Week 17: Your Gut, Disease and the Immune System

All disease begins in the gut.

Although he died 2,386 years ago, the author of this quote - Hippocrates - is, more than any other person, responsible for how medicine is performed today, establishing clinical practice as the profession's dominant methodology, and asserting that natural factors - not gods and superstition - were the source of illness. Even millennia before the advent of the machine age and modern science allowed us to look into - and measure - human biological processes, he understood the gut's key role in creating and maintaining our health. 

The gut - which is also called the gastrointestinal (GI) tract - is comprised of multiple organs that begin where we ingest foods and end with where we expel them. Its primary job is to process nutrients from that which we eat. Beyond being responsible for the digestion of food, one's GI tract, which includes the esophagus, stomach, small intestine, large intestine and rectum - in addition to contributory organs like the pancreas, liver and gallbladder - does, more than any other system in the body, determine the state of our well-being. As such, gut health is of fundamental importance, and accordingly, it deserves an exploration and a deeper understanding.

The GI tract is host to the majority of the 100 trillion microorganisms that are not part of your body, but are instead hosted by it. According to Dr. Joseph Mercola, some 90% of the genetic material in your body is not 'you', but rather "the bacteria, fungi, viruses and other microorganisms that compose your microflora." Together, according to him, "your body's microflora influence your genetic expression [whether or not genetic predispositions are 'triggered'], your immune system, your brain's development, mental health and memory, your weight, and risk of chronic and acute diseases, from diabetes to cancer." In just one example of our guts' deep-reaching influence, a 2012 Time Magazine article quotes from the website Autism Speaks, stating that "up to 85% of children with autism also suffer from some kind of gastrointestinal distress." The question that this astounding fact begs is, what is the relationship between these two conditions?

The GI tract is home to the body's enteric nervous system. This system is often referred to as 'The Second Brain', because - as explained in an illuminating Scientific American article - "it contains 100 million neurons, more than in either the spinal cord or the peripheral nervous system". The article goes on to say that the enteric nervous system operates independently from that of the brain, and that when the two do communicate, 90% of the exchange travels from the gut to the brain - not the other way around. Dr. Emeran Mayer - a professor of physiology, psychiatry and behavioral sciences at UCLA - believes says that "A big part of our emotions are probably influenced by the nerves in our gut." Both of our 'brains' contain neurotransmitters, and some 95% of serotonin - that all-important chemical that regulates mood, social behavior, appetite, sleep, memory and sexual desire - resides in the bowel. Indeed, our 'second brains' seem to be regulators of many processes that most of us probably believed were the dominion of our 'primary brains'.

As important as these neurons are in regulating much of what we consider our psychological 'human-ness', there are other considerations with regard to our guts that directly affect our physical health, and is why, fundamentally, we are discussing the subject here.

The Immune System

The human immune system, which as we all know, is responsible for fending off infectious organisms and disease, resides primarily - approximately 70% of it - in our GI tracts. Disorders of the immune system can result in autoimmune diseases, such as lupus, multiple sclerosis, celiac disease, irritable bowel syndrome and psoriasis, among others, which together afflict between 7% and 20% of all Americans - affecting women far more than men, up to 75% more, according to the American Autoimmune Related Diseases Association, or AARDA. The immune system also regulates inflammatory diseases, like appendicitis, bursitis, rhinitis and ulcerative colitis - the latter affecting 500,000 to 2 million Americans, and from which my own brother died more than twelve years ago. The National Center for Biotechnology Information (NCBI) pulls no punches, and states that 'Chronic inflammation is a major cause of age-related diseases and cancer.' Supporting NCBI's position, a 2006 paper published by the Yale Journal of Biology and Medicine states that an environment friendly to inflammation is at the root of the diseases that claim the most dollars and lives in industrialized nations today: heart disease, stroke, diabetes, and many cancers. 

On the subject of cancer, it's worth repeating a key line from our Week 3 post: that 'an estimated 1/3 of all cancer deaths are due to nutritional factors, including obesity'. Clearly, the health of our GI tracts directly influences the health of our bodies, since these tracts are not just the gateways for the foods we ingest and the nutrients that we cull from them, but equally important, they are the force that protects our bodies from an endless supply of toxins, pathogens and harmful bacteria that we also ingest daily. Thus, the health of this fundamental biological system is largely dependent upon of the types and qualities of food and drink that we choose to put into it.

