The disastrous microbiome consequences of fiber deficiency

What happens when you fail to ingest fiber in your daily dietary routine?

By the term “fiber,” I am referring specifically to fibers, carbohydrates, and other factors that are not digestible by humans but metabolizable by microbes in the gastrointestinal (GI) tract. I am NOT referring to the fibers that provide “bulk” such as bran or cellulose obtained from, say, bran breakfast cereal, fiber that is not digestible by humans nor by the majority of microbes in the human GI tract (in contrast to the ruminant GI tract that does harbor microbes that can degrade cellulose).

Lack of such fibers occurs, for instance, in ketogenic, carnivorous, and excessively strict low-carb diets in which there is a preponderance of protein-rich animal products such as beef, pork, fish, poultry, etc. and a lack of plant matter such as legumes, vegetables, root vegetables. The absence of plant matter yields a diet lacking fibers, polyphenols, lignans, β-carotene and other carotenoids, vitamin K1, sulforaphane and other factors. Note that the hunter-gatherer microbiome has been shown to be enriched in fiber-metabolizing species such as Prevotella and spirochetes largely lacking or absent from the modern microbiome.

Here’s an example from someone who followed a carnivorous diet for several weeks and then, after having developed a disruption of bowel habits and abdominal discomfort, had a stool analysis run (via DNA sequencing). This was submitted by a 50-some year old woman in excellent physical shape, at or near ideal weight, with no significant health problems including no type 2 diabetes, hypertension, heart disease, autoimmune conditions, etc.

Among the findings:

• A marked excess of Proteobacteria/Enterobacteriaceae—These are the Gram-negative fecal microbes of colonic dysbiosis and perhaps small intestinal bacterial overgrowth, SIBO. (Because SIBO is distinguished by its location, i.e., the small intestine, and not just species composition, we cannot identify SIBO from a stool sample; we can only suspect that SIBO is present.) An excess of these species is inflammatory in both the GI tract and throughout the body when endotoxin breakdown products enter the bloodstream.
   
• Increased Hexa-LPS Index—Think of this form of “hex-acylated” lipopolysaccharide endotoxin (originating from Gram-negative Proteobacteria, especially E. coli) as the most toxic form of endotoxin likely to set in motion inflammation in the intestinal wall and then into the rest of the body when it gains entry into the bloodstream. This amplifies toxic effects such as insulin resistance, inflammation, weight gain in abdominal fat, etc.
   
• Moderate increase in hydrogen sulfide (H2S)—Low levels of H2S are normal, as it is a normal signaling molecule in the GI tract. However, at high levels, such as that developing here, it is toxic to the intestinal lining and becomes a risk factor for inflammatory bowel disease and colon cancer.
   
• Dramatic increase in ammonia—Excess ammonia is yet another result of excessive reliance on animal proteins along with lack of fiber. Ammonia is an intestinal irritant and can provoke abdominal discomfort, irritability, confusion, brain “fog,” and toxicity to brain tissue. High levels of ammonia have also been associated with promoting colon cancer.
   
• Excessive secondary bile acids—This is a frequent occurrence when diet lacks fibers and is protein-heavy, a shift in bile acids towards microbial-derived bile acids such as lithocholic and deoxylitholic acids, known risk factors for promoting colon cancer.
   
• Lack of Urolithin A—This microbial metabolite has a variety of effects including stimulating muscle growth and mitophagy. Urolithin A was present at unusually low levels, likely due to the lack or loss of species producing this metabolite from polyphenols that were meant to come from plant matter.

These are therefore presumptive acute effects of this relatively recent dietary shift. Studies looking at changes that develop over a longer timeline suggest that these changes persist and are accompanied by additional distortions in microbial composition, as well as metabolites. One of the patterns she has not yet developed in this several-week long experience is a reduction in species diversity, i.e., loss of hundreds of bacterial species that develops when you “starve” microbes. Akkermansia muciniphila populations also remain at healthy levels although this is also likely change over time as this species is starved of fibers and turns to human mucus for nutrition, over-proliferating and adding to intestinal inflammation and endotoxemia.

(She did not have a baseline analysis prior to making this diet change for comparison. But the changes are so characteristic of a fiber-depleted, meat protein-based diet that it is likely a safe assumption that the above changes are recent.)

Thankfully, reversing these unhealthy changes can be accomplished by adding back plant matter for their fiber, polyphenol and other components. We can expect a shift away from Proteobacteria; reduced levels of H2S, ammonia, LPS, secondary bile acids; increased Urolithin A. It would likely help to include our “yogurts” that restore small intestinal- and colon-colonizing and bacteriocin-producing species such as L. reuteri, L. gasseri, and B. subtilis along with all our other efforts to restore a healthier GI microbiome.

I hope that you can see that my concern with these fiber-depleted lifestyles is that we are likely to witness an uptick in colon cancer in coming years should people stay on these diets chronically. You might view these diets as a perfect storm of changes that cultivate a microbial milieu that is a setup for carcinogenesis. Do not interpret these remarks as an endorsement of vegan or vegetarian diets. As more and more people are experimenting with different diets, some of them extreme, it is becoming clear that a varied diet that includes animal proteins and fats along with plant matter is the basic formula for health. Ironically, despite the constant need some people have for dietary novelty, we are coming back full circle to the diet that humans have evolved to need over thousands of generations, no fancy labels required.

The original IHB post is currently found on the: ⎆Infinite Health Blog, but accessing it there can require an unnecessary separate blog membership. The copy of it above is complete, and has been re-curated and enhanced for the Inner Circle membership.