Carolina Holistic Medicine | Functional & Alternative Medicine | Charleston, SC

Living with microbes

Living with microbes: A need for a paradigm shift

Living with microbes: A need for a paradigm shift

JP Saleeby, MD


A new paradigm and way of thinking is emerging in the post-antibiotic era.  The driving force behind this new approach is the failures of antibiotic therapy in the arena of infectious disease with mounting resistance, persister cells and the lack of emerging new antibiotics by the pharmaceutical industry.  Antibiotic resistance even with conservative antibiotic use and antimicrobial stewardship programs has not mitigated the problem we are facing today.  The viral pandemic of the 2020-2022 has revealed many holes in the ‘’old way of thinking’’ about infectious diseases.  Through the prism we now see the world things must change and at a fundamental level.

The old-school way of dealing with infections has been to annihilate them.  This goes back to the early days of the discovery of the germ-theory.  When antimicrobials were first discovered by Professor Alexander Fleming in 1928 when he noted that a penicillin derived from mold killed bacteria at his lab at St. Mary’s Hospital in London the world responded by searching for more.  The theory at the time was that abnormal microbes colonizing the body caused disease and that they should be eradicated.  This held out well until the development of microbial resistance in the past two decades, by the constant bombardment of microbes by synthetic antibiotics.  The microbes were smarter than we gave them credit.  For millions of years microbes developed ways to fight toxins and invading viruses by elaborate defense mechanisms we are not just beginning to understand.  The failures we now see with older antibiotics and their inability to kill as effectively; our immune system not properly adapting to emerging vaccines to irradicate bacterial and viral illnesses; and the clinical observations of how to deal with difficult microbes such as Borrelia, Babesia and some viruses like the Epstein Barr virus (EBV) and the emerging novel corona virus (SARS-coV2) and others necessitate change.  

The new paradigm is not to think of eradication, but rather to think in terms of balance and co-existence to the point that microorganisms (viruses, bacteria, spirochetes and parasites) are taken down to a point where our immune system (primary defense mechanism either innate or adaptive) can keep them in check and not remain in a pathological or harmful way to the host organism.

After years of treating resistant chronic Lyme disease (CLD) patients the realization is that cure is impossible and the best we can hope for is a remission state.  Biofilms, persister cells, drug resistance, drug ineffectiveness, rapidly mutating and smart microbes have all played a part in lingering disease due to many different microorganisms.  Collateral damage caused by powerful synthetic drugs in efforts to fight infections has taken a toll on patients.  Do not get me wrong, at times of severe infections and sepsis, these powerful agents will save lives.  The long-term use and mis-use of antibiotics (for example in viral illness) can be quite harmful to humans.

How to deal with acute and chronic infections?  In the setting of a mild acute illness alternatives to antimicrobial drugs may be as simple as the plethora of natural agents we use in herbal medicine.  Effective and less collateral damage (untoward effect) such as dysbiosis or corruption of the normal oral, gut and skin microbiome can be achieved.  We also would see less emerging antibiotic resistant opportunistic microbes emerging during treatment.  In the more severe life-threatening infections that is where more powerful drugs may have a part but for limited use and time.  For the chronic illnesses such as Lyme disease, EBV, CMV, HHV6, Mycoplasma, H. pylori, yeast overgrowths and similarly viral burdens we are now seeing with the coronavirus SARS-coV2 with Long-COVID and post COVID syndromes there must be another better way.

The better way is a shift in the paradigm of infectious disease away from eradication to symbiosis.  Achieving a balance where good microbes keep bad microbes in check in is a simplistic way to imagining this model.  How is this achieved?  The trick is to use more natural remedies to force a balance and reclaim a health microbiome.  The microbiome is not limited to the gut, it is also not limited to bacteria.  We have to think of things in a more holistic way.  The oral, intestinal, dermatological tissues are involved as well as prokaryotic bacteria, spirochetes, viruses and parasites classified as protozoa, helminths and ectoparasites.

My practice as a Lyme Literate Medical Doctor (LLMD) has taught me much about symbiosis and balance.  Chronic infections are proinflammatory, disrupt the delicate hypothalamic-pituitary-adrenal axis (HPA-axis) hormonal system and can lead to other illnesses and disorders such as autoimmunity.  So, I depart from the distraction my basic medical education instilled in me to ‘’kill’’ the organism responsible for the ‘dis-ease’ and now focus on how to reach homeostasis and keeping humans in a symbiotic relationship with its microorganisms.

Much like the Quercus virginiana (live oak) tree has a symbiotic co-existence with the Tilladsia usneoides (Spanish moss) and Pleopeltis polypodioides (resurrection fern) organisms where they live in harmony without each suffering the other’s presence.  We should take a life lesson from this relationship and many others found in nature when we pursue a cure for an ailment.

Next article will cover Phages:  The war between viruses and bacteria and how the human race can benefit.


Yusuf (JP) Saleeby, MD is founder and director of the Carolina Holistic Medicine centers in SC and professor of medicine at the Priority Health Academy.

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