sep). Does Soil Contribute to the Human Gut Microbiome?, Microorganisms, 7(9): 287. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6780873/

Cho, S. I., Yoon, S. & Lee, H. (2021). Impact of comorbidity burden on mortality in patients with COVID-19 using the Korean health insurance database, Nature, 11: 6375. https://www.nature.com/articles/s41598-021-85813-2

Fields, H. (2015, Nov). The Gut: Where Bacteria and Immune System Meet, Johns Hopkins Medicine. https://www.hopkinsmedicine.org/research/advancements-in-research/fundamentals/in-depth/the-gut-where-bacteria-and-immune-system-meet

gilbertlab (2021). How your Gut Affects your Immune System: A Symbiotic Relationship. GilbertLab.com. https://gilbertlab.com/immune-system/gut-microbiome-symbiosis/

Golden-Tevald, J. (2021). Modern Agriculture and Human Gut Health, MorningStar Family Health Center. http://morningstarfhc.com/modern-agriculture-human-gut-health/

Hirt, H. (2020, July 31). Healthy soils for healthy plants for healthy humans, Science & Society. https://www.embopress.org/doi/full/10.15252/embr.202051069

Valdes, A. M., Walter, J., Segal, E., & Spector, T. D. (2018). Role of the gut microbiota in nutrition and health. BMJ (Clinical research ed). 2018;361:k2179. https://www.bmj.com/content/361/bmj.k2179

Velasquez-Manoff, M., (2015, November 12). How the Western Diet Has Derailed Our Evolution, Nautilus. https://nautil.us/issue/30/identity/how-the-western-diet-has-derailed-our-evolution

Weaver, J. (2021, July 12). A fermented-food diet increases microbiome diversity and lowers inflammation, Stanford study finds, Stanford Medicine News Center. https://med.stanford.edu/news/all-news/2021/07/fermented-food-diet-increases-microbiome-diversity-lowers-inflammation