The Human Genome Project Benefits Gut Microbiome Research. Human Genome Project Facts Confirm Diet Affects Gut Microbiome which Affects Obesity and Depression. The Gut Microbiome Complements the TCM Sanjiao Function

  How does Human Genome Project Benefit Gut Microbiome Research? How do Human Genome Project Facts Confirm Diet Affects Gut Microbiome which Affects Obesity and Depression? How does the Gut Microbiome Complement the TCM Triple Energizer Function?

Always ahead of his time, Hippocrates stated, ‘Walking is man’s best medicine.’ I believe that if Hippocrates was still alive today, he would be a naturopath or an acupuncturist. Having a scientific background, I appreciate that antibiotics, statins, antihistamines, steroids, etc. are all modern and powerful medications and have their place, but I do not believe for a second that they should be consumed like jelly beans on a daily basis. Every xenobiotic medication has the potential to behave as antibiotics and wreak havoc on our microbiome—some more than others. A massive amount of research is being performed on our microbiome by numerous diverse sectors of the medical arena. Many researchers conclude that they have discovered a new organ, namely our gut microbiome. In this Chapter, I discuss in detail many of the remarkable findings being made on a daily basis by researchers investigating the gut microbiome.

The vast majority of our human physiology comes from our gut microbiome! The Human Genome Project revealed that the vast majority of our human physiology remarkably came from somewhere other than our 25,000 genes. This revolutionary finding lead to an understanding of epigenetics, which is the body’s capability of manifesting variable genetic expression within our epigenome without changes to the primary nucleotide sequences of our DNA itself. The greatest interface with our environment involves our gut microbiome, which is composed primarily of bacteria that amplify our genomic library 150 fold. In the article ‘How to Build a Healthy Microbiome, before, during, and after Birth’, Mercola (165) states, ‘The gut is also responsible for metabolizing food that we couldn’t otherwise, for producing nutrients that we couldn’t otherwise, and even for detoxing chemical exposures that we couldn’t otherwise.’ Non-human genes from our gut microflora are assisting us way more than anyone ever thought possible.

This enlightening book is easy to understand, and is essential reading for everyone wishing to know more about the wondrous biochemical and biological processes that are being performed inside our body by genes that are not even our own human genes. These remarkable feats are being discovered and verified by modern scientific research on a daily basis. This informative book can be securely purchased by clicking the ‘BUY NOW’ button at the bottom of this page.

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Summary of Chapter 42

The Human Genome Project revealed that the vast majority of our human physiology remarkably came from somewhere other than our 25,000 genes. This revolutionary finding led to an understanding of epigenetics, which is the body’s capability of manifesting variable genetic expression within our epigenome without changes to the primary nucleotide sequences of our DNA itself. The greatest interface with our environment involves our gut microbiome, which is composed primarily of bacteria that amplify our genomic library 150-fold. Many of our genes ‘slipped into our DNA from microbes living in our bodies’ (166). This mechanism is called horizontal gene transfer. Mercola states, ‘Bacteria slip genes to each other, and it helps them evolve. And scientists have seen insects pick up bacterial genes that allow them to digest certain foods. Humans may have as many as hundreds of so-called foreign genes they picked up from microbes.’ Mercola explains that the human genome consists of about 23,000 genes. He then emphasizes that the combined genetic material of the human gut microbiome is somewhere between 2 million and 20 million. It is incredible that even the gene that determines your blood type (A, B, or O) is a foreign gene. A human study (168) involving seven healthy volunteers found that consumption of a dairy drink containing three different strains of probiotic microorganisms caused changes in the activity of hundreds of genes six hours after consumption of the drinks.

There is no doubt that the status of the gut is largely responsible for human health. But how is our gut composition initiated? What are the contributing factors to gut health? When does our microbiome start? Mercola (165) answers these questions by stating, ‘Adding to a long list of “oops!” in the history of medicine, it was long-held that the womb was a sterile environment. We now have broadened our appreciation of the ubiquitous nature of microbes to encompass their special place in the placenta, umbilical cord, and fetal membranes.’

