Born of a Love Affair Between Our Genes and Our Microbes
“Humans without microbes are sick. Microbes without humans have no home.”
(Rodney Dietert, PhD, The Human Super-Organism, 2016)
For the past century, scientists have assured us that they knew what made us tick – the genetic code of course! Experts agreed that instructions conserved over millions of years were stored in the DNA which controlled our birth, growth, and death; these instructions were inherited and transmitted through the generations. This theory served as an elegant scientific replacement for the ‘Creator God’ theory of previous millennia. Yet neither theory could be demonstrated – both relied on faith – and now there’s new information that renders both theories obsolete.
It is true that one can see the double helix of our genetic code with sophisticated instruments. DNA can reliably establish paternity, even prove guilt or innocence of a crime, and help figure out evolutionary relationships over great expanses of time. But nobody ever saw what was “inside” the DNA. Then along came the Human Genome Project which spent $3 billion in search of the secrets of the genetic code. When the project was completed in 2003, former U.S. President Bill Clinton said: “Today we are learning the language in which God created life.”
Actually though, our genome has turned out to be more like a musical theme from which a master jazz player can produce a variety of interpretations. The jazz player is the exterior environment. The musical performance does not arise from an internal preset score. In fact, as Rodney Dietert, Cornell University’s professor of immunotoxicology and author of The Human Super-Organism puts it, the “control of gene use is epigenetics.”
When big projects fail, they do so spectacularly and in ways that can lead to new insights. The Human Genome Project failed because it asked the wrong question, equivalent to “Tell me your program.” The answer was: “Sorry, all programs currently are, and always were, and always will be under construction.” No one-to-one relationships were discovered between genes and intelligence, sexual orientation, criminality, diseases (disappointing for Big Pharma), or anything else.
Epigenetics Studies Life’s Impact On Genes
What was ultimately revealed to researchers was the fact that all gene expression is dependent to varying degrees on the body’s microbiome. So the mere 25,000 human genes alone could not even begin to explain our complexity, seeing that the banana has the same number of genes as we do.
The Greek word “epi” means “above” (ie. in addition to). In 2001, the journal Science devoted an entire issue to the introduction of the new science of epigenetics and defined it as “the study of heritable changes in gene function that occur without a change in the DNA sequence.” In other words, the DNA is silent unless spoken to.
We now know that close to “99% of the genetic information within the space we call ‘you’ is not from your genome” (or your DNA, your mammalian genes) explains Dietert. In fact, almost 99% of your genetic information is accrued from your life experience, including influences ranging from environmental poisons to foods, and even emotional states and attitudes to such a degree that genetic activity can be activated by your memories, feelings, and thoughts in under two seconds. (Rossi; 2002)
This dialogue between the world and our genome is made possible by the microbiome resident within us which consists of trillions of bacteria, fungi, and earth’s most ancient creatures, the archaea. We, unlike the banana, acquired this vast internal population over millions of years. And it is because of this immense super-organism we embody that it doesn’t matter that we only have as many genes as the banana. Had the banana in its evolution acquired this empire of regulatory support, bananas today would be very interesting indeed!
Dietert says “the microbiome is your body’s ultimate gatekeeper” for many reasons; chief amongst them is its role in creating the immune system. No biological defense action or repair process is possible without the bacteria populating the microbiome. When the microbiome’s membership is complete (with trillions of microbes), we are healthy. But if it is decimated by poisons and starved due to poor nutrition, then we become sick and die.
Damaged Microbiome Linked to All Diseases
The diseases now known to be caused and/or mediated by a compromised microbiome are the so-called Non-Communicable Diseases (NCD) such as Alzheimer’s, asthma, certain types of autism, all autoimmune diseases, all cancers, all gastro-intestinal diseases, hypertension, many lung diseases, food allergies, Lupus, various liver diseases, obesity, osteoporosis, periodontal disease, psoriasis, rheumatoid arthritis, certain schizophrenias, sudden infant death syndrome, both types of diabetes, and some mental health problems. This list is not controversial – it is known by science. The age of ‘idiopathic’ (unknown cause) disease is over. The causes of this relatively recent epidemic of NCDs (less than a century) are now known to include:
- Antibiotic overuse (especially in food-producing animals to prevent disease, as well as its unnecessary uses in medicine);
- The processed food revolution and diets deficient in fermented and raw foods;
- Heavy spraying of genetically modified crops with toxic pesticides (the prime example of an extremely harmful pesticide, Roundup, suppresses the liver’s detox system called cytochrome P450 and kills the microbiome-created enzymes that keep our guts healthy and orchestrate amino acid biosynthesis);
- Urbanization, and wrong-headed safety measures such as flame retardants, pesticides;
- A great many drugs, food additives and especially emulsifiers (polysorbate 80 and carboxymethylcellulose) also used in medicine, toxic metals;
- Caesarean birthing (which bypasses the normal channels for infusing bacteria into the baby) and lack of breastfeeding (which supplies the infant with crucial bacteria).
