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The Science Behind the Anti-Antibacterial Movement

Let me first start with this fundamental key:
One Bizarre Theory Replaces Another
In the early 19th century, a few scientists extrapolated a new and bizarre theory: that disease was caused by tiny organisms and each illness had a corresponding germ.
After a few years of examining sterile cultures slides and a bit of playing around with vaccines, these scientists were able to convince the world that their germ theory of disease was, indeed, true.
This outlook was convenient (and perhaps, perfectly poised to take root at this time in history during America’s industrialization) because it was methodical and specialized in its approach to understanding both the cause and treatment of disease. It allowed us to breakdown, the cause of an ailment to one small, fundamental unit which provided us a simpler way to understand a disease (ex. one germ for each disease). [*]
A treatment was then established based on this approach allowing generalized (‘one size fits all’) and massive quantities to be produced at an industrious scale. This approach was able to keep cost and time at a minimum while treating an increasing population. [*]
However, this mechanical approach to health is now diminishing…
Some biologists have even begun to speculate a new theory (I imagine just as absurd as germ theory was originally thought of back in the early 19th century): that humans are not individual entities, but rather complete ecosystems dependent on billions (100 trillion +) of bacteria and viruses (quadrillion +) to establish, maintain and actively influence health.[*][*]
Much of this information would have Pasteur rolling over in his grave…. who would think that viruses would be shown to help keep people disease free?[*][*]

Enter the field of Microbiomics.
If you have not heard of the human microbiome or microbiomics then, with great reverence, let me provide some mind blowing information for you to digest (no pun intended).

Microbiomics (….and why it’s absolutely mind blowing)
The ‘specific causes’ of diseases that revolutionized medicine a century ago is going through a conceptual evolution (time to get on board) – the way scientists think about disease and normal physiology is transforming. [*]
When I was in 7th grade, I remember the Human Genome Project being the next biggest and greatest thing science had going on…. now that it has been completed, however, a new phase has emerged: the Human Microbiome Project (HMP)….and it is changing everything. [*]
The HMP is an initiative to sequence the genomes of all the microbiological flora for a variety of body sites which play a “vital and interactive role” with our human DNA, immunity and disease. As bacteria, microbes and viruses in our bodies are modified under environmental pressure (ex. antibiotics and cesarean section birth), so is the regulation and replication of our genes (yes, our DNA). The two are intimately connected. [*] 

Far from being the ‘master molecule’ in our physiology, our DNA is demoted to simply another set of cellular genomes jostling for influence within us, reacting to and being regulated by, a set of microbial genomes that outnumber our own 10 to 1. [*]
Try to think of the bacteria, microbes and viruses that reside in our bodies as it’s own sensory motor organ which reacts much like our own nervous or immune system.[*]
Our microbiome encodes physiological traits that we were able to bypass in evolution; for example, the ability to “harvest certain nutrients and energy from food that would otherwise be lost because we lack the necessary digestive enzymes”. [*]
The Death of Germ Theory
The major conceptual doctrine of Pasteur’s germ theory is the role of causal pathogenic agents in disease. For example, diseases are separable from the patient and bacteria or virus in a human host equals disease. [*]
Even before the study of Microbiomics, it was clear that many individuals harbor dangerous bacteria (even at in large quantities) and suffer no ill effects.[*]
Certain diseases, such as herpes virus infection, which seem to fit neatly in the germ theory framework began to reveal a beneficial relationship that conferred immune advantages:


After clearance of acute infection, latent herpesvirus confers resistance to bacterial infection. To be specific, protection correlated with 100-fold reduction in bacterial burden in the spleen and liver.

2007 Nature [*]

“We now demonstrate that herpesvirus infection triggers systemic, PROFOUND IMMUNE MODULATION, with the potential to alter significantly the kinetics and nature of host response to foreign antigens.