It has been estimated for some time that 80–85% of our immune system is located in our gut, so reseeding our gut on a daily basis with healthy probiotic organisms is extremely important for our overall physical health. However, note what researchers have recently discovered regarding psychological health. Amongst the statements are ‘sufficient amounts of probiotic gut bacteria from birth may be essential for future psychological health’ (167); ‘the presence of gut microbiota regulates the set point for hypothalamic-pituitary-adrenal (HPA) axis activity’ (167); ‘probiotic microorganisms caused changes in the activity of hundreds of genes six hours after consumption of the drinks’ (168); ‘gut bacteria may influence mammalian early brain development and behaviour’ (169); ‘presence of gut microorganisms during infancy permanently alters gene expression’ (169); ‘gut bacteria altered genes and signaling pathways involved in learning, memory, and motor control’ (170); and ‘there is a critical period early in life when gut microorganisms affect the brain and change the behavior in later life’ (170). According to the authors of one study (167), ‘Acquisition of intestinal microbiota in the immediate postnatal period has a defining impact on the development and function of the gastrointestinal, immune, neuroendocrine and metabolic systems.’

It is astounding that the genetic code of our gut microflora overrides human genetic code. The article entitled ‘Microbiome’ (171) advises that we essentially use the genetic code of the microflora in our gut to do numerous things that we can’t do ourselves—for example, making different vitamins and digesting food components that our own human enzymes cannot digest. Even our moods and cravings can be dictated by our gut microbiome. Your gut bacteria provide a significant source of many essential nutrients, including amino acids, vitamins, lactase, coenzyme Q10, and three other major substances, including the energy source substance (adenosine triphosphate or ATP), tryptophan, and serotonin.

Your human DNA is largely controlled by your gut flora. Mercola (83) points out, ‘Beneficial bacteria also play an enormous role in your genetic expression—continuously helping flip genes off and on as you need them. Your genetic expression is 50 to 80 percent controlled by how you eat, think and move, and your genes change daily—if not hourly.’ He poignantly continued, ‘You may be surprised to learn that 140 times more genetic influence comes from your microbes as from the DNA in your own cells. Your genes control protein coding, which determines your hormones, weight, fertility, mood and others.’

It is interesting that we believe that our body is our own, but in reality, on a cellular basis, only one tenth of our cells are human (172). The other 90% of the cells in our body are all hitchhikers, mainly made up of harmless bacteria and other not-so-harmless organisms that have made our body their residence. There are 100,000 billion of these organisms in our guts. That means, on a cell-to-cell basis, we are 90% microbial and 10% human! Professor Jeffrey Gordon (172) from the St. Louis School of Medicine at the Washington University, points out that as there are 10 times more microbial cells in our bodies than there are human cells. There are also 100 times more functional microbial genes in our bodies than there are genes in our entire human genome.

While the ancients were aware that Xie Qi (Evil Qi, Incorrect Qi) existed, they perceived its presence as Fong Qi in its numerous forms (Cold, Hot, Damp, Dry). They were not aware as we are now that there are thousands of different individual microscopic life forms that can hitchhike on us for months, years, or a lifetime. They were not aware these organisms could poison us with their potent enterotoxins and neurotoxins to produce symptoms and signs specific to that organism. These potential ‘Lingering Pathogens’ include viruses, bacteriophages, prions, virions, bacteria, yeasts, fungi, moulds, dinoflagellates, spirochetes, mites, algae, paramecium, nematodes, etc. Likewise, the ancients were not aware that there are hundreds of varieties of beneficial microflora living in our gut and in our lungs, mouth, nasal passages, ear canal, sinuses, fallopian tubes, vagina, stomach, skin that are absolutely essential for us to maintain optimal health and well-being. Note the incredible significance of that. These friendly commensal bacteria happily live in our airways and lungs, producing natural antibiotics (bacteriocins—Wei Qi) to fight pathogens (Fong Qi). Their function is ‘to induce Th1 response and anti-inflammatory interleukin (IL)-10, antimicrobial peptides, FOXP3, secretory immunoglobulin A (sIgA) production’. Could this western scientific jargon be a portion of what the ancients called Wei Qi? Now let’s consider health aspects associated with the microflora that inhabits our mouth.

In the article titled ‘Oil Pulling the Key to Oral Health’, the author, Dr Valerie Malka (175), states, ‘More than 95 percent of people in modern society have some form of tooth decay or gum disease. Medical research has shown a clear and direct link between oral health and a multitude of chronic diseases, something ancient healing traditions have known for centuries. Oil pulling, the simple daily routine of swishing vegetable or coconut oil in your mouth, spitting it out and rinsing, has been reported to also prevent, improve or treat chronic diseases such as asthma, diabetes, headaches, chronic fatigue and colitis.’