Noncommunicable diseases are preventable and often reversible, but that would require a new way of practising medicine, Dietert explains – and he is about as conventional a scientist as one can get. Doctors would, for example, be found guilty of malpractice if their antibiotic treatments (when absolutely necessary) are not accompanied by probiotic supplementation before, during, and after therapy. If this strikes you as astounding, read his book and be flabbergasted some more.
How Our Microbes Dance With Our Genes
Many of our microbiome members often defy standard biological doctrine by transferring, swapping, or exchanging genes amongst each other right across different species and genera boundaries and without bothering to reproduce first – that’s called horizontal transfer. It is rather like a human transferring or swapping genes with an ape just by touch. The primary job of all these billions of bacteria, viruses, and archaea is to switch genes on or off at the right time and for the necessary purposes. Genes don’t follow predetermined, immutable, ancient programs as the Human Genome Project had hoped to find. And no, one size never fits all: each of us has a different microbiome due to differing exposure and personal histories and global environments. Researchers in Germany’s Max Planck Institute describe the action of the microbiome on your genes as “writing your very own personal book of life.” You did not learn that in biology class, did you?
Microbes protect and promote our lives: they make many vitamins and their metabolites make serotonin, dopamine, GABA, acetylcholine, norepinephrine and more. Not surprisingly, disrupting microbiome bacteria can affect entire systems: Dr. Derrick MacFabe, at the University of Western Ontario, found that by altering the concentration of one such bacterial metabolite, the short-chain fatty acid propionic acid, baby mice behaved like autistic children by becoming completely antisocial and obsessing with a ball. As another example, a slight reduction in your gut of the bacteria called Akkermansia causes a form of obesity-promoting inflammation. Even “your ancestors’ lousy childhoods or excellent adventures might change your personality, bequeathing anxiety or resilience by altering the epigenetic expressions of genes in the brain.” So writes Dan Hurley in Discover Magazine, May, 2015, describing the work of McGill University’s neurobiologist Michael Meany and geneticist Moshe Szyf.
The microbiome is now referred to as a newly recognized organ, writes Dietert: “Researchers working on hormones see it as another endocrine organ (like the thyroid) managing hormones. Nutritionists and biochemists often see it as a second liver because of its remarkable digestive and metabolic capacities. To immunologists it is an organ designed to train the immune system, and neurobiologists and psychologists view it as an organ that controls human cognition and behavior.”
Epigenetics In Action
– In 2002, which seems now a very long time ago, a landmark study was published in the New England Journal of Medicine on cancer in identical twins. Their genome was identical and so were their microbiomes at birth. After studying the life histories of more than 23,000 pairs of identical twins from 1886 to 1995 to ascertain if cancer might be an inescapable fate built into our DNA, the researchers stated: “We conclude that the overwhelming contributor to the causation of cancer in the populations of twins that we studied was the environment.” In the early 1990s, nothing much was known about the microbiome. Now we know that it was toxic environmental exposures that compromised the microbiome of the twin that developed cancer.
– Amazingly, experiences can be transferred via so-called epigenetic tags from fathers to their children. During the 19th century, starvation episodes in parts of Sweden resulted in the kids of fathers who had survived the starvation period then producing children with maximal resilience. The offspring lived on average 32 years longer than those without starved fathers, into three generations each.
– Rats who had been exposed simultaneously to electric shocks and the scent of cherry blossoms produced pups who reacted with fear to cherry blossom scent even though they had never experienced an electric shock. This reaction persisted for three generations as well. Again, the epigenetic tag was transferred via the fathers’ sperm.
