This blog is intended solely for educational purposes and should not be construed as health or medical advice. INTRODUCTION: PART 2B This post is a continuation of Introduction Part 2A, where I started discussing the various roles microbes play in the human body and how we use the GAPS diet to target the cell regeneration process in the digestive system. For full context, please read my two earlier posts. Furthermore, I will delve into how gut flora is passed on to the baby. I have little-known and important information to share, so I encourage you to read the entire post. In this post all quotes will be from Dr. Natasha Campbell McBride's latest book, "Gut and Physiology Syndrome," published in 2020. BLOG Since it has been a while since my last blog post, I'll provide a brief review of the previous ones. This award-winning photo from the Stanford School of Medicine's Center for Human Microbiome Studies shows a mouse colon colonized by human microbiota. In this image, the microbes appear as colorful entities above the green mucus layer produced by the gut wall itself. The photo effectively illustrates the mucus layer as a barrier between the microbes and the colon cells, indicated here by the blue nuclei. In a healthy individual, microbial cells outnumber human cells by approximately 10 to 1, as demonstrated in this photo. Microbes residing on the gut's absorptive surface, with its tiny fingerlike protrusions called villi, secrete various substances such as polypeptides, glue-like adhesions, glycoproteins, proteoglycans, and others to form biofilm, their 'home.' All microbes create these 'homes,' resulting in a complex community of varying microbes living in a mixture of their biofilm, filling all the deep crevices and crypts between the villi of this absorptive surface. The biofilm is part of the green mucus layer, not clearly visible in this photo. Remember, this is not a chaotic microbial mass but a highly organised system, much like the soil beneath our feet. Speaking about soil research, Dr. Natasha writes: "The most active place in the soil is an area around plant roots because the roots secrete sugars. A myriad of microbes live in this area feeding on these secretions, none so important as fungi called mycorrhiza. These fungi create an extension of the root system of the plant; they attach themselves and grow a fine network of long filaments with many branches, spreading to a large area around the root. Through mycorrhiza all plants growing in an area are connected to each other underground; two trees may be many metres away from each other, but they are connected through this fungal network sharing information, nutrition and water...researchers now talk about the whole planet being wrapped in a fungal 'blanket' of fine filaments- a network probably much more sophisticated than our World Wide Web...This network is dynamic: new filaments grow all the time and connect to the whole network, while other filaments disappear. This fungal network provides soil with a fine structure, a road system of a sort, and a myriad of small creatures (bacteria, viruses, archaea, protozoa and other) live on this structure Just as we -humans- build our homes along streets, lanes, and roads that deliver goods back and forth for us, the microbes build their 'homes' along the micorrhizal 'road system'." Could our microbial ecosystem be structured similarly? According to Dr. Mc Bride, without a doubt. Recent microbiome research has identified some 60-70 species of different fungi in the gut of healthy people; future research will probably discover more. Dr. McBride writes: "These fungi provide our microbial community with a structure; their network of thin filaments makes a 'road network' in the gut flora. Along this network smaller creatures can build their homes (their 'houses, villages and towns') and thrive. Nutrients, information and water are delivered to their 'homes' via this 'road network' and wastes are taken away. So, our ability to benefit from the food we eat, would "depend greatly on the fungal population inside our gut flora!"      In my last post, I discussed three primary roles of microbes in the human body: 1) protecting us from invaders and toxins, 2) aiding in the digestion and absorption of food, and 3) orchestrating the cell regeneration process. Microbes have additional functions, and I will elaborate on a few significant ones here. There are nutrients so crucial to the functioning and maintenance of the body that the body does not depend on food intake but rather produces them itself. A fourth major role of microbes is the synthesis of some nutrients. They actively synthesise the whole B vitamin group and vitamin K2 as well as some amino acids and other molecules. Dr Natasha writes: "...Mother Nature has provided us with our own little factory inside our digestive system to produce these substances for us all the time. There is a very complex 'conversation' going on between the body and the gut flora, where the body asks for so much vitamin B12, for example and the gut flora releases it in the right amount and the right chemical shape for the body to use." It is possible to obtain B vitamins from foods, with liver being an excellent source for the complete range of B vitamins. However, the primary source of B vitamins comes from healthy gut flora. Vitamin K2 plays multiple roles in the body; for instance, without it, the body cannot properly utilize minerals, especially calcium. A deficiency in K2 can prevent calcium from reaching the bones and teeth resulting in osteoporosis and tooth decay. Calcium may then accumulate in soft tissues, such as blood vessels, leading to high blood pressure and heart disease, in the brain calcifying important structures, in the joints and tissues causing arthritis, and in the liver and kidneys causing stones. Although a few fermented foods, like high-fat cheeses and natto, can provide K2, microbes are the main and sometimes sole source of this vitamin. Needless to say, if your microbiome is compromised, this entire process will not function effectively, eventually leading to nutritional deficiencies and ultimately disease. Another significant role of microbes is the production of neurotransmitters, chemicals utilized by the nervous system. These neurotransmitters serve as messengers between nerve cells and fulfill various other functions in the body. Current research demonstrates a link between the gut and the brain, revealing that many neurotransmitters produced in the gut are eventually transported to the brain. For instance, serotonin and dopamine are largely produced in the gut, with about 95% of serotonin and approximately 50% of dopamine originating there. Serotonin is known as the "happy" neurotransmitter, contributing to feelings of contentment, relaxation, and joy. If the gut fails to produce sufficient serotonin, a person may feel negative and depressed. Dopamine is our "motivational" neurotransmitter, helping