the hygiene hypothesis, vaccinations, antibiotics, and how to heal your gut


“For decades it has been obvious that early exposure to a farm environment, meaning an abundance of microbes, a diverse microbiota, eliminates allergies and many autoimmunities.  The Hygiene Hypothesis explained how early exposure to abundant microorganisms could eliminate allergies, as an early exposure to antigens that trained the immune system….    Your immune system is critical to your health and damage to your immune system is the typical beginning to most diseases.  Damage to the immune system starts in the gut, where the aggressive and suppressive halves of the immune system develop in response to particular species of bacteria.  Those essential bacteria grow on the food in your diet that is not digested in the stomach and absorbed as nutrients in the small intestines, i.e. prebiotic fiber.  Thus, you eat to feed yourself and your gut bacteria.  Without the gut bacteria, you would be deficient in vitamins, your immune system would cease to function and you would be constipated.  Fixing your diet and gut microbiota will cure your diseases.”   Dr. Art Ayers from Disease Genes in the Gut Microbiota

“According to the ‘hygiene hypothesis’, the decreasing incidence of infections in western countries and more recently in developing countries is at the origin of the increasing incidence of both autoimmune and allergic diseases….    Public health measures were taken after the industrial revolution by western countries to limit the spread of infections. These measures comprised decontamination of the water supply, pasteurization and sterilization of milk and other food products, respect of the cold chain procedure, vaccination against common childhood infections and the wide use of antibiotics. In countries where good health standards do not exist, people are chronically infected by various pathogens. In those countries, the prevalence of allergic diseases remains low. Interestingly, several countries that have eradicated those common infections see the emergence of allergic and autoimmune diseases…  The geographical distribution of allergic and autoimmune diseases is a mirror image of the geographical distribution of various infectious diseases, including HAV, gastrointestinal infections and parasitic infections.”  From the April 2010 issue of Clinical and Experimental Immunology (The ‘Hygiene Hypothesis’ for Autoimmune and Allergic Diseases: An Update)

“Keeping a delicate balance in the immune system by eliminating invading pathogens, while still maintaining self-tolerance to avoid autoimmunity, is critical for the body’s health. The gut microbiota that resides in the gastrointestinal tract provides essential health benefits to its host, particularly by regulating immune homeostasis. Moreover, it has recently become obvious that alterations of these gut microbial communities can cause immune dysregulation, leading to autoimmune disorders.”  From the January 2012 issue of the medical journal Gut Microbes (The Role of Gut Microbiota in Immune Homeostasis and Autoimmunity)

“The hygiene hypothesis stipulates that microbial exposure during early life induces immunologic tolerance via immune stimulation, and hence reduces the risk of allergy development.”  The opening sentence of the brand new study from the journal Pediatrics (Allergy in Children in Hand Versus Machine Dishwashing)

“All disease begins in the gut.”  -Hippocrates

Remember how we were taught to fear certain things like DIETARY FAT, SALT, and CHOLESTEROL from the time we were little?  And how one after the other, these have been shown to play little or no part in disease — or at least in the way we have been led to believe that too much of them causes disease?  These, however, are small potatoes compared to something else that humans have become increasingly worried about since the days when Louis Pasteur first postulated his germ theory — the theory that microscopic bugs are the ultimate culprits behind all sickness and disease.  While we now know that there are any number of other factors in the development of diseases, the germ theory is alive and well, and working overtime.  But it hasn’t always been so.

The Developer of Chiropractic, DR. BJ PALMER (1882-1961) hypothesized that, “If the ‘germ theory of disease’ were correct, there’d be no one living to believe it.”  But he wasn’t the only one.  A number of famous contemporaries and colleagues of Pasteur himself (1822-1895) did not buy into his ideas either.  They believed that while germs might play an important role in the development of disease, it’s a susceptibility to the germ and not the germ itself that cause people to get sick.  After all, how can (in the words of BJ’s father, DD), “two factory workers be exposed to the exact same environmental conditions on a daily basis and one gets sick while the other remains well?  Let’s see what people much smarter than I had to say about the matter back in the day.