Bacteria educate our immune system, digest our food, synthesize vitamins and neurotransmitters, and fight off invaders for us. But they are far too small to have an impact, beneficial or adverse, if they act as individuals. The mechanism the bacteria use is a process called Bacterial Quorum Sensing. A protein enzyme inside the bacterium makes the hormone molecule that is secreted into its surroundings. The bacterium has a sensor for that molecule. The molecule fits the sensor specifically like the correct key fits the lock it was designed for. When sufficient molecules abound, the lock is opened in all the bacteria, and all the bacteria get the message and thus simultaneously act. All bacterial niches have dynamic mechanisms like this. So all bacteria can ‘talk’ to one another, using different chemical ‘words’, and then they are able to turn on group behaviors when the threshold for the specific chemical word is reached. But the process is only successful when all the cells participate in unison. It is like every cell votes, the votes get counted, and then all the cells respond to the vote. Bassler (177) believes there are hundreds of different actions and functions that bacteria carry out in this collective behaviour of communication.

It has been established that diverse commensal bacteria, predominantly Bacteroides, occupy our Large and Small Intestines at birth, thanks to the bacterial loading inherited from our father and primarily our mother during the birthing process. The dominantly Bacteroides microbiome we inherit at birth has recently been shown to have a large effect on the expression of our DNA and also moulds our emotional makeup and is with us until the day we die. I believe that the gut microbiome we inherited in some way impacts our own human DNA inheritance in a much greater manner than scientists give credit for.

The author of The Economist article (58) entitled ‘The Human Microbiome: Me, Myself, Us’ succinctly stated what I have believed for the last three years. He/she stated:

One way to think of the microbiome is as an additional human organ, albeit a rather peculiar one. It weighs as much as many organs (about a kilogram, or a bit more than two pounds). And although it is not a distinct structure in the way that a heart or a liver is distinct, an organ does not have to have form and shape to be real. The immune system, for example, consists of cells scattered all around the body but it has the salient feature of an organ, namely that it is an organised system of cells. The microbiome, too, is organised.

A faulty microbiome can poison us, causing ‘foggy brain’ and psychiatric conditions. Myhill (182) points out that some patients have bacteria, yeasts, and possibly other parasites present in their upper gut, so rather than foods being digested, they are being fermented into ethyl alcohol, propyl alcohol, butyl alcohol, and possibly methyl alcohol. These would subsequently be metabolized by the liver into acetaldehyde, propylaldehyde, butyraldehyde, and possibly formaldehyde respectively. Alcohol and aldehydes result in ‘foggy brain’, ‘toxic brain’, feeling ‘poisoned’, and so on. Alcohol also disturbs blood sugar levels, which makes the sufferer crave sugar and refined carbohydrates, which are the very foods the contaminating microorganisms in the upper gut require to ensure their own survival. Myhill concludes, ‘This is arguably a clever evolutionary ploy by bugs to ensure their own survival!’

An article written in 2012 in The Economist titled ‘The Human Microbiome: Me, Myself, Us’ (58) discussed how a lot of carbohydrates would also be indigestible and unavailable to us if we only had access to human-derived enzymes. The massively more diverse genome of our gut microbiome has correspondingly greater digestive capabilities, and even complex carbohydrates succumb to its power. Carbohydrates of all sorts are ceaselessly munched and their reduced units churned out as small fatty-acid molecules—particularly formic acid, acetic acid, and butyric acid—which can pass through the gut wall into the bloodstream, where biochemical pathways release energy from them. It is estimated that 10–15% of the energy used by an average adult is generated via this process, thanks to our gut microflora.

A critical point to note is that we acquire our Bacteroides colonies at birth and retain those bacteria for the rest of our life (182). As mentioned previously (172), humans have 30,000 genes, while the numerous diversified bacteria that hitchhike on us have between them 3,000,000 genes (which is 100 times more genes), expressing themselves throughout our entire body at all times. Could they be associated with and contributing to our Yuan Qi? Further, Bacteroides are literal powerhouses of energy production as Bacteroides are estimated to generate more than 500 Kcal of energy per day, which makes them very significant source of energy! (182). Could this be one of the ways that the Triple Burner produces qi, which is circulated throughout the entire body?

