“Microbiome is defined as the collection of microbes or microorganisms that inhabit an environment, creating a sort of “mini-ecosystem”. Our human microbiome is made up of communities of symbiotic, commensal and pathogenic bacteria (along with fungi and viruses) all of which call our bodies home.

These communities exist in unique, complementary blends, and inhabit everything from our skin and genitals, to our mouths and eyes, and of course our intestines. The clusters of bacteria from different regions of the body are variously known as microbiota, including, for example, your skin microbiota, oral microbiota, vaginal mirobiota and gut microbiota, also known as “gut flora”.” 


What is the Microbiome?

Simply put it is the symbiotic community of microbes/cells from many sources that all work together to make us, “Us”.   Do you remember playing a game growing up naming body parts in a song?  The leg bone is connected to the hip bone…?  The concept was to learn how one part connects and affects another.   It also places an order to things; foot bone was never connected to the arm bone.  On a cellular level it is much the same with the variety of microbes that make our bodies function or not.

When the human body experiences “dis” ease of all kinds it is because something has happened to affect and affect the harmony or our cells.   We each have our own individual harmonious balance, our own defined combinations of cells.  No two the same, like snowflakes.  We each have our own genetic mix of our parental DNA (pre/post conception/inception) that makes us different from even our siblings.  Life experiences from birth to date are just as independent and individual.  What might be a mild emotional trauma on one child could be devastating to another, placing that child’s immune system in more jeopardy.   The cascade of biological fallout during an extreme stress reaction can have lasting effect on the microbiome and how ones gut deals with it. 

Before I go any further I think I will explain using the song as my impetus:  The gut neurons are connected to the brain neurons…as strange as that sounds there are actually more in the digestive track than your brain.

Most people are familiar with the term or concept of fight or flight reaction.  In its most simplistic terms it is the bodies’ response to fear/stress/necessity.  When a tiger wants to eat you, but he’s securely in a cage, our bodies naturally acknowledge the threat is possible but not likely.  So there might be some stress/fear response.  If the tiger was free and within reach the response would be increased to help us protect or get away from the tiger.  In each situation, your brain received a message and it sent a message to the rest of your body.   The body’s job is to respond in our best interest.  When there is little threat your body would send signals to body parts telling them to be ready, be on guard.   

There are a variety of different processes that happen with hormones like cortisol and neurotransmitters like NorEpinephrine that get released that travel from one neuron to another; the Vagus nerve being the main route used, until they get to their destination.   Turns out there are more neurons in the gut then in the brain and the majority of the immune system brains are also located down below.   Perhaps the old saying the way to a mans heart was through his stomach,  is partially accurate, it is at least a direct line to the brain and so much of how the body functions. 

 Now, if the tiger was going to eat you, that message would be faster, more urgent and hopefully sufficient to aid your escape.   Once safe your brain tells your body it is okay to rest and recover.   Hopefully that is the last of the tiger and your body can rebalance itself or return to normal.  

Not all tigers have strips.  Some children live with tigers and the switch is activated frequently.  If  balance is disrupted and healing or balancing is accomplished before balance is altered again, a new normal is established.  The order of things changes and when this happens it gives different cells more work and the normal pathway cells are left bored/restless/unproductive.   Meanwhile, the body has tried to adapt or find balance internally.   Reoccurring stress would not allow the cells the break/healing time they need to return to harmony.   During the healing process we need certain cells stronger than others; specific microbes have essential duties to help us eliminate bad/damaged/dead cells.   When not given enough time before needed again(new stress) the immune system starts to break down, creating ‘dis’ease.  Stress fallout makes the body weak and vulnerable to other diseases and from rogue cells trying to take over control.    

Much the same way there is a place for certain microbes and when they relocate themselves that’s when balance and functional break down.  They are normal parts of who we are, but because some cells were exhausted, it allows others to wander about unchecked.  When in appropriate location and numbers they help our bodies function, when the delicate balance is knocked off the once helpful cells become dysfunctional and harmful.

This figure depicts different microbes and other organisms that have been intimately associated with humans as commensals or potential pathogens.

Adapted from Glausiusz, Discover Magazine, June 2007, as well as images courtesy of the National Institutes of Health, National Cancer Institute, Centers for Disease Control, and Wikipedia

The numbers correspond to images of organisms and approximate anatomic locations where these organisms may reside on the human body.

1. Trichophyton and Epidermophyton are filamentous, parasitic microbes that cause athlete’s foot.   2. Vaginal microbiota, mostly Lactobacillus species secrete lactic acid and other antimicrobial compounds that prevent pathogen overgrowth.   3. More than 500 species of bacteria, weighing approximately 3.3 pounds in the average human adult, live inside the gastrointestinal tract.   4. More than 100 strains of human papillomavirus (HPV) can infect humans, causing a variety of warts from the common wart to plantar and flat warts.