  • DR. CLAUDE BERNARD:  Dr. Bernard (1813-1878) was a French physiologist who has been praised as, “one of the greatest of all men of science“.  Among his numerous scientific accomplishments were his development of double-blinded studies as well as coming up with the concept of “HOMEOSTASIS” — the body strives to keep its internal environment constant.  It was Bernard who wrote that, “The terrain is everything; the germ is nothing“.  In other words, the soil is far more important than the seed. 
  • DR. ANTOINE BECHAMP:  Dr. Bechamp (1816-1908), a chemist and biologist as well as a fellow Frenchman, was a rival of Pasteur.  Although his “Microzyma” theory is certainly interesting, I’m not sure it’s much more than that.  Bechamp believed that germs could not invade a healthy host; but could easily invade, thrive, and multiply in an unhealthy host. Sort of like the old “Rats in the Dump” lecture that Dr. Fred Barge used to give.  Dumps attract rats, but they certainly don’t cause them.
  • DR. ILYA ILYICH MESHNIKOV:   Dr. Meshnikov (1845-1916) was a Nobel Prize-winning Russian biologist, zoologist, protozoologist, and immunologist, who happened to be one of our earliest “Gut Health” researchers.  A popular online encyclopedia says this about Dr. Meshnikov.  “Mechnikov also developed a theory that aging is caused by toxic bacteria in the gut and that lactic acid could prolong life. Based on this theory, he drank sour milk every day. He wrote three books: Immunity in Infectious Diseases, The Nature of Man, and The Prolongation of Life: Optimistic Studies, the last of which, along with his studies into the potential life-lengthening properties of lactic acid bacteria (Lactobacillus delbrueckii subsp. bulgaricus), inspired Japanese scientist Minoru Shirota to begin investigating a causal relationship between bacteria and good intestinal health, which eventually led to the worldwide marketing of kefir and other fermented milk drinks, or probiotics.”  Meshnikov was so adamant that germs were not the cause of disease that he ate cultures of live Cholera to prove it.
  • DR. RUDOLF VIRCHOW:  Probably the most brilliant of all these men, Dr. Virchow (1821-1902) — a German / Prussian medical doctor — was also an, “anthropologist, pathologist, prehistorian, biologist, writer, editor, and politician, known for his advancement of public health. He is known as the founder of social medicine, veterinary pathology, and to his colleagues was known as the ‘Pope of Medicine’.  He was said to have published over 2,000 scientific articles and 1858’s Cellular Pathology is still regarded as the text that earned him the title of “Father of Modern Pathology”.  As an interesting side note to this issue; despite being an agnostic, he was an adamant ANTI-DARWINIST.  It was Virchow who said, “If I could live my life over again, I would devote it to proving that germs seek their natural habitat — diseased tissue — rather than being the cause of diseased tissue; i.e. mosquitoes seek the stagnant water, but do not cause the pool to become stagnant.

If you’ll go back and look through my posts on ANTIBIOTICS (particularly THIS ONE), you’ll quickly notice that I have shown you from the peer-reviewed literature that they are causally related to things like Asthma (HERE), Allergies (HERE), and various skin conditions, including Eczema.  And even though the studies we are discussing today do not deal with either of them, we also know that this class of drug is intimately related to health problems like OBESITY, DEPRESSION, and any number of other Chronic Inflammatory Degenerative Diseases.  This is because 80% of your Immune System resides in your Gut (HERE).  A failure to achieve and feed our bacterial diversity from early in life can mean a tougher row to hoe health-wise as we get older (HERE and HERE).