Microflora and Health

Chief among our choices of how to best feed our bodies is an assessment of how those foods interact with the microflora (the bacteria and fungi) - within our guts. "These microbes influence digestion, allergies and metabolism," according to a 2015 article on the subject in The Atlantic, and importantly, the presence or absence of different bacteria change the expression of disease. Take autism: California Institute of Technology microbiologist Sarkis Mazmanian has linked one bacterium to the expression - and subsequently management - of autism symptoms in mice. He was awarded a 2012 MacArthur Genius Grant for his ongoing work on the subject. He believes that adjusting gut bacteria could be a viable treatment for Autism, along with other neuro-developmental disorders. Another study, by neuroscientist John Cryan at the University College of Cork in Ireland, found that feeding mice the bacterium lactobacillus - found commonly in fermented foods like yogurt, kefir and pickles - resulted in reduced levels of hormones linked to stress. Similarly, Oxford University neurobiologist Phil Burnet fed 45 human volunteers a substance that fosters the growth of both lactobacillus and bifidobacteria (again, found in fermented foods), and discovered that they reduced the production levels of cortisol - the stress hormone - in his subjects when exposed to stress-inducing stimuli. The consumption of these bacteria generated similar results to those seen when subjects take anti-depressants or anti-anxiety medications. His team's conclusion, as reported by NCBI: "The ingestion of probiotics modulates the processing of information that is strongly linked to anxiety and depression."


Many of us have seen this word and wondered what exactly it meant. We've been told that so-called probiotic foods - or supplements - are good for us; or that they might keep us 'regular'; or at least ease digestive problems. But most of our collective knowledge stops there. Adding confusion to the subject, we in the 'germophobe' West have been inculcated with the idea that bacteria are harmful. Accordingly, we have developed anxieties around keeping our bodies, children and homes pathogen-free. Topical agents like anti-bacterial soaps, sprays and hand sanitizers have proliferated, while the widespread use of medically prescribed antibiotics has likewise soared. According to researchers at Princeton University, global use of antibiotics has risen more than 36% in just 10 years, from 2000-2010. And while no one can argue that the correct administration of antibiotics like penicillin has saved countless lives since their introduction in the 1940's, the rise in antibiotics use and anti-bacterial everything brings with it three major - and somewhat worrisome - consequences. 1: Our bodies have lost some of their innate ability to manage reasonable exposure to a variety of pathogens. 2: Our guts' microflora is severely compromised when fed a regimen of antibiotics, and must be repopulated artificially. 3: Psychologically, our belief that bacteria are generally bad, and that anti-bacterials are generally good, leads to a misunderstanding of just how symbiotic the relationship between 'us' and 'them' is - and that without (good) bacteria, we would not exist. Probiotics are - as the name implies - the opposite of antibiotics; and as such, science is increasingly finding that the ingestion of probiotics can trigger or support the re-establishment of a balanced micro-biome in our guts.

It's worth repeating here that each and every one of us carries some 100 trillion microorganisms within us, comprising 90% of our genetic 'selves', and that this symbiotic relationship - when in balance - allows us to function, feel, maintain health and live long lives.  

Our ancestors knew this. In most global cultures, the regular, ritual ingestion of probiotic foods - that is to say foods in which thriving colonies of gut-healthy bacteria proliferate, via fermentation - can be found. Turks and Russians gave us kefir. Eastern Europeans provided sauerkraut. Koreans created kimchi. Japanese tripled down with natto, miso and tempeh. Chinese invented kombucha (before it was perfected by the Japanese). Indian cucumbers were fermented by Mesopotamians to create pickles. And today, most of the Western world consumes yogurt, which also originated in Turkey. Unexpectedly, some types of cheese contain some amount of probiotics that survive the aging process, including gouda, mozzarella, cottage cheese and cheddar, according to NCBI - but only if they are raw, as pasteurization (heat treatment) kills its bacteria and denatures its enzymes. Finally, even bread can be probiotic - sourdough bread, that is. Made with a 'starter' leavening agent, sourdough was the de facto form of bread for all of human history, until baker's yeast slowly replaced it beginning just 150 years ago.

