You are your microbiota

December 2nd 2017  |   in Health and fitness   |   20 min. read

Photo by Kyle Ellefson

All disease begins in the gut.


We all the know this famous quote of our great father of medicine and for centuries we have been presuming he meant nutrition is the key to health. Well, it is, but the story behind this quote is more profound you might expect. What Hippocrates referred was not necessarily what we put in our gut, but what already exists there: bacteria.

Since Louis Pasteur came with his Germ Theory, we have been labeling bacteria as bad guys and putting the blame on them for all our misfortune - disease. If that is true, why are we still alive?

Bacteria is the primordial life form. We have evolved from bacteria. Also, animals, plants, and humans have evolved in nature, constantly exposed to bacteria. Thus, is bacteria the culprit? It turns out, the majority of bacteria we all fear is actually our friend because we are the hosts of a living ecosystem called microbiota.

The microbiota (microbiome)

According to the Department of Chemistry & Biochemistry at the University of Colorado, “the human microbiota consists of the 10–100 trillion symbiotic microbial cells harbored by each person, primarily bacteria in the gut. The human ‘microbiome’ consists of the genes these cells harbor.” Furthermore, “the Meta-HIT consortium reported a gene catalog of 3.3 million non-redundant genes in the human gut microbiome alone, as compared to the ∼22,000 genes present in the entire human genome. Similarly, the diversity among the microbiome of individuals is immense compared to genomic variation: individual humans are about 99.9% identical to one another in terms of their host genome but can be 80-90% different from one another in terms of the microbiome of their hand or gut.”[1]

What this research suggests:

Our microbiota is our “genetic footprint”, as researchers call it. It determines our DNA, our health requirements, our mood, our mindset, our metabolism, it determines who we are.

This confirms what Lucretius Carus said: “One man’s meat is another man’s poison”. Our requirements are determined primarily by our microbiota. And it is not something static, but dynamic.

Our microbiota is constantly changing, it is dynamic. It adapts to our environment, to our health status, to our nutrition, our exercise, our feelings, our thoughts. Briefly, it adapts to our lifestyle.
How does it do that? By changing the variety of microbial species.

If you pay a visit to good old doctor Google and search on “microbiota species list”, you will be overwhelmed with what you find. Every species of bacteria have an impact on our body, especially on our DNA. As we learned, our bacteria have the biggest influence on our DNA, because their genetic material programmes our genetic material: they run our genes on and off (epigenetics studies this process). When they change, we change. The question is, what do we change into?

Louis Pasteur was right partially, there are some bacteria that are not beneficial to us. We can create such bacteria by our way of living.

The Hygiene Hypothesis

Some research studies found that in countries where there is less sanitation and people are living more close to nature - exposed to germs - there are less autoimmune diseases and less disease risk factors.
The Hygiene Hypothesis suggests the cleaner we are, the sicker we are. And if we think about it, it is true. The more disconnected and urbanized we have become, the sicker we have become. And the Big Bang of unhealthiness occurred after the industrial revolution, in the last 100 years. It so makes sense.

According to a recent article in Nature by the Stanford microbiologist Justin Sonnenburg, “Consumption of hyperhygienic, mass-produced, highly processed and calorie-dense foods is testing how rapidly the microbiota of individuals in industrialized countries can adapt.”[2]

Just to be straight, I am not suggesting you should stop washing your hands or something. I am suggesting to rethink bacteria and microbes. Whenever you are using antibiotics, antifungal, antibacterial, and antimicrobial, it is actually anti-you. When you think of “you”, you are referring to 10% of the actual “you”. 90% of you is microbes.

See antibiotics only as a last resort, when your life depends on it. Antibiotics are like atomic bombs, they destroy every living (“anti - bios”, “against life”), both good and bad.

Gut microbiota

The vast majority of our microbiota is in our gut, which is also the most affected by our lifestyle and vice versa.

According to Wikipedia, “the gut microbiota has the largest numbers of bacteria and the greatest number of species compared to other areas of the body. In humans, the gut flora is established at one to two years after birth, and by that time the intestinal epithelium and the intestinal mucosal barrier that it secretes have co-developed in a way that is tolerant to, and even supportive of, the gut flora and that also provides a barrier to pathogenic organisms.”[3]

According to a research article in the National Institutes of Health, “The intestine is adapted to bi-directional host–flora exchange and harbors a diverse bacterial community that is separated from the internal milieu by only a single layer of epithelial cells. Resident bacteria outnumber human somatic and germ cells tenfold and represent a combined microbial genome well in excess of the human genome (Shanahan, 2002). Collectively, the flora has a metabolic activity equal to a virtual organ within an organ (Bocci, 1992).” Furthermore, “Enteric bacteria form a natural defense barrier and exert numerous protective, structural and metabolic effects on the epithelium (Fig 1B). Their influence on intestinal physiology has been shown in comparative studies of germ-free and colonized animals. Germ-free animals are more susceptible to infection and have reduced vascularity, digestive enzyme activity, muscle wall thickness, cytokine production and serum immunoglobulin levels, smaller Peyer’s patches and fewer intraepithelial lymphocytes, but increased enterochromaffin cell area (Shanahan, 2002). However, reconstitution of germ-free mice with an intestinal microflora is sufficient to restore the mucosal immune system (Umesaki et al, 1995)”[4]

This reveals the importance of the gut microbiota to the immune system, especially in the anti-inflammatory mechanism.