A brand new study from the medical journal Pediatrics (Allergy in Children in Hand Versus Machine Dishwashing) concluded that, “We found a lower prevalence of reported allergy in children aged 7 to 8 years from families who use hand dishwashing instead of machine dishwashing. This effect was further potentiated if they also ate fermented food or bought food directly from farms. We speculate that these lifestyle factors reduce allergy development via increased or more diverse microbial exposure, stimulating the immune system to develop in a more tolerant direction.”  That, my friend, is the Hygiene Hypothesis in action.  Exposure to germs — especially in children — leads to less chronic disease later in life.  Remember this because it is going to be very important in a moment.

According to the “Hygiene Hypothesis” article from Clinical and Experimental Immunology, The human gut is the natural niche for more than 1,000 different species [of bacteria]. Immediately after birth, the human gut is colonized with different strains of bacteria. This commensal microbiota is important in shaping the immune system, for other basic physiological functions, as well as for the integrity of the intestinal barrier.”  Let’s talk about some of the ‘meat’ that’s in these two sentences. 

  • MORE THAN A THOUSAND SPECIES OF BACTERIA:  Depending on who you read, the human Gut should contain somewhere between 500 and 2,000 different strains of bacteria.  This is known as the “MICROBIOME“.
  • TEN TIMES THE NUMBER OF BACTERIA IN YOUR MICROBIOME AS THERE ARE CELLS IN YOUR BODY:  Although I cut it out of the quote above because I’m not sure how to do exponential numbers on my computer (10 to the 14th power), your body contains 10 times as many bacteria as you have cells.  In other words, there’s a bunch of those little critters living in and on your body.
  • GUT COLONIZATION STARTS IMMEDIATELY AFTER BIRTH:  This is not technically true — or at least is shouldn’t be.  As long as you were not born via C-Section, colonization actually starts during the birth process (HERE).
  • THESE BACTERIA SHAPE YOUR IMMUNE SYSTEM:  We know from quotes found at the top of the page and any number of others I could have come up with had I wished, that an absence of bacteria in youth leads to a whole host of very chronic diseases later on (chiefly CHRONIC INFLAMMATORY DISEASES and AUTOIMMUNE DISEASES — the links contain lists of both).  Dr. Art Ayers, whom I quoted from at the top of the page, is a Ph.D researcher whose chief area of study is the link between GUT HEALTH and INFLAMMATION, and his website (Cooling Inflammation) is largely devoted to this fact. 
  • GUT BACTERIA ARE RESPONSIBLE FOR ANY NUMBER OF PHYSIOLOGICAL FUNCTIONS:  HERE are a few of them, but this list is growing by leaps and bounds with every new study published on the topic.
  • THE “INTEGRITY” OF THE INTESTINAL BARRIER IS CRITICAL FOR YOUR HEALTH:  A loss of ‘integrity’ in the intestinal barrier is commonly known as LEAKY GUT SYNDROME, although the medical community knows it by another name; Increased Intestinal Permeability.  A Leaky Gut is intimately linked to Chronic Systemic Inflammation, as well as almost every disease process you can name.  By the way, many of the same conditions that leave one with a Leaky Gut, can leave one with a “Leaky Brain”, where the “Blood / Brain Barrier” is similarly affected.
  • COMMENSAL BACTERIA ARE IMPORTANT:  The word “commensal” means, “an animal, plant, fungus, etc.) living with, on, or in another, without injury to either.”  I believe that we could probably refer to the relationship as ‘symbiotic’ (both organisms gain benefit from each other) rather than commensal.  When your ratio of good bacteria to bad bacteria is disrupted, you end up with something called DYSBIOSIS.  Interestingly enough, Dysbiosis can occur when you get your ratio of good bacteria to other good bacteria out of kilter as well (HERE).  This is why PROBIOTICS are never a long-term solution to Chronic Gut-Related Health Issues such as the Autoimmunity these authors keep mentioning (HERE is more information on this).


