Dead garden

Remember how I likened the gastrointestinal (GI) microbiome to a backyard garden? To start your springtime garden, you clear the soil of twigs, rocks, and weeds. You then plant seeds for cucumbers, tomatoes, and zucchini, followed by watering and fertilizing over the growing season to harvest a bounty of vegetables after two or three months. Cultivating bowel flora in your GI tract follows similar principles.

What if you forgot to water and fertilize your garden and it didn’t rain for, say, two weeks? You will probably salvage few, if any, vegetables at the end of the growing season and instead you may have a garden of weeds. Bowel flora is like that, too: If you fail to “water and fertilize” them, they begin to die off and “weeds” begin to appear, i.e., microbial species that introduce adverse effects.

Let’s also accept that, unlike the nice garden you began with, your GI microbiome is already “damaged” from all the exposures of modern life: multiple antibiotics, glyphosate and other herbicides, stomach acid-blocking and anti-inflammatory drugs, statin cholesterol drugs, synthetic sweeteners, food additives, etc. You therefore begin the “growing season” after having lost hundreds of beneficial microbial species, allowing anywhere from mild to severe degrees of overgrowth of unhealthy, mostly fecal, microbes. It’s as if you start the growing season not with a properly prepared 10×10-foot plot for your garden, but a garden where the soil is clay, hardly any topsoil remaining, soil nutrients depleted through use of herbicides, pesticides, and other chemicals.

If you therefore fail to nourish your microbes for a few weeks or longer, a number of important unhealthy additional changes have been documented that amplify the damage inflicted by all these modern factors:

    • Further loss of species diversity-–In nearly every study looking at this question, there has been a marked reduction in the number of species inhabiting the GI tract, adding to the loss of diversity that modern people have developed. Recall that greater species diversity is a sign of health; low species diversity a sign of poor health.
    • Marked reductions in Bifidobacteria species—Species such as B. longum and B. infantis are important for gut and overall health, as they produce beneficial metabolites. Bifidobacteria species are consistently decimated when you are deprived of prebiotic fibers. If you are ketotic, ketone levels in intestinal cells are sufficient to inhibit proliferation of Bifidobacteria species.
    • Increased Fusobacterium nucleatum—This is an important development, as Fusobacterium is looking like a major contributor to colon cancer. Implant this microbe into a normal mouse colon and colon cancer develops. Specimens of human colon cancer are filled with Fusobacterium, as are metastatic lesions in liver and lung. (Note that Fusobacterium originates in the mouth and colonizes the colon by gaining access to the bloodstream, not via swallowing, a perfect example of bacterial translocation.)
    • Increased E. coli—and some other species of Proteobacteria. These are the Gram-negative species that yield endotoxin that enters the bloodstream, causing endotoxemia that “exports” inflammation, insulin resistance, and other harmful effects to other parts of the body to cause skin rashes, cognitive impairment, depression, anxiety, coronary heart disease, fatty liver and other conditions. Some strains of E. coli are believed to add to risk for colon cancer, also.
    • Overgrowth of Akkermansia muciniphila and Bacteroides caccae—Several studies have now documented overgrowth of these two species that are consumers of intestinal mucus. (Muciniphila = “mucus lover.”) These two microbes are perfectly happy when you feed them prebiotic fibers. Deprive them of fibers, however, and they are uniquely able to consume intestinal mucus as an alternative energy source. This erodes the intestinal mucus barrier, allows microbes to contact and enter the intestinal wall, cause intestinal inflammation and colitis, and increases entry of endotoxin into the bloodstream, i.e., endotoxemia.
    • Increased Desulfovibrio speciesDesulfovibrio species have been associated Parkinson’s disease and colon cancer. Desulfovibrio species exert many of their effects via production of hydrogen sulfide, H2S.

Failure to take in adequate quantities of prebiotic fibers and related compounds is common in people following ketogenic or carnivorous lifestyles, unless specific effort is made to include foods like asparagus, leeks, dandelion greens, and onions. It also happens in low-FODMAPs diets that some people follow to reduce symptoms of irritable bowel syndrome. As if our microbiomes weren’t’t already damaged beyond recognition, the confused thinking that goes on in the world of diet makes it worse by leading people down paths that introduce even greater damage to an already-damaged GI microbiome. In my programs, we may be intermittently, but not purposefully, ketotic. We include carnivory, but also include foods rich in the fibers that nourish microbes. And we never fall for the short-sighted mistake called a “low-FODMAPs” diet that ignores the underlying cause of food intolerances, small intestinal bacterial overgrowth, SIBO. People following these dietary mistakes are lulled by the upfront beneficial effects such as weight loss or reduction of bloating, not recognizing that they are setting themselves up for long-term health problems.

Say you witnessed a lion gore a gazelle, tearing open its abdomen and settling down to gnaw through its intestines, liver, heart and other organs and limbs. You are so disgusted that you capture the lion, isolate it in a cage and feed it kale and spinach, what some label “superfoods.” How long will the lion survive? Perhaps a few weeks, but then you would have a dead lion on your hands. You defied the lion’s basic nutritional needs programmed into its genetic code, accumulated over millions of years of life and adaptation. As a member of the species Homo sapiens, you likewise have basic needs programmed into your genetic code, acquired over the 3+ million years our species has walked the planet. Part of the needs programmed into your genetic code is to rely on the metabolic products of microbes living in your GI tract, so reliant that humans have lost enzymes to digest or process some components of diet that we now rely on our resident microbes to deal with. Wild Homo sapiens were, yes, hunters, but also gatherers of wild berries and other fruit, flowers, insects, fish and shellfish, bird’s eggs, roots, and nuts. You eat what you must to survive. Don’t allow these modern armchair interpretations of diet send you off-course and engage in a lifestyle that is contrary to your genetic programming.