Thus, whereas the immune evasion capabilities and lifelong persistence of herpesviruses are commonly viewed as solely pathogenic, our data suggest that latency is a SYMBIOTIC RELATIONSHIP with immune benefits for the host.”
So long we’ve swallowed the metaphor of an endless “war” on infectious diseases which involved a search for the microbial ‘cause’ of each and every disease  (of course, followed by the anti-microbial cure). This ideal has served its purpose and now we can no longer allow it to be our sole guide in medicine. [*]


“A new paradigm is needed that incorporates a more realistic and detailed picture of the dynamic interaction among and between host organisms and their diverse populations of microbes, only a fraction of which act as pathogens.” (Forum on Microbial Threats, 2006) [*]
A New Understanding of Disease


Quick Personal Backstory: My recent “antibiotic debacle”

About a month ago, my two year old was sent home from daycare for pink eye. I was expected to get a prescription for antibiotics for her to return. I was hesitant to say the least, my daughter has never received antibiotics and I wasn’t certain that all cases of conjunctivitis were caused by a bacteria. When we visited the nurse, she instructed me that only bacteria cause pink eye and my concern on delaying antibiotics was not sound. She went ahead and prescribed antibiotic eye drops.


Within 10 minutes of doing my own research once I returned home, I found this to be completely untrue. In fact, the majority of conjunctivitis cases are caused by a virus (NOT BACTERIA). Not to mention, the data very clearly illustrates that antibiotics for conjunctivitis is a complete over kill and often times does more harm than good.[*][*]

I made a deal with my husband, let’s wait one day before we administer the medication. We waited and her condition improved on its own. I suspect if we used the antibiotics, we would attribute her recovery to the drugs – luckily, we waited.

Medication we use via the ocular route (via eye drops) is just as important to research as ingested or injected drugs. Eye drop medication enters the bloodstream via mucous membranes lining the surface of the eye, the tear drainage system, and the nose. Once in the bloodstream, the medication can cause side effects in other parts of the body, including slow heart rate, dizziness and headaches.[*]


The outdated, traditional interpretation of disease correlates health as a matter of being “clean” and in order to obtain and maintain health we are advised to completely obliterate anything that’s not a human cell. [*]
Now, of course, microbiomics does not suggest health is all rainbows, ponies and singing kumbayah - our bacteria ecosystem can (and does) go awry. Certain species within us can overpopulate, resources decline, diversity is reduced (via antibiotics) and the interdependent processes can collapse.[*]
A new metaphor replaces the old – an understanding of ‘balance’ and ‘harmony’ supersedes the traditional thought of specific causation (one germ for each disease). Rather, human health is a matter of “having ones physiological process and predispositions aligned to promote homeostasis”. [*]

“It may turn out that diseases caused by microbial pathogens are best seen not so much as an invasion by a hostile organism, but rather as a kind of holistic dysfunction of the microbiome.” [*]

Simply revolutionary.
The greatest benefit to the health and wellness of a human body is not sterility, but rather “on maintenance of the symbiotic relationship between the host and the intestinal microbiotia”.[*]
This model, based on the latest science has to offer, suggests there are no diseases that exist separate from ourselves (ex. viruses floating around getting people sick) – only sick people whose processes within the body are not in balance. Recovering our health, therefor, is a matter of controlling the forces that influence the homeostasis within us.  Our health becomes a matter of our own responsibility. [*]
Antibiotics –Use with Extreme Caution (better yet, don’t use at all)
Our internal bacteria (particularly those located in the intestines) are essential to our health and “play an active role in nutrition, development, metabolism, pathogen resistance, and regulation of immune responses”. Antibiotic use, even for a short duration, has been “shown to disrupt these coevolved interactions leading to acute or chronic disease”.[*]
For every one human cell, there resides 10 bacteria cells within the human body (with viral particles expected to be a hundred times greater). Science, research and data continue to reaffirm that they play an active role in not only maintaining our normal physiology but also protecting us from: [*][*][*]
-respiratory infections
-acute intestinal infections
-type II diabetes
-cardiovascular diseases
-several forms of cancer

In addition to being numerous, our microbes are also “enormously varied” – with over 1,000 bacterial species residing within us. [*]

In fact, all plants and animals can be considered superorganisms; composed of a variety of species – bacterial and viral. [*] 

This variation in species is critical to health and is why antibiotics have been shown (repeatedly) to be permanently harmful (especially to children).

