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September 16.2022
16 Minutes Read

The Human Microbiome

The Human Microbiome By Teresa Ducoffe

This information is simply revolutionary and changes everything about health and hope, whether you’re looking to regain your health or simply maintain. There’s too much illness and disease in our world and our current medical model is not serving us and in fact, it’s failing us with chronic disease.

This information focuses on your gut microbiome, the complex colonies of microbial life within us. Think of it as a newly discovered organ in your body, one that inter-connects with all other organs and regulates our immunity, overall health, and mental state. This is about understanding and working with your microbiome. If you have a serious health problem, chronic illness and diseases like autoimmunity, obesity, diabetes, IBS, autism, Parkinson’s, fatigue, Lyme’s, and cancer the list goes on possible hope has arrived with fixing the microbiome. It’s our very own internal ecosystem of beneficial bacteria, fungi, and viruses that help fight disease and keep us healthy.

Because your health is everything, learning about your microbiome may be the most important exercise of your life. It’s the hottest topic of the day, “ The Gut Microbiome ”.

What builds or destroys good bacteria? How do we create a healing process that begins in the microbiome, spreads to your entire body, and impacts your entire life? Because health is wealth and starts at the very core, the microbiome.

The medical community has long viewed microbes as something to destroy. Why is that? Our understanding of microbes was born in illness and searching for cures for things like measles, influenza, and small pox. The idea that microbes are bad and hold only one role in our echo system is not only a misunderstanding, it’s actually dangerous to us as individuals and as a species.

Some say the famous French scientist, Louis Pasteur (1822-1895) the father of the germ theory, said on his death bed, “ The Microbe is Nothing.

The Terrain is Everything ”. The medical community has become more aware that microbes keep us healthy and control our ability to ward off disease, run digestion, and immunity. Nurturing healthy bacteria is important in this new millennium. New generations of medicines are being developed that kill only the bad bacteria and leave the good bacteria alone. Bacteria’s are being explored to be used as carrying agents to cure illnesses like cancer.

How has your gut been nurtured in the last 30-40 years? What’s the environment of your gut like? Everyone’s gut is unique because of what we eat. Did you know everything you eat has an effect on the microbiome? The most important thing you can do is fix your microbiome.

What is the gut microbiome? It refers to a community of microbial life that live in and on our bodies – the gut, skin, organs, and even in the blood.

Every organ has a microbiome of its own. They are so different that you could have 70% different microbes on the right and left hand. We have between 2-6 pounds of microbiome in our gut.  They modulate our immune system; they are us. They are our fungal organisms, bacteria, viruses, and little one-cell protozoa. So, viruses and bacteria are not all bad for us. They're the reason we breathe oxygen and why plants breathe carbon dioxide. They are in every cell of the body the most important one being the mitochondria, which uses oxygen available within the cell to convert chemical energy from food in the cell to energy in a form usable to the host cell. We are one big symbiose, which is defined as an interaction between two different organisms living in close physical association, typically to the advantage of both, in big communities. When these communities get out of balance, we get an illness like autoimmunity, diabetes, obesity, mental health issues, and cancers.

You have thousands of organisms living within the digestive tract that have their own genetics and genes, different from our genes.

One gram of stool has more bacteria in it than there are stars in the known universe. There are 100 trillion microscopic species in the entire human body - more than a billion in just one drop of fluid in the colon alone. That is incredibly profound!    You might ask are most of those friendly or are they hostel to the body? Normally, in a healthy body very few are hostel. It might be 1000 out of 10,000 that surrounds the bad bacteria holding it in check.

If hostile bacteria get out of check your immune system sees those bacteria and their debris, because they die and release their contents to the gut mucosa, as hostile and our immune system calls out the “guards” and starts doing battle.

So, the gut and the microbiome are a major contributor in how our immune system is working and is a very important part of this emerging story.

Bacteria, single-celled organisms located at every corner of the Earth and in our own gut, make up our microbiome. Bacteria, unlike humans, are prokaryotes, which make up the majority of creatures on Earth. Within our own body, bacteria release chemicals that work to convert compounds and materials that we cannot digest on our own. We’re now just beginning to understand the vast complexity of our relationship with the bacteria in our bodies and guts.

This gives us a place to intervene to make the environment gut-friendly. Do you see how important your microbiome is? When you think about being healthy or eating healthy have you directly tied that outcome to having healthy communities in your microbiome? It’s important and many of us have a lot of microbiome to repair from the antibiotics and other environmental triggers we have been exposed to but the body is forgiving.

