Human coprolites from Hinds' Cave

Photo courtesy Texas Beyond History

Now, before you throw your arms up in frustration, know that my programs are all low-carb. You will also recognize that my programs, whether labeled “Wheat Belly,” “Undoctored,” “Super Gut” or otherwise, are not just about diet. My programs begin with diet, but then go further by addressing common nutrient deficiencies unique to modern life, and show you how to manage the gastrointestinal (GI) microbiome using multiple strategies. Results are therefore dramatically superior to results obtained with diet alone.

The problem with low-carb diets falling under labels such as ketogenic, carnivorous, Atkins’, low-FODMAPs or others is that in most versions there is no emphasis on cultivating GI microbes. This has serious consequences for long-term health, even if you experience substantial upfront benefits such as weight loss, reduction in blood sugar and blood pressure, etc. These dietary approaches, of course, emphasize consumption of meats, organs, poultry, fish, shellfish, eggs, cheese, etc. The inclusion of vegetables varies from program to program, but starchy plant matter such as potatoes, yams, and grains are generally shunned, similar to my programs. Legumes and fruit are also verboten. And, because they are simply diet programs and not necessarily programs for health, most end there, also failing to address common nutrient deficiencies.

Let’s view all this from the viewpoint of the GI microbiome. Due to many modern factors, everyone in the modern world has lost hundreds of bacterial species in the GI tract, i.e., we have lost species diversity. This is important because, of all the varied and complicated ways to “grade” the human GI microbiome, one consistent pattern emerges: the greater the species diversity, the better are measures of health; the lower the species diversity, the poorer are measures of health. For example, GI species diversity in slender people is substantially greater than that of obese people. Species diversity of someone without cancer or without type 2 diabetes is greater than someone with cancer or type 2 diabetes. Over and over again, measures of species diversity has held up as a reflection of health (although whether cause or effect remains debatable). But, because of exposures such as antibiotics, glyphosate and other herbicides, preservatives with antimicrobial properties and other factors, modern GI species diversity is far less than it used to be. This includes, by the way, loss of numerous microbes that performed important functions for the human host. (Lactobacillus reuteri is one perfect example, ubiquitous in mammals and human hunter-gatherers, lost by nearly everyone in the modern world.)

So all of us begin our journey with reduced GI microbial species diversity, even if you begin with apparent outward health. Failing to nourish microbes on your low-carb journey therefore leads to:

  • Further reduction of species diversity
  • Further reduction in Bifidobacteria
  • Increase in Proteobacteria (esp. E. coli, Fusobacterium nucleatum)
  • Increased Desulfovibrio
  • Increased mucin degraders: Akkermansia muciniphila and Bacteroides caccae overgrowth

So an already depleted GI microbiome is further depleted. The loss of Bifidobacteria and other butyrate-producing species means that, over time, the metabolic benefits of this fatty acid are reduced, impairing benefits on such things as blood sugar, blood pressure, and sleep. (No, the beta-hydroxybutyrate of ketosis does not fully compensate for the lack of microbe-produced butyrate, as demonstrated in experimental models.)

The increase in Proteobacteria, especially Fusobacterium nucleatum, is especially concerning. Abundant evidence suggests that F. nucleatum is a major driver of colon cancer. Recall that this microbe originates in the mouth, especially in people with bleeding gums, gingivitis, and periodontitis, and colonizes the colon via the bloodstream (not by swallowing), where it takes up residence and, given the experimental and human evidence, provokes cancer. Overgrowth of E. coli (though it differs with strain) adds to this effect. The increase in Desulfovibrio, a producer of hydrogen sulfide gas, may be yet another driver of colon cancer risk.

The increase in mucin-degrading microbes means that, deprived of dietary fibers from plant matter, they turn to consuming intestinal mucus. This has been shown to allow microbes to directly contact and inflame the intestinal wall, allowing entry of bacteria themselves as well as toxic breakdown products, especially endotoxin, that enters the bloodstream: endotoxemia. This is the process that drives insulin resistance, increased blood sugar, type 2 diabetes, skin rashes, joint and muscle pains, coronary disease, brain effects such as depression, Alzheimer’s dementia, and many other conditions. Abnormal proliferation of mucin-degrading species therefore poses major risks for long-term health.

In other words, Homo sapiens are reliant on intake of fibers from plant matter that are indigestible by human digestive enzymes, but are “digestible” by GI microbes. Human hunter-gatherer populations forage for roots, tubers, and other sources of such fibers (though varies with seasonal availability). Recovery of ancient fossilized fecal material (as shown in the photograph above), while not yielding the full array of fecal microbes from ancient people, do show that fiber intake was abundant, far greater than in modern populations. (Most of the fiber recovered is indigestible cellulose fiber that even most microbes cannot metabolize, but it provides an indirect proxy for overall plant matter intake.) Factors associated with nourishing microbes with various plant fibers is therefore programmed into the human genetic code—we are reliant on the many effects yielded by our resident microbes. Failure to keep them happy is a major risk for numerous human health conditions.