The human microbiome – acute and chronic illness

Earlier this month, the New York Times published Microbes, a love story, in time for Valentine’s Day.  Yes, your microbes are what make you sexy… and brainy, and healthy, and what have you.  After all, inside our own bodies we are outnumbered ten to one (in the intestines alone there are 500-1000 different species of bacteria, and ten times as many living in it as human cells in the entire body).  This micro-biologic life in and on the human body is called the MICROBIOME.  The understanding of the microbiome is going mainstream and challenging the medical community to rethink many assumptions of health and illness, but, not nearly fast enough.  Doctors still prescribe broad-spectrum antibiotics or other biocides all too often, and all too soon!  (See my post on biocides.)  On the other hand, probiotics have taken the non-conventional health world by storm, and dirt is the new superfood!

But, let’s understand this human microbiome first.  This mass of micro-organisms collectively weighing over 3 lbs. forms a continuous living shield, or bio-film, of nonhuman tissue that covers every square inch of skin, colonizes every orifice and lines most of the respiratory, gastrointestinal and urogenital tracts.  It plays a crucial role in almost every aspect of life including immunity, digestion, respiration, social interaction, sexual attraction, bonding, and reproduction.  Survival without it as NASA scientists have determined is nearly impossible.  Incidentally, it was the scientists working at NASA who first discovered the effects of depleting the microbiome while studying the results of long journeys into space in a bacteria poor environment.  Later on, the National Institute of Health (NIH) delved deep into it using genetic sequencing technology, and called it the Human Microbiome Project (HMP).  Amazingly, just as the human organism is completely dependent on the microbiome for growth and development and survival, the microbiome is also completely dependent on the human organism for its survival.  THIS IS TRUE SYMBIOSIS.  The more diverse the bacterial spectrums present in the human microbiome, the more stable and healthy the resulting super-organism.  Germophobes, take heed!  The erstwhile antibiotic premise that germs are bad and that impeccable hygiene is the cornerstone of human health is not correct anymore.  This emerging reality shifts away from the fear-based relationship one has with the environment and instead informs us to nurture and educate the complex microbiota within.  A self-sufficient, successfully operating ecosystem then becomes perfectly capable of dealing with pathogenic microbes (the “bad guys”) on its own, as and when the need arises.

It all starts at birth, as the baby makes its way down the birth canal and inoculates itself with a heavy dose of the mother’s vaginal flora.  Thereafter, the infant is a sponge for new bacteria and viruses, getting the nourishment and protection it needs mostly from mother’s milk while it figures out what is “self” and “friends of self” and what is not.  This process impacts all levels of development.  The nervous system, the limbic system, the immune system, the digestive and respiratory systems, and the sexual and reproductive systems all develop based on complex interactions with the microbiome.  Reduced biological exposure and microbiome diversity, particularly during early infancy is associated with significantly increased risk of developing immune related allergic and inflammatory conditions in childhood, adolescence and adulthood.  Cesarean section, formula feeding and overly hygienic conditions around these events dramatically reduce and limit exposure and accumulation of normal bacterial flora from the mother.   The earlier in life that bacterial exposure takes place the greater likelihood that immune system maturity and tolerance to these organisms will develop.  After this crucial neonatal time period passes, newly introduced organisms are more likely to trigger an oppositional immune reaction, or an infection.  Psychological trauma is another major factor known to influence and alter the gut microbiota.  Stress-induced alteration of the gut microbiota early in life may elicit long-lasting immune consequences and increase the risk of developing stress-related disorders later in life.  Throughout every activity for the rest of life, we are exposed to multitudes of bacteria, viruses, fungi and parasites and the overwhelming majority of these organisms enter long-term complex relationships with the body, ultimately helping it survive in the environment.

Role of Acute Illness and the Immune System

Your microbiome is influenced by where you live, how much time you spend outdoors, people you work and live with, your diet, traumas you have experienced, etc..  The composition also changes at different points in life: adolescence, pregnancy, old age, etc.. Traveling abroad will often make people sick due to the change in environment, food, water, etc.  Seen through the lens of environmental science, acute infections are part of the normal negotiation process between the immune system and the microbiome, in fact they may even be considered essential training processes. Childhood infectious diseases were once considered necessary rites of passage for children.  Acute infections can result from first-time encounters between bacteria (or viruses) that the immune system has never seen before, but they can also result from changes in the balance of organisms in the microbiome, for example from the use of an antibiotic.  When that happens, some organisms that were previously held in check, may now overgrow and become invasive, triggering an immune compensatory response (such as the occurrence of yeast infections after antibiotics).  To reestablish balance, the immune system and the microbiome must adjust.