The study also reveals how the microbiota teaches the immune system to distinguish pathogens and foreign invaders from the body’s own cells. “Host defense requires an accurate interpretation of the microenvironment to distinguish commensal organisms from episodic pathogens and a precise regulation of subsequent responses. The epithelium provides the first sensory line of defense and active sampling of resident bacteria, pathogens, and other antigens is mediated by three main types of immunosensory cell”.

Another importance of the gut bacteria is in metabolism, digestion, and nutrient absorption and synthesis.

“The intestinal microbiome has a metabolic activity that is both adaptable and renewable (Bocci, 1992). Through the production of short-chain fatty acids, resident bacteria positively influence intestinal epithelial cell differentiation and proliferation and mediate other metabolic effects (Fig 1B; Shanahan, 2002). Together, this complex metabolic activity recovers valuable energy and absorbable substrates for the host and provides energy and nutrients for bacterial growth and proliferation. Colonization increases the uptake of glucose in the intestine and, compared with colonized mice, germ-free mice require a greater caloric intake to sustain a normal body weight”.

Any disruption to the gut microbiota leads to inflammation and nearly every existant disease, especially autoimmune disease, allergies, infections and so on.
“Innate immune responses to the commensal flora educate the immune system and influence adaptive responses to exogenous antigens. With increased sanitation and hygiene in developed nations, genes that were once survival factors in an earlier era could become risk factors for immune-hypersensitivity disorders in a modern sanitized environment”.

The cure is also in the gut: “The 2005 Nobel prize in Physiology and Medicine awarded to Robin Warren and Barry Marshall is a reminder that the solution to some human diseases does not reside solely within the host but rather might be found at the interface with the microbial environment. Manipulation of the flora is becoming a realistic therapeutic and prophylactic strategy for many infectious, inflammatory and even neoplastic diseases within the gut.”

There is also correlation between gut microbiota imbalance and ulcers, inflammatory bowel disease, irritable bowel syndrome, diabetes mellitus, asthma, Alzheimer’s disease, Parkinson’s disease, Crohn’s disease, infections, liver disease, cancer, autism, obesity, and schizophrenia.

Besides being an organ, the gut microbiota acts like a second brain, because of the gut-brain axis and the relationship between our gut microbiota and nervous system - the enteric nervous system. According to Wikipedia, “The enteric nervous system is one of the main divisions of the nervous system and consists of a mesh-like system of neurons that governs the function of the gastrointestinal system; it has been described as a “second brain” for several reasons. The enteric nervous system can operate autonomously. It normally communicates with the central nervous system (CNS) through the parasympathetic (e.g., via the vagus nerve) and sympathetic (e.g., via the prevertebral ganglia) nervous systems.”[5]

So, the quotes “Listen to your gut!” and “I am having butterflies in the stomach!” are not just metaphorical as we thought. Whenever our gut microbiota is feeling bad, we are also feeling bad: depression, anxiety, mood disorders and so on. Also, whenever the gut microbiota is feeling well, we are feeling well. It seems that 70% of the serotonin (“happiness” hormone) is produced by our gut microbiota.

“The relationship between gut flora and humans is not merely commensal (a non-harmful coexistence), but rather a mutualistic relationship. Human gut microorganisms benefit the host by collecting the energy from the fermentation of undigested carbohydrates and the subsequent absorption of short-chain fatty acids (SCFAs), acetate, butyrate, and propionate. Intestinal bacteria also play a role in synthesizing vitamin B and vitamin K as well as metabolizing bile acids, sterols, and xenobiotics. The systemic importance of the SCFAs and other compounds they produce are like hormones and the gut flora itself appears to function like an endocrine organ,[11] and dysregulation of the gut flora has been correlated with a host of inflammatory and autoimmune conditions. The composition of human gut flora changes over time, when the diet changes, and as overall health changes.” Furthermore, “The gut flora can produce a range of neuroactive molecules, such as acetylcholine, catecholamines, γ-aminobutyric acid, histamine, melatonin, and serotonin, which is essential for regulating peristalsis and sensation in the gut. Changes in the composition of the gut flora due to diet, drugs, or disease correlate with changes in levels of circulating cytokines, some of which can affect brain function. The gut flora also release molecules that can directly activate the vagus nerve which transmits information about the state of the intestines to the brain. Likewise, chronic or acutely stressful situations activate the hypothalamic–pituitary–adrenal axis, causing changes in the gut flora and intestinal epithelium, and possibly having systemic effects. Additionally, the cholinergic anti-inflammatory pathway, signaling through the vagus nerve, affects the gut epithelium and flora. Hunger and satiety are integrated in the brain, and the presence or absence of food in the gut and types of food present, also affect the composition and activity of gut flora.”