5.Pediculus humanus capitis, the head louse, may have co-evolved with recent H. sapiens.

6. Oral Streptococcus species form biofilms that may be 300–500 cells in thickness on the surfaces of unbrushed teeth.   7. Demodex mites inhabit the follicles of the eyelashes and infest about 20 percent of people under the age of 20.   8. After initial infection with the varicella-zoster virus (chickenpox), the virus remains dormant in nerve ganglia and may cause disease due to re-activation later in life.   9. Approximately 1/12 of the human genome consists of DNA from fossil viruses that infected human ancestors millions of years ago.  10. Prevalent bacterial genera on the human skin include Streptococcus, Staphylococcus, and Corynebacterium.

The types and functions of certain bacteria and viral are only now being explored, so information is new and unfolding, however there is certainly lots of evidence to suggest that we need to revisit our approach to bugs.  Louis Pasteur started the germ theory and the ideal that bugs were bad and needing to be eliminated.  In following that approach our society has become increasingly offensive towards bacteria and viruses without understanding their role in our survival.  Processes to sterilize our environment have altered our worlds and in turn our bodies have been altered.  

Like many of life challenges, exposure to bacteria and friends help strengthen the host by training the immune system.  We have eliminated and are attempting to eliminate things that we have only started to understand their role.  The old dogma started by Pasteur continues to try to divide bugs into submission, looking at them as a threat instead of a learning tool for our microbiota.   Like learning to ride a bicycle, we all needed to fall and scrap a knee on the journey.  To risk nothing is to gain nothing, struggle creates strength.   Bugs challenge and educate our immune systems, their role is crucial for its development.  

It is actually the premise behind the vaccination rational.  That exposure to the virus/bacteria in small altered amounts helps the body develop immunity.  The concept is sound.  The vaccines are not.  They force nature on a man-made schedule.   They put toxic substances inside the vaccines that cause devastating damage to make the “bug” viable.  The Vaccine industry is not interested in increasing immunity they are only interested in profiting from the fear created by science paid for by them.   Vaccines are not a safe option when considering improving immunity, nature has already created the perfect system, we need only find our way back to it. 

     How do you help heal and support your microbiome?


Let's look at what alters it and how to stop the destruction first.  To do so I need to start at the moment of our conception, as we acquire our microbiome from our mothers.  Everything that happens to the woman carrying the fetus has an effect on its developing microbiome.  Like our genes, all the microbes passed in utero become bits and pieces of who we are.  A healthy diet, positive maternal experience, a pregnancy free of antibiotics/trauma/disease,  a natural delivery ( C-sections reduce essential exposure to cervical microbiome, decreasing the immunity transferred to baby) insert link here  all contribute to the best combination of needed microbes.  Each deviation interrupts the exchange needed to pass along a stable functional immunity.  This process also continues during the exchange of breast milk from mother to infant.   Formula can supplement the nutrients needed to keep the body functional, but most formulas are not complete enough to consider other needs like that of the immune system with the addition of pre/probiotics.  

Probiotics has become a more frequently used term in the last decade, prebiotics is a newer term.   Probiotics are the healthy bacteria the body requires to keep the system running smoothly. 

Many have been identified and are growing in popularity;  Lactobacillus acidophilus,Bifidobacterium longum, Lactobacillus Rhamnosus gg, etc.

 These can be found in a range of supplements, but are also found in fermented foods; like kefir, sauerkraut, kimchi.   Prebiotics are foods that support and feed those microbes we want running the show, bacteria like Lactobicilicus plantarum, an important boss bacteria that can manage the bugs beneath them on hierarchy of microbes.  

Each life experience either adds to, maintains or takes away from the balance of our individual microbiome.  Each of these aspects leave an imprint on our immunity, our bodies either are nurtured to balance or they remain off balance, skewing even further as each ‘experience’ pushes it further from center.   Accumulating effects of dysbiosis leads to ‘dis’ ease.

Diet (quality and diversity)

Exercise (physical wellbeing activities; dancing, walking, swimming, yoga, etc.)

Stress (mental, emotional, financial, interpersonal)

Use and/or exposure of environmental toxins (EMFs, Heavy Metals, GMOs, Chemtrials, etc.)


The variety of treatment intensity or duration is as diverse as the individuals with health/gut issues.  Problems left neglected for years can create what they call leaky gut, requiring a different diet than those who are related to a short course of antibiotics or experience that has altered their system.    It has been a two year journey since my 13 month multiple antibiotic/antimalarial/antimicrobial protocol, and I am still working on healing my gut, but feel 75% of the way there.   Like the damage, healing is accumulative.  No one approach works with everyone completely.  I feel it is important to use the right tools to solve the right problems, and not use a hammer or approach for every issue.    There are many  tools that can help heal, becoming informed about your options is the first step to recovery.