The first response to an acute infection is usually an acute inflammation such as fever which is just one of the tools used by the immune system to help it resolve the infection more efficiently by inhibiting the pathogens from multiplying.  Rushing to treat with anti-pyretic, anti-inflammatory, and steroidal medicines that are used to reduce this inflammation only end up impairing the immune system, making it impossible to fully resolve the infection.  The person may “feel better” in the short term due to the suppression of the inflammation.  But, what happens to that pathogen that has infiltrated the microbiome?  Well, then the recommendations for the antimicrobials follow.  Treatments using antibiotics, antivirals, antifungals, etc.  then proceed to damage the microbiome and further prevent the immune system from negotiating with the microbiome to incorporate and deal with the pathogen effectively.  Inevitably, these interventions prevent both the immune system and the microbiome from maturing. Permanent or lasting immunity cannot result under these circumstances, and the result – RECURRING infections.  Autoimmune conditions potentially also develop when the immune system is thus prevented from reacting to foreign antigens and ends up eventually attacking antigens within the body.

In reality, only the combined activity of both the immune system and the microbiome results in a healthy response.  This article, Microbiota talks cholera out of the gut, describes a study that provides an example of how gut resident bacteria can protect the host by reducing the pathogenicity of invading organisms, rather than simply competing for resources.  Acute infections thus are inevitable events in immune system development and diversification of the microbiome.
A quick side note: the systematic eradication of many childhood infectious illnesses through routine vaccination also prevents the immune system from experiencing the routine challenges of acute illness that helps it mature and provide lifetime immunity along the way, and therefore, deserves a re-evaluation.  Bacteria and viruses are intelligent life-forms and they have a directive to survive, they are going to mutate if necessary, as we are seeing with “superbugs”.  True herd immunity is this learning and negotiation and this ability to accommodate each other in a way that creates greater health in us and maintains the circulation of these bacteria and viruses within the society.  Support the process, not suppress it.  Most acutes can be safely, effectively and efficiently treated with homeopathy, gemmotherapy, tissue salts, the right foods and herbs, etc. without destroying the microbiome!

Let me re-emphasize that the stability of one’s health is directly related to the diversity of the microbiome and the integration of these communities of microbiologic life in conjunction with the host, that is the human body.  Microbiome damage and lack of diversity have both been associated with the tendency to develop many physical and mental illnesses. More and more medical conditions have been linked to either the failed diversity or the damaged ecology of the microbiome.  Disruption of these highly evolved and finely tuned bacterial relationships in the microbiome leads to failures of immune regulation, modulation, maturation, and tolerance.  When these functions are interrupted, the stage is set for the development of a host of CHRONIC health problems.

Chronic Inflammatory, Allergic, and Autoimmune Illness

Nearly half of all Americans have been diagnosed with at least one chronic health condition and at the current rate of growth, this number is expected to increase by another 42% over the next few years.  The incidence of chronic illness in children has also more than tripled since 1960 with asthma, learning disabilities, ADHD, and autism to name a few.  There is a virtual epidemic of chronic illness with nearly 70% of all deaths attributable to one or more of these conditions.  Unless we understand, and get on board with the importance and role of the microbiome, unfortunately that’s the reality we will have to be dealing with for a while to come, as most disturbances of the microbiome are iatrogenic: the result of well intentioned, but misguided medical interventions.  We have literally traded in epidemics of acute diseases for epidemics of chronic inflammatory diseases.  One of the most important lessons of the HMP is that humans must learn to live within the world of microbiology. “We’ve just spent the better part of a century doing our unwitting best to wreck the human-associated microbiota with a multifronted war on bacteria and a diet notably detrimental to its well-being.”

From experience with working with a wide array of chronic ailments in my homeopathic practice, I have observed the workings of the human microbiome first hand through remedy actions.  A fever, an acute incidence of diarrhea or a cold, and temporary aggravation of certain symptoms are some of the common reactions to well-chosen constitutional remedies that are prescribed for ANY chronic condition after a thorough intake and analysis of the person’s life history.  Followed by wellness and resolution of the chronic symptoms, immediately or gradually improving layer by layer depending on the person’s vitality and level of suppression that the microbiome has undergone in its lifetime.  Although the mechanism behind homeopathy is not well understood by many, neither was the human microbiome until it was studied with the most advanced scientific machinery available.  Homeopathy is a truly remarkable modality that synchronizes the actions of the body with the microbiome to promote natural healing and immune maturation.

According to researchers at California’s Institute of Technology (Caltech):
“A healthy, mature immune system depends on the constant intervention of beneficial bacteria. ‘It goes against dogma to think that bacteria would make our immune systems function better, … But the picture is getting very clear: the driving force behind the features of the immune system are commensals.'” – J. Ackerman, The Ultimate Social Network.

Needless to say, it behooves us to choose healthcare and treatments that work in conjunction with the microbiome, not against it.

Further reading:
The Human Microbiome Project (HMP)
The effect of infections on susceptibility to autoimmune and allergic diseases
Harvard study shows how antibiotics disrupt babies microbiomes
Aliens Inside Us: A (Mostly Friendly) Bacterial Nation
An Epidemic of Absence. A new way of understanding allergies and autoimmune diseases
Commensal bacteria control cancer response to therapy by modulating the tumor microenvironment
Microbial Manifesto: The Global Push to Understand the Microbiome
Postraumatic Stress Disorder: Does the Gut Microbiome Hold the Key?

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