“Medicine has done a fantastic job in dealing with infectious disease (antibiotics, vaccinations, public health), and with trauma.  Unfortunately however, the “one disease, one cure” efficacy of antibiotics has blinded medicine into thinking a “magic bullet” awaits every disease and condition.  Looking at our success with degenerative disease like diabetes, autoimmunity, cancer, neuro-degeneration, and cardiovascular disease paints a bleak picture.”  Paleo proponent Robb Wolf from his article, Evidence Based Medicine: Fraud, Double Standards and Ignorance
What does all of this mean in practical terms?  In plain English, it means we are TOO CLEAN — both inside and out.  And it’s DESTROYING OUR COLLECTIVE MICROBIOME.  We take way too many Antibiotics (or drugs that have ANTIBIOTIC-LIKE EFFECTS), and are the recipients of way too many VACCINES that contain way too much bacteria-destroying MERCURY and ALUMINUM.  Follow along as I show you how the “Hygiene Hypothesis” sheds some light on this issue, leaving the waters a bit murkier than the dogmatic in the “mandatory vaccination” camp would have you believe.  

We are currently in the throes of a battle over the government’s right (or not, as I would argue) to force any number of vaccinations on you and your family — something I predicted would come about as the result of socialized medicine (HERE).  Unfortunately, people like myself, who believe in healthcare choice have been given the nearly-Satanic label of “anti-vaxxers”.   Forget labels for a moment.  What people should be paying attention to in this debate is what’s happening to our nation’s children.  If you go to any of the hundreds of “Vaccination Education” sites across the web (HERE are a few of the bigger ones), you can read the tragic stories and watch the heartbreaking videos of thousands upon thousands of children who were completely normal — until they had their vaccinations.  Mere coincidence?  That’s what the government would have you believe. 

But let’s put the conspiracy theories aside for a moment, ignore the acute vaccine reactions of the previous paragraph, and look at the evidence (even though most of us would have to agree that “EVIDENCE-BASED MEDICINE” is quite often a joke) that there could be a link between vaccinations and chronic health issues.  What sorts of health issues do children who react to vaccines almost always end up with?   They end up with that ugly triad of SIBO/IBS, IBD, and other “Gut Health” issues (HERE are some other examples).  They wind up with a potential plethora of AUTOIMMUNE DISEASES, which have absolutely EXPLODED in our society in recent decades.   And they end up with NEUROLOGICAL PROBLEMS of varying degrees of severity.   But should we be surprised?   Not according to the Hygiene Hypothesis.

If you go back and carefully re-read the quotes from the peer-reviewed literature at the top of the page, the diseases in the previous paragraph are just about what you might predict / expect as the result of our declaration of war on poverty and disease over five decades ago.  Despite spending $22,000,000,000,000 tax payer dollars on this fifty-year ‘war,’ America has fewer people working, more poverty, more people on government PROGRAMS, and more chronic illness — way more chronic illness. 

Don’t get me wrong; we’ve done a pretty good job of stamping out the acute childhood illnesses that everyone used to get (measles, mumps, chicken pox, WHOOPING COUGH, etc, etc, etc). Unfortunately, because of increasing ANTIBIOTIC RESISTANCE, wiping out acute bacterial infections like UPPER RESPIRATORY INFECTIONS, EAR INFECTIONS, and SINUS INFECTIONS is proving less effective every day.  But what has this “War on Disease” done for the health of American people? As per the Hygiene Hypothesis, we’ve simply traded one set of diseases for another.

Because our children are not growing up on farms, in gardens, playing outside, or getting any of the typical childhood diseases that everyone used to get (diseases that even pro-vaccine experts have shown “train” your Immune system); and because we are flooding their systems FROM BIRTH with Antibiotics, Vaccines (at least in the way they are administered today), and any number of NASTY DRUGS; and because on top of all this we are feeding them a steady diet of food that is of such low quality that we really cannot call it “food”, we are destroying their Guts, and thereby destroying their Immune Systems.  In doing so, we have traded the acute (short term) diseases mentioned in the last paragraph, for chronic (long-term) diseases that can be impossible — or at the very least, difficult and costly — to defeat. 