You can restore your microbiome and as you heal your microbiome, watch for changes in your mood, your attitude, and your opinions.

Doctors are finding that the body is an extraordinarily complex ecosystem with a collection of a hundred billion cells with more bacterial, viral fungal cells than human cells.

What is microbiome and what role does it play in helping disease? Mark Hyman, MD, Director of Cleveland Clinic Center for Functional Medicine says for most of medical history we have basically ignored the gut flora and the gut microbiome which is this host of bacteria. Elie Metchnikoff in the 1900’s coined the work Dysbiosis, which is the imbalance in our gut microbiome and how it might be related to disease. There are 10 times as many bacterial cells as your own cells. There are 100 times as much bacterial DNA than your own DNA.

Literally, you’re only about 1% human . Those bugs aren’t just waste they’re interacting with your biology every minute. They control levels of information such as the permeability of your gut, or leaky gut, brain chemistry, hormones, metabolism, and nutrient levels. They even control what you absorb and don’t absorb. Microbiome is the most important thing in our life that is controlling our health and we’ve completely ignored them. We are just learning how to diagnose it, treat it, or help people fix the microbiome in their gut.

Claire Fraser, PhD, Director Institute Genome Sciences, Univ. of MD for the past 12 years has focused on understanding the structure and function of all the microorganisms that live with us in our GI tract. We know that these microbes that share our space with us from birth to death are critically important in health and disease. Our studies are figuring out how they contribute, and to understand what a healthy microbiome is and to leverage that to improve overall health and minimize disease.

Dr. Zach Bush, Endocrinologist, Internist, Palliative Care, discovered that that right before an autoimmune disease, the microbiome collapses. There’s a sudden drop in microbiome diversity and then you have an autoimmune disease. Another sudden drop and then you have a stroke. That’s the general concept. But this observation starts to answer how the diversity of a microbiome translates into health.

Dr. Martin Blaser, Dir. Human Microbiome Program at NYU, thinks we will find that the microbiome is important in just about all chronic diseases that have risen dramatically in recent decades. Since World War II and the widespread use of antibiotics, a whole group of diseases have become much more common and pervasive like Celiac and inflammatory bowel disease, diabetes, obesity, cancer and autism to name a few. His theory is the changed microbiome and loss of diversity are underlying all of it.

Dr. Zach Bush believes if we could teach our children how to interact with the soil again, take care of it, interact with the microbiome and let it take care of us, we’ll decrease our disease process, our disability and increase our productivity and creativity.

Many experts are saying that we’ve entered the decade of the gut microbiome. Thousands of research papers have been published on the subject in recent years. There isn’t a field in medicine that hasn’t been informed by gut microbiome studies. With an evidence-based model, you have to consider gut diversity, diet nutrition, lifestyle, and the various variables that impact the bacteria in our gut.

According to Dr. Claire Fraser, not only are we a system of multiple organs and tissues that work together but living in us and on us. It is this incredibly complex ecosystem of microbes that play an important role in health and disease by interacting with each other and interacting with us as a host. We know that microbiome contributes in so many ways that we can no longer ignore the fact that when we think about approaching a disease, diagnosis, and treatment we have to consider the impact and implications of the microbiome.

Sarkis Mazmanian, PhD of Caltech, in the gut-brain connection doctors, look at how events in the gut, specifically microbial events, affect everything from mood and emotion to neurodegeneration. Whether there are specific bacteria that either promote or protect against diseases. We have a rich nervous system, not just in our brain, but in our intestines. So, the entire nervous system has actually been studied for many decades and these two nervous systems talk to each other. The nerves in the gut communicate with the brain through the vagus nerve directly in terms of neuronal connections, but also through soluble molecules , molecules that are secreted in the gut and then they activate the enteric nervous system as well as the central nervous system. We discovered this connection is how the gut microbiome regulates the activity level of our immune system. So, when we look at chronic inflammatory diseases, they’re all caused by a hyperactive immune system.

Rheumatoid arthritis is probably the most well-known disease that’s caused by simply a hyperactive immune system. We’re starting to learn how the gut microbiome regulates the immune system, can calm it down, and prevent this damage that is completely unnecessary because we’re not continuously infected.  