Thus, the gut microbiota is a second brain and an endocrine organ and it is a constant bidirectional communication with us. When we are stressed, angry, sad, frustrated our gut microbiota responds, and we respond further. It also dictates our energy management.

In a study, when a group of mice without developed gut microbiota received a gut microbiota transplant from obese mice, they gained more fat storage without increasing their food intake. Also, when fat mice received gut microbiota transplant from lean mice, they started to burn fat storage and become leaner.

Natural birth and breast milk

The human vagina is full of bacteria and breast milk is one of the most oligosaccharides dense food. But newborns cannot digest oligosaccharides. No, but the gut microbiota do, and that is their role. The human breast milk is meant to feed the gut microbiota and that is why children born by Cesarean procedure and are fed with milk formula instead of mammal milk are more prone to malnutrition, infections, and diseases. Not to mentions the major drugs and vaccines they receive with further destroy the microbiota.

Our lifestyle programs our microbiota programs our life

I believe you agree with me that in last century our lifestyle has changed to destroy our microbiota. We have been disconnected more and more from nature and have begun to believe that nature is our enemy. The food industry and pharmaceutical industry with all their influence on the health care system made health a lottery win.

This applies especially to the Western lifestyle, a pro-inflammatory and pro-oxidative lifestyle:

These, in addition to sedentary lifestyle, indoor lifestyle, and the chemical toxins and pollutants mentioned previously in this article create a macrobiotic and genetic bomb that kills us.

There you have it! The reason you are sick and fat! No bad luck, no God, no genetic lottery. It’s all up to you.

Pro-microbiota lifestyle

The reason we have evolved in symbiosis with these bacteria is that they are so adaptable to change. They are the primitive form of life and they can change and adapt faster than the host, a more complex organism. Thus, the same way they have gone bad, they can go back good. How? By reverting your commit (to speak in a software developer language). In English, by reconnecting with your human nature and traditions and reversing the industrial revolution impact.

Forget everything you have been taught for 100 years, and go back to the ancient knowledge and traditions and, most important, common sense. Listen to your body and to your environment. Your lifestyle should not be universal, nor static as all the medical advice suggest. No, you are in a continuous change, as weather, as nature, as day-and-night. You are in a continuous cycle and you need to adapt.

You are unique. You and your neighbor cannot live exactly the same lifestyle. Your microbiota is unique to you and you need to live conformably. If you live in Germany, you cannot live like a person in Japan. If you live in Iceland, you cannot live like a person in Italy. You have the different history, different environments, different seasons, and, hence, different microbiota.

When life gives you lemons, you make lemonade.

The Natural Lifestyle

The standard dietary guideline is this: eat clean (anti-oxidants and anti-inflammatory.

What can you do is the experiment and find what is good for you. But you will need a baseline:



Food and drink

Mindful eating


There you have it, friends. I hope I helped you and inspired you with this article and I hope you will rethink the way you live and you see yourself. As an extra and conclusion for this article, Dr. Axe offers two very nice infographics for a pro-microbiota lifestyle and fact about the microbiota[6].

Image credit: Dr. Axe, “The Human Microbiome”

Image credit: Dr. Axe, “The Human Microbiome”

Also, to summarize in one quote everything we learned today.

Eat clean, live dirty.

Dr. Robynne Chutkan

You are the farmer of your inner garden. Grow it well and you’ll harvest health, fitness, and well-being!


  1. Luke K Ursell, Jessica L Metcalf, Laura Wegener Parfrey, and Rob Knight, Defining the Human Microbiome, Nutr Rev. 2012 Aug; 70(Suppl 1): S38–S44 doi: 10.1111/j.1753-4887.2012.00493.x
  2. Justin L. Sonnenburg & Fredrik Bäckhed, Diet–microbiota interactions as moderators of human metabolism, Nature 535, 56–64 (07 July 2016)
  3. Wikipedia, Gut flora
  4. Ann M O’Hara, and Fergus Shanahan, The gut flora as a forgotten organ, EMBO Rep. 2006 Jul; 7(7): 688–693 doi: 10.1038/sj.embor.7400731
  5. Wikipedia, Gut-brain axis
  6. Dr. Axe, The Human Microbiome: How It Works + a Diet for Gut Health
  7. YouTube, Dr. Robynne Chutkan | Revitalize | Why The Microbiome Is The Future Of Medicine

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