Let’s see how many of these chronic conditions we can rattle off in ten seconds.  Mark, set, go. CANCER, MS, EPILEPSY, AUTISM, RA, DJD, THYROID PROBLEMS, FIBROMYALGIA, SEXUAL DYSFUNCTION, NEUROPATHY, PARKINSON’S, ALZHEIMER’S, ANEMIA, GLUTEN SENSITIVITY, PR, MUPS, ADD/ADHD, DIABETES, SKIN PROBLEMS, and on and on and on and on and on and on….  All you have to do is do is pick one out of a hat, do a bit of research on it, and you’ll see that incidence has gone through the stratosphere.  And it’s all occurred as the American people (both children and adults) are being increasingly inundated with vaccines and antibiotics.

I would never for a moment try and convince you that vaccines are the only reason for this explosion of Chronic Conditions.  However, claiming that incredible amounts of Antibiotics given early and often, as well as today’s absurd Vaccination Schedules, plays no role in the chronic “sickening” of America, should make the astute observer at least stop and ponder. Especially if we understand and apply the Hygiene Hypothesis to the equation.  But real quickly, let me bring this to where the rubber meets the road — the debate over the Measles Vaccine.

I’ve followed Niel Miller and his “Think Twice” website for years (I also own one of his books that’s probably about 20 years old — back when there was no internet).  A couple weeks ago Miller wrote a short piece for The Age of Autism website called WHY PEOPLE CHOOSE NOT TO VACCINATE, concerning the effect of childhood infectious diseases (most particularly Measles) on the probability (it decreases it) of developing Cancer later in life.  In other words, vaccinating against Measles increases your chances of developing Cancer — something we also know about Antibiotics (HERE).  It’s a fascinating read that goes right along with today’s post, which is backed up with plenty of peer-reviewed literature.  He even gives us a great example of an INVISIBLE AND ABANDONED STUDY concerning the known problems with THIMEROSAL (Mercury) in vaccines and its relationship to Autism.


How does one go about healing the Gut?  Although there are any number of products that I use in my clinic, I firmly believe that most of this can and should be done dietarily.  And while I am a fan of Probiotics for the short haul, be aware that they are not a good solution over the long haul (HERE). Below are the things I have found helpful for healing a messed up Gut.

  • STOP BEING SO DAD-BLAMED CLEAN:  Remember back when people bathed maybe once a month?  I’m not suggesting we go back to that, but if you are using chemical cleaning products in your house or on your body, you may want to rethink some things (HERE).  Especially when you realize that most of these also happen to be XENOESTROGENS.   There are increasing numbers of articles on the world-wide web that describe people who “cure” chronic conditions (particularly SKIN CONDITIONS) simply by bathing less and without chemicals.
  • GO PALEO:  Instead of sitting here and giving you a whole list of dietary guidelines, I’ll give you only one — GO PALEO.  Going “Paleo” means that you get plenty of FIBER, but have no fear of DIETARY FAT.  Coconut Oil (especially the organic stuff that has a coconutty taste) is excellent for helping heal the Gut. The truth is, there are any number of foods, HERBS, products, etc, that can help in this process of healing the Gut.  Do due diligence as you research, but make the foundation of whatever you do food.
  • GET OUT IN THE GARDEN:  I’m a big fan of organic gardening and GETTING DIRTY (we went out and tilled and planted the patch for our greens, spinach, and lettuce, just before the snow barrage started three weeks ago).
  • HAVE MORE SEX:  If there’s a better way of swapping bacteria and upgrading your Microbiome’s diversity, I haven’t discovered it yet. 
  • FOLLOW THE EXPERTS:  If you want to get a handle fixing your Gut, there are any number of individuals I would read.  Make sure to start with Dr. Art Ayers.  Go to his FERMENTED VEGETABLES REPAIR GUT FLORA, and then read things from the people on his recommended sites.  I would never for a moment consider myself an expert (I just read a lot), but I did create a post for you to get started with getting your life back (HERE).
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