2007 The ISME Journal, Multidisciplinary Journal of Microbial Ecology

Long-term and persistent impact on human intestinal microbiota is a direct response from antibiotic exposure which never return to its original composition (during the 2 years of the study period). [*]
Antibiotics use in Children and Immune-mediated Disease
Antibiotics hold the possibility to be useful in some cases, but must be used with caution to protect long term health.
If you take anything away from reading this collection of data, please:

Several studies of antibiotic treatment has shown that the gut microbiota is profoundly and persistently altered by broad-spectrum antibiotic therapy. Data has shown that bacteria communities do not return to their initial state even after antibiotic treatment is withdrawn. [*]
During infancy and childhood, appropriate microbial stimulation and colonization is required for the development of a healthy, functional immune system. [*]
It is “well known that early life events occurring during critical windows of immune development can have long-term impact on immune-mediated disease. Antibiotic use in children has been shown, with significance, to increase such diseases as: diabetes, inflammatory bowel disease, asthma (requiring the use of inhaled corticosteroids), eczema. [*][*][*][*][*][*][*][*][*]
Antibiotic use must be critically evaluated, not just for ourselves but especially for children.  Each time we administer antibiotic medication it results in a ten-fold reduction in the amount of beneficial intestinal bacterial present. [*] 
With the use of antibiotic drugs,significant alternations are seen in the expression of pro-inflammatory cytokines” and Th1 immune maturation which has profound effects on our immune system. [*][*]
Take Care of Your Health by Giving Your Microbiome Some Love

My preference is to eat and drink foods that promote a healthy flora (versus relying on supplements) while being mindful of the lifestyle choices that can hurt me (moderation is key, of course)….
Focus on Prebiotics
-Foods with prebiotics are garlic, onions, almonds and asparagus.
-Foods with the fiber inulin promote beneficial flora: bananas, high-fiber veggies like peas and beans.
Avoid Sugar (especially artificial sugar)
-Sugar and starch promote the growth of harmful bacteria in the body
-Yogurt may have probiotics, but they are often LOADED with sugar. Be careful!
Eat more Fermented Foods (just a quarter to a half cup per day will do ‘ya)
-Homemade sauerkraut, kefir (watch the sugar here too), kombucha, miso soup
-Smoking, caffeine, alcohol, consuming heavily-processed foods

It may go completely against what we all have been taught in high school biology class, to think that bacteria and viruses make our immune system function better, but the science is becoming evident: A healthy, mature immune system depends on the constant intervention of beneficial bacteria.[*]
Humans (all mammals, in fact) have co-evolved over millions of years to establish a dynamic, complex check-&-balance system with our microbiota. It shouldn’t be all that surprising that our immune system (particularly our mucosal immune system) has developed an intricate connection that mediates the balance between health and disease.[*][*]

Both innate and adaptive immune function has evolved to require microbial interactions during their development. [*]

The microbiota provides critical signals that promote maturation of immune cells and tissues, leading to protection from infections by pathogens. [*]
We must become more aware of our symbiotic relationship with the bacteria within the body (especially our children’s). This starts with not stereotyping all bacteria as bad. In fact, although a few may be problematic, these account for far less than 1% that exist in our body.[*]

Take care of your ecosystem – it sure takes care of you!


You can't learn everything from the laboratory, that's what he used to say. The whole is more than the sum of its parts, he told us. The whole behaves differently from the parts, and has different properties. That's what he taught us, and he was right. It's out of fashion to say these days, when we spend our time scrutinizing the interactions of eukaryotic microbes, but it's true, nevertheless. It's still true.

(M. Drabble, The Sea Lady, 140–1)


  1. We obsess too much about germs... it's called soap people.

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