Copyright FFFL 2016

Copyright FFFL 2016

For thousands of years, these foods have been ingested by our forebears for their curative, digestive benefits. As an area of scientific study, it is no more than 25 years old, though growing rapidly. As often happens, science is catching up with what cultural trial and error knew all along: that a healthy gut leads to a healthy self; and that certain foods can help foster that balance. According to Harvard Medical School, so-called 'probiotic therapy' "can help treat several gastrointestinal ills, delay the development of allergies in children, and prevent and treat vaginal and urinary infections in women." According to the American Nutrition Association, dysbiosis - or an imbalance in your gut flora caused by too few beneficial bacteria and an overgrowth of bad bacteria, yeast, and/or parasites - has been implicated in the following conditions: chronic inflammation, auto-immune diseases, neurological afflictions (including Parkinson's), psoriasis, colon and breast cancer, chronic fatigue, fibromyalgia, acne and eczema. They suggest four steps in the rebalancing of the gut, which is widely referred to as the 'Four R Program':

  • Remove toxins

  • Replace stomach acids and digestive enzymes

  • Repopulate (Reinoculate) good bacteria

  • Repair the bowel lining

The ingestion of probiotic, fermented foods help in all four categories. A good primer on the Four R Program can be found here, courtesy of Jeffrey Bland, Ph.D.

The use of probiotic supplements - which are manufactured, not naturally occurring, and are, like all supplements, outside of regulation, as we discussed at length in Week 10 - is of potential, but unclear benefit. One key reason is that we as consumers cannot be guaranteed that what is advertised on the bottle/jar/box is in fact what is in the supplement, either in quantity or in quality. Some third-party consumer groups, like Consumerlab.com, have found that eight of probiotic supplements they tested contained less than 1% of the purported live cultures. Echoing this sentiment, neurologist Dr. Natasha Campbell-McBride - the creator of the GAPS Diet (Gut and Psychology/Physiology Syndrome) - says that even if the probiotic supplements we take were to include what they advertise, fermented foods contain some 100 times the number of probiotic bacteria as the supplements. Put another way, she says that "Literally, one serving of vegetables was equal to an entire bottle of a high potency probiotic! So clearly, you're far better off using fermented foods." She further discusses another benefit of fermented foods, namely, that the fermentation process can increase the bioavailability of nutrients. In her interview with Dr. Mercola, she illustrates the point using cabbage, whose Vitamin C, she says, becomes 20 times more bioavailable than in 'fresh' form, where the nutrient is bound in the cellular structure of the host plant. She also cautions against overwhelming the body with probiotic foods if it is not used to them, and instead introducing it slowly into your system so as to acclimate it. You can find a great host of general information on her website, here, and about probiotics in particular here, including their introduction into your diet, as well as dosages. She believes that it takes approximately six months of consistent probiotic ingestion for the average gut to "remove the pathogenic flora and start re-establishing normal gut flora." The following graphic charts the range and breadth of probiotic foods indigenous to global cultures and - thanks to an increasing awareness of these foods' health benefits - largely available today at both up- and down-market food stores nationwide.

Copyright FFFL 2016

Copyright FFFL 2016

For an excellent abstract by the NCBI on the effects of antibiotic use on the immune system and health, click here.

We at FFFL recommend the regular - daily - inclusion of fermented foods in your diet, both because of their contribution to gut health and because as these are whole (albeit fermented) foods, they are also full of vitamins, minerals and phytonutrients. We further suggest you vary your intake, since each food contains different bacterial strains (some contain beneficial yeasts, as well); and because no two foods have the same nutrient profile, variation is central to a healthy diet. We recommend looking for 'raw' probiotic foods, as pasteurization and cooking (i.e.: high temperature) denatures the food's enzymes and kill its bacteria. And one last time, these foods have been successfully included in the human diet for thousands of years; they are not medicine, per se; and they are as old as human society. They are all, as we have consistently advocated, heart- and gut-healthy, live, healing, whole foods, produced by nature.