– Transgenerational epigenetics has been observed especially after famines. In the winter of 1944/45 the Nazis starved the population of the Netherlands, and between 1958 and 1961 Mao starved some three million Chinese through his Great Leap Forward policies. The babies whose mothers were starved during pregnancy in the Netherlands were more prone to develop Type 2 diabetes and dyslexia, and the children of those Chinese who had survived the great famine were overwhelmingly more likely to have metabolic syndrome, schizophrenia, and anemia. This, too, was multigenerational.
– Last year, researchers at Johns Hopkins University School of Medicine found that a deficient epigenome can turn on you and initiate the metastasizing cascade of pancreatic cancer.
– Women exposed to DDT transferred via their ova the propensity to develop asthma and obesity to their children into the third generation, even when the children and grandchildren themselves were not exposed to DDT.
– Most disturbing is the finding that abused children have the same epigenetic tags as the cherry blossom and shock-exposed rats mentioned above, resulting in mood disorders, increased anxiety, specific immune deficits, and more. Fortunately, therapeutic methods have been developed to help them. It seems logical to feed their microbiomes as well.
Cultivating a Healthy Microbiome
Dietert provocatively asks in his book on the human super-organism: “Will you do no harm?” We need to become “microbiome whisperers” and listen to what these new discoveries can teach us. Health should no longer be viewed as a DNA-mediated fate but rather as a microbiome-mediated choice. Often we are indeed victims, not of ancient cast-iron DNA messages but of toxic circumstances created by others for profit – and that includes many medical practices which use microbiome-toxic drugs handed out carelessly by microbiome-ignorant doctors. However, we are free to take charge by learning to work with our bodies, question our doctors, and clean up our environments. The scientifically studied solutions include meditation, nutrition, breastfeeding, loving interaction, detox protocols, strategic supplementation, and more, which can activate our genes and move them towards healing.
One new line of research is an outright bomb shell! Researchers with the National Institutes of Health have in 2015 and 2016 published the results of their work showing that the microbiome cannot effectively function in directing our genes unless the required substrate is present inside and outside every one of our cells. That microbiome-regulating substrate is vitamin C! I hear Linus Pauling cheering from the Great Beyond: “I told you so!”
This research from the Gaofeng Wang group shows, for example, that while it was known that the microbiome takes charge of the immature B-cells as they emerge from the bone marrow, and educates them into T-cells for our immune system, nobody knew until recently that the very birth of the B-cells depends on the presence of vitamin C in the latticework of the bone marrow. As T-cells measurably diminish, specific cancers develop.
The researchers also point out that drugs are developed by using rats as test subjects at the start, but they are animals that make their own vitamin C, unlike humans. Those drugs are then put into people who cannot synthesize their own vitamin C and are already deficient in it, as evidenced by their illness. The toxicity of the drugs further reduces vitamin C inside and around the person’s cells and also kills off much of their microbiome whose work of transforming B-cells into useful cancer-fighting T-cells becomes a losing battle. Environmental medicine expert, Dr. Sherry Rogers, comes to mind as likes to say that “drugs make the sick get sicker quicker.”
This information is vital not only for treating cancer, but for understanding that the presence of vitamin C in early embryonic stages is absolutely key. Vitamin C is “a micronutrient with functions far beyond scurvy prevention,” the Wang group states, and suggests that cancer is in effect a type of deadly scurvy.
Dietert envisions what the medicine of the future will have to become. Diagnostic disease labels will give way to checking out a person’s microbiome status first and foremost, and doing what can be done to correct it – and it can be done. Symptoms are a cry for help from essential bacteria being exterminated. We can make choices that our microbial support system requires. Who would have thought that mainstream medical research would make a 180 degree turn and start teaching us profound respect for bacteria and viruses!
- International Scientific Association for Probiotics and Prebiotics (ISAPP) https://www.isapp.net
- R. Dietert, The Human Super-Organism, Dutton 2016. Part Three: Caring for Yourself is made of 5 chapters devoted to practical application of microbiome knowledge to affect positive epigenetic results.
- D. Church, The Genie in Your Genes: Epigenetic Medicine and the New Biology of Intention, EP 2009. https://www.EpigeneticMedicine.org
- V. Camarena & G. Wang. Epigenetic role of vitamin C in health and disease, Cellular and Molecular Life Sciences, vol. 73:1645-1658, 2016.