Dr. Tom O’Bryan, the author of Autoimmune Fix, writes about how the microbiome talks to the immune system, that there’s a cross communication from the immune system that’s inside the lining of the gut to the microbiome that’s on the outside of the gut. This crosstalk is going on all the time, back and forth. What happens is we develop a microbiome over time that is so inflammatory it begins tearing the gut lining by itself. The microbiome then triggers the immune system to go after some of the microbiomes so you get inflammation going on constantly until the microbiome changes.


Did you know that 90% of our health is determined by social, behavioral, and environmental factors? Dr.  Robin Berzin states only 10% is determined by medical interventions when you’re later in the disease process. We’re not preventing, we’re not always curing, we managing disease once it’s gotten out of control. Most doctors with their digital tools in day-to-day medicine don’t capture these social determinants of health. So, that 90% is what you’re eating, your relationships, supplements, your exercise, the genomics, the microbiome, your and your family’s health history, and your environmental exposures are captured in the electronic records. As a result, the doctors are looking at a very small piece of you. Functional medicine looks at all aspects of you, what you’re eating, and your entire personal history from birth to now, along with diagnostic data looking at the microbiome and genomics. We then take this information in function health and use that whole picture to help guide you to better health.

Dr. Helen Messier, Chief Medical Office has had significant success in reversing many autoimmune diseases in her practice………here’s what she has to say:

“When you address the microbiome and gut health, in so many cases you could not just halt or reverse their symptoms you could reverse these chronic diseases” .

“The one thing I’ve learned is that we’re not really human…We are a human microbial ecosystem and we live in an Earth microbial ecosystem. We are a small player. It’s a paradigm shift. We used to think that we’re individuals and humans and we’re so special, but we are actually part of a much bigger system. And what I’ve learned is that our microbiome is fundamental to everything that we are and everything we do. Our entire environment gets filtered through this microbiome, these microorganisms and transformed by these microorganisms before they affect our human body, our diet definitely, but the air that we breathe, everything, even our thoughts get transformed and filtered by our microbiome. ”

One of the emerging themes from microbiome research is that our own genome isn’t sufficient to induce or promote all the different functions or activities of the human body. That we rely on impetus signals from the microbiome.

Bacteria in our gut provide signals or cues to our development function just as our own genome does. It’s possible that we have two genomes our own and our microbial genome.

Dr. Messier goes on to say, “All of these functions that we used to think were just human, our microbes do them from metabolizing hormones and stress hormones, and changing the foods that we eat. They control our biological rhythms and our sleep cycle or circadian function. They are the first ones to metabolize all drugs that we take in. So, a drug can be effective or not depending on our unique microbiome. We have clearly seen that in cancer and diabetic therapy. You can transfer the effect of the drug by transforming just the microbiome and not the drug. So, it’s that fundamental interface of our environment and us. We eat to feed them and we give them a home.

Drug companies are researching the microbiome because science has found that certain bacteria may be blocking the effect of the drugs people are taking. We’ve also learned that our primary detox organ and nutrient generator is the microbiome, a change in the way we look at health. It communicates with the immune system and the nervous system, promoting a healthy microbiome to help bolster our immune response and fight off disease. It’s a beautiful dance and synergistic relationship that we have with these organisms.”

We categorize people according to symptoms and geography and not according to the causes or the mechanisms and then give them a drug. This style of medicine has proven ineffective for chronic disease and we’re entering a new era where our understanding of the microbiome is changing everything.

Let’s begin with birth and early development. We’re learning that the seed colonies we are born with are important for our overall health.

In fact, they can lead to chronic disease later in life. A healthy pregnancy, delivery, and breastfeeding are a key parts of the solution.

Dr. Zach Bush states when a baby is born through C-section it never sees the flora from the mom’s vaginal canal, so is born sterile. The baby is put on a hospital gurney and immediately inherits the hospital flora instead of the mom’s flora. The baby is most likely to get invasive strep infections in the ears and throat over the first 18 months of life because of its flora and by the time their nine months old the pediatrician gives a dose of antibiotics for the first ear infection. A lot of children from then until age 12 receive antibiotics for chronic ear infections. The doctors finally remove the tonsils that are now riddled with chronic strep. Now the main immune system of the upper respiratory tree has been removed so the child is more prone to viruses.

Those first few days after birth are more important than we previously thought.