In 2014, a test group investigated, using a living bacterial skin tonic created by AOBiome. The tonic looked, felt, and tasted like water, but each spray bottle contained billions of cultivated Nitrosomonas eutropha, an ammonia-oxidizing bacteria (AOB) that is most commonly found in dirt and untreated water. The article stated, ‘AOBiome scientists hypothesize that it once lived happily on us too—before we started washing it away with soap and shampoo—acting as a built-in cleanser, deodorant, anti-inflammatory and immune booster by feeding on the ammonia in our sweat and converting it into nitrite and nitric oxide.’ One subject had not showered for twelve long years. Did he stink? No, the bacterial spray he had engineered kept him smelling fresh. There is no doubt that gut and skin microorganisms are absolutely essential for continued good health and vitality and for smelling good into the bargain.

REFERENCES:

(58) Anonymous, ‘The Human Microbiome: Me, Myself, Us’, The Economist ( 2012). From the print edition: Science and Technology.

(83) Mercola, J., ‘Global Health Problems Reflect Our Disconnection from the Earth’ (2015). Available from <http://articles.mercola.com/sites/articles/archive/2015/02/28/how-modern-lifestyle-caused-global-problems.aspx>.

(165) Mercola, J., ‘How to Build a Healthy Microbiome, before, during, and after Birth’ (2014). Available from <http://articles.mercola.com/sites/articles/archive/2014/12/29/healthy-gut-microbiome.aspx>.

(166) Mercola, J., ‘Fiber Provides Food to Your Gut Microbes that They Ferment to Shape Your DNA’ (30 March 2015). Available from <http://articles.mercola.com/sites/articles/archive/2015/03/30/fiber-fermentation-gut-health.aspx?e_cid=20150330Z3_DNL_B_art_1&utm_source=dnl&utm_medium=email&utm_content=art1&utm_campaign=20150330Z3_DNL_B&et_cid=DM71100&et_rid=895005487>.

(167) Neufeld, K. M., N. Kang, J. Bienenstock, J. A. Foster, ‘Reduced Anxiety-Like Behavior and Central Neurochemical Change in Germ-Free Mice,’ Neurogastroenterology & Motility 23/3 (2011), 225.

(168) Daniells, S., ‘Breakthrough Study Shows Personalised Nutrition Future for Probiotics’, (updated 15 September 2010). Available from <http://www.nutraingredients.com/Research/Breakthrough-study-shows-personalised-nutrition-future-for-probiotics>.

(169) Diaz-Heijtz, R., S. Wang, F. Anuard, Y. Qiana, B. Björkholmd, A. Samuelssond, et al, ‘Normal Gut Microbiota Modulates Brain Development and Behavior,’ PNAS, 108/7 (2011), 3047–52.

(170) Diaz-Heijtz, R., S. Wang, F. Anuar, Y. Qian, B. Björkholm, A. Samuelsson, et al., ‘Bacteria in the Gut May Influence Brain Development’ (2013). Available from <http://ki.se/en/news/bacteria-in-the-gut-may-influence-brain-development>.

(171) Wikimedia Foundation Inc., ‘Microbiome’, (updated 23 March 2014 at 04:10). Available from <http://en.wikipedia.org/wiki/Microbiome>.

(172) Mercola, J., ‘How Bugs Become Instantly Resistant to Insecticide by Swallowing Bacteria’ (09 May 2012). Available from <http://articles.mercola.com/sites/articles/archive/2012/05/09/how-bug-becomes-instantly-resistant-to-insecticide-by-swallowing-bacteria.aspx>.

(175) Malka, V., ‘Oil Pulling the Key to Oral Health’ (2015). Available from <http://www.wellbeing.com.au/article/Features/Body-Health/Oil-well_1562>.

(177) Bassler, B., ‘How Bacteria “Talk” (2009). Available from <http://www.ted.com/talks/bonnie_bassler_on_how_bacteria_communicate?language=en>.

(182) Myhill, S., ‘Fermentation in the Gut and CFS’ (updated 19 May 2014 at 09:34). Available from <http://www.drmyhill.co.uk/wiki/Fermentation_in_the_gut_and_CFS>.

ACKNOWLEDGEMENT:

I wish to sincerely thank Dr Paul U. Unschuld for the selfless and tireless work he has committed to make many ancient Chinese medical classics available in English for study and research. My book is based predominantly around his scholarly work ‘Nan-Ching: The Classic of Difficult Issues’. I also wish to sincerely thank Professor Unschuld for permission to use citations of his translation in my book. His translation of ‘Nan-Ching: The Classic of Difficult Issues’ can be purchased from the following link: https://www.amazon.com/Nan-ching_The-Classic-Difficult-Comparative-Studies/dp/0520053729

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