Definitions of epigenetics:
- R. Dietert & J. Dietert, The Completed Self: An Immunological View of the Human-Microbiome Superorganism and Risk of Chronic Disease, Entropy, vol. 14, 2012. The absolute interdependence of all immunological function with the microbiome is elucidated in detail. Most of Dieter’s research is available for free onhttps://www.rodneydietert.com/
- C. Deans & K. A. Maggert, What do you mean “Epigenetic”?, Genetics, April 15, 2015 provides an excellent history of the concept and what it has evolved into today
- B. Weinhold, Epigenetics: The Science of Change, Environmental Health Perspectives, March 2006, explains the mechanisms of epigenetics and the links to disease via environmental toxins.
- S. Mukherjee, Same but Different: How epigentics can blur the line between nature and nurture, The New Yorker, May 2, 2016. The article discusses how epigenetics is based on unique personal experience and mental states even in identical twins.
Harmful epigenetic effects and their transgenerational effects:
- M.K. Skinner et al. Ancestral dichlorodiphentyltrochloroethana (DDT) exposure promotes epigenetic transgenerational inheritance in obesity. BMC Medicine Vol. 11 (1) 2013. The authors show that epigenetic harm caused by DDT is heritable and continues its harm across generations specifically with regard to obesity.
- A. Samsel & S. Seneff, Glyphosate’s suppression of Cytochrome P450 enzymes and amino acid biosynthesis by the gut microbiome: pathways to modern disease, Entropy vol. 15, 2013. The effect of the herbicide Roundup on the detoxification pathways of the body are detrimental epigenetic changes discussed here in detail.
- M. Pandika, Air pollution causes epigenetic changes that may trigger asthma, Discover Magazine July 23, 2015
- N. Ma et al. Fetal and neonatal exposure to nicotine leads to augmented hepatic and circulating triglycerides in adult male offspring due to increased expression of fatty acid synthase. Toxicology and Applied Pharmacology January 2013
- S. Guerra et al. Maternal Pregnancy Obesity is an independent risk factor for frequent wheezing in infants by age 14 months. Pediatric and Perinatal Epidemiology, Vol. 27 (1), 2013
- D. Simmons, Epigenetic Influences on Disease, Scitable Nature Education, Vol. 1 (1), 2008
- V. Hughes, Epigenetics: The sins of the father – The roots of inheritance extend beyond the genome, Nature March 5, 2014
- Mercola.com April 11, 2012, explains epigenetics in the context of cancer: https://tinyurl.com/7vcayr2
Harmful epigenetic effects due to emotional stresses:
- D. Hurley, grandma’s experiences leave a mark on your genes, Discover Magazine, June 25, 2015
- Summary of presentations made at the annual meeting of the Society for Neuroscience in 2013 in ScienceDaily, Nov. 11, 2013. The presentations included the discovery of new genetic mechanisms underlying long-term memory and how epigenetic changes can block its formation.
- N.D. Powell et al. Social stress up-regulates inflammatory gene expression in the leukocyte transcriptome via adrenergic induction of myelopoiesis. Proceedings of the National Academy of Sciences vol. 110 (41), 2013
- S.E. Romens et al. Association between early life stress and gene methylation in Children, Child Development, July 2014
- K. Gapp et al. Implication of sperm RNAs in transgenerational inheritance of the effects of early trauma in mice. Nature Neuroscience, vol. 17 (5) May 2014
Helpful to epigenetic activity ensuring health:
- E. L. Rossi, The Psychobiology of Gene Expression, Norton, 2002
- E. Yong, Breastfeeding the microbiome, The New Yorker July, 2016
- I. C. G. Weaver et al. Reversal of maternal programming of stress responses in adult offspring through methyl supplementation: altering epigenetic marking later in life. The Journal of Neuroscience, vol. 25 (47), Nov. 23, 2005
- P. Kaliman et al. Rapid changes in histone deacatylases and inflammatory gene expression in expert meditators. Psychoneuroendocriology, vol. 40, 2013
- J. I. Young et al. Regulation of the Epigenome by Vitamin C. Annual Review of Nutrition, July 17, 2015
- E. Ho & F. Domann eds. Nutrition and Epigenetics, CRS Press 2014. A scholarly series of research articles by many authors expert in all aspects of nutrition in health and disease as mediated by the epigenome.