Part of the answer may be in how their microbiome was primed at an early age according to Dr. Datis Kharrazian. Within the first six months to two years, we lay the foundation of the gut microbiome. Breastfeeding and the way we feed our children within the first two years are critical. Then the gut microbiome becomes relatively stable. It will fluctuate with its environment but the “base” colonies are believed to be established. As we grow, if taking antibiotics, being hospitalized, having an injury, or eating a lot of junk food the microbiome is adversely affected and less bio-diversified. There was a recent study that also showed BPA exposure in the first four months of life can change the microbiome permanently. BPA’s are found in plastics and are everywhere in the modern world. We know that various chemical exposures can have an effect on our microbiome as well.

This is really important to educate new mothers on the care of their newborns and the importance of breastfeeding. There are so many things that can’t be made in a formula that’s in breast milk, especially polysaccharides, which prime our microbiome. They feed and boost the healthy bacteria in the early days that take hold and continue to support our health for life.

When a baby comes down the birth canal it gets smothered in bacteria from the vaginal tract called Prevotella. In the first 7 months of pregnancy, very little of this bacteria is present but flourishes in the eighth month and becomes the dominant species. Prevotella signals to close tight junctions in the gut lining helping the baby separate from mom and prepare the baby for the outside world it’s just entered. When breastfed, the colostrum which is rich in antibodies like bifidobacteria and fructooligosaccharides, nourishes the pre-biotics which then nourishes the bacteria.

So individuals who are born through the vaginal canal and are breastfed develop a full spectrum of microbes much earlier than individuals who are born through C-sections because of the use of antibiotics and sterilizing rinses. Doctors are now learning that microbiome inoculation, by swabbing the mother’s vagina and smearing on the baby’s face, can help transplant some of the mom’s healthy colonies to the baby.

The most common illnesses that are affecting our society today, diabetes, obesity, and heart disease can all be traced upstream to the fetal experience in utero. This is HUGE!

In the medical revolution the food system profits off of cheap processed materials that come from taxpayer subsidies. These ingredients sprayed with toxic pesticides harm our microbiome causing much of the disease we suffer from today, yet cheaper than carrots and broccoli. Twinkies have 14 ingredients that are subsidized by taxpayers, carrots have none.

The food industry feeds the medical business which wastes trillions of dollars chasing symptoms that come from poor lifestyle decisions. The best disease from a business perspective is a chronic disease because a person has it all their life. If you manage the chronic disease but do not reverse it by addressing the root cause, you have a patient for life using drugs to control their symptoms for life. Do doctors go into medicine just to manage disease or actually heal people and reverse that disease?

When you compare the diets of Europeans and tribal Africans, the foods and bacteria were completely different. African culture didn’t have any of the autoimmune diseases we experience in Europe and the United States.

There is published research specifically showing that pancreatic cancer is caused by the gut microbiome coming from a leaky gut moving into the pancreas and shutting down the immune system.

The Mayo Clinic published their research on breast cancer caused by the microbiome and liver cancer caused by the gut microbiome. This is a good argument for looking for the root cause and not just what’s presenting.

Dr. Zach Bush states, “ To find out that the microbial life can intelligently figure out the difference between a cancerous cell and a human cell and induce the opposite response with their mitochondria, you start to realize we’re barely human. To be human and alive means you have 20, 30, 40,000 species of bacteria, five million species of fungi, and 300,000 species of parasites speaking to the mitochondria within your cells to coordinate the constant repair.

There is constant transformation, regeneration, and repair, making us stronger, not weaker. So the extraordinary message to the future of science and medicine is if we keep killing the smallest things among us we will die.

If we start to support the fundamentals of life and we start to take care of the mitochondria and take care of the microbiome they will, in concert, build the most resilient healing machines ever on the planet.”

No matter if your root colonies came from mom or not there’s plenty of data suggesting that you can increase your diversity and resilience. Life is forgiving. It adapts. Double down on getting better and live more probiotically NOW!

The Human Genome Project allowed us to understand our genes and we realized that the environment has a major influence on our genes, what they call the “epigenetic effect”. The next major breakthrough has been the Human Microbiome Project where we’re trying to understand what the genes in the trillions of microbes is code for, everything from immunity, enzyme production, antibiotics, and more.  Action is simply revolutionary and changes everything about health and hope, whether you’re looking to regain your health or simply maintain it.

There’s too much illness and disease in our world and our current medical model is not serving us in fact, it’s failing us with chronic disease.

Written by Teresa Ducoffe.

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