us wake up ready to face daily challenges. Individuals whose gut cannot produce this neurotransmitter may lack motivation, a major symptom of depression. Depression is a GAPS condition, Dr. McBride's clinical experience has shown that when treated with the GAPS protocol, irrespective of digestive symptoms or not, the production of seratonin and dopamine normalise. Microbes are also responsible for the production of the neurotransmitter gamma-amino butyric acid (GABA). If these are not produced a person will suffer from anxiety, panic, insomnia and depression as well as being proned to drug and alchohol abuse. It is often hard for these people to believe that their mental symptoms have anything to do with their gut, however, Dr. McBride has found that once successfully treated with the GAPS protocol their symptoms disappear. The gut has been referred to as the "second brain" of the body. However, some researchers now go further, labeling it the "first brain" and others even considering it an endocrine organ due to its own complex nervous system, hormone production, neurotransmitters, and various other substances. A group of researchers has even reported the discovery of an 'estrobolome', which consists of bacterial genes involved in estrogen metabolism within the gut. The gut produces around 40 hormones, with microbes playing a role in this process. These microbes produce their own hormones, which metabolize our hormones. For instance, research has demonstrated that steroid hormones excreted into the gut via bile are converted by a common bacterium, Clostridium scindens, into androgens, such as testosterone. From androgens, the gut flora can generate estrogen and other steroid hormones. Recent studies have demonstrated that microbes can affect our behavior, mood, and thoughts by producing active endorphins, which are substances that make us feel good as Dr. Natasha explains: "Every food craving you experience is likely driven by your gut flora; the microbes in your gut are addicted to that specific food and compel you to consume it by creating an overwhelming urge... Our bodies function as an ecosystem; they are not solely ours. They comprise a community of various life forms, coexisting and collaborating in the same space. Our lifestyle choices can alter the entire ecosystem, leading to numerous consequences."  There is of course so much more that I could say about the roles of microbes but I will conclude here and will now discuss how gut flora is passed to the baby. The baby's microbiome comes from the microbiomes of both the mother and the father (through sexual activity). Recent research has revealed that the uterus is not sterile (infact, nowhere in the body is sterile micobes are ubiquitous), it has a rich microbial community dominated by Lactobacilli, which plays a crucial role in conception and pregnancy. According to Dr. Natasha, women with abnormal uterine flora may struggle to conceive or maintain a pregnancy, making it a significant cause of infertility. Placenta has now been found to have it's own microbiome which surprisingly is similar to oral flora. Consequently, the baby's gut flora begins to develop in utero, during pregnancy, as the baby ingests microbial fluids from both the uterus and placenta. However, the majority of the baby's gut flora is acquired during birth when the baby passes through the mother's birth canal, ingesting a multitude of microbes present there. The mother's vaginal flora comes from her bowel, while the father's flora comes from his groin area. If either parent has abnormal gut flora, it will be passed to the baby at birth. A child starting life with abnormal gut flora will have a weakened immune system and constitution. If a child is born via c-section, this vital step of passing through the birth canal is missed. Research has shown that babies delivered by c-section have lower microbial diversity and lack bifidobacteria, a critical species essential for the development of the immune system and gut. Dr. Natasha Campbell McBride writes: We have an epidemic of abnormalities of gut flora in the world...As gut flora passes down the generations, this epidemic worsens. Before talking about the health of any child in my clinicI I always talk about the health of the parents and grandparents; and a typical scenario has emerged. After the Second World War the grandparents, who generally received healthy gut flora from their parents, may have had a few courses of antibiotics, which slightly damaged their gut flora. They passed this partially damaged gut flora to their children. Their children were born at a time when breast feeding was going out of fashion (replaced by artificial formulas), when antibiotics were given to children for every cough and sneeze, and when junk food was increasingly becoming a large part of children's diet. All these factors created generations of people with far more damaged gut flora than in their parents. The gut flora of women, on average, is more damaged than that of men because many of them took contraceptive pills for quite a few years before having children. The pill has a very damaging effect on the gut flora and the immune system of the woman. So, by the time the younger generation decides to have children, their gut flora is far more seriously damaged than in their parents' generation and that is what they pass to their babies. The situation is worsening with each generation. The epidemic of GAPS or abnormal gut flora increase every year. Moreover, many women and men are unaware that pregnancy serves as a way for a woman to detoxify her body. From a young age, women in today's society accumulate increasing levels of toxic chemicals in their bodies due to factors such as poor food and water quality, pestcides, personal care chemical products, hair dyes, makeup, and daily environmental exposures. Additionally, as women choose to have children later in life, their toxic load increases. During pregnancy, this accumulated toxic load is unloaded (dumped) into the baby, this high toxic burden further compromises the health of the child (if it survives). The firstborn child typically receives the highest level of these toxins, while subsequent pregnancies benefit from the mother's cleaner body, unless she has been exposed to significant amounts of toxins again. Tests on newborns' umbilical blood have detected around 287 toxins, including mercury, pesticides, and fire retardants. In a healthy mother, breast milk serves as a probiotic food and an additional source of microbes for the baby, which is why breastfed infants develop healthier gut flora compared to those who are bottle-fed. Breast milk is considered the ideal food because its composition is similar to that of the mother's blood. According to McBride, it contains live and active immune cells, immunoglobulins, enzymes, growth factors, hormones, neurotransmitters, and many other components. All of these vital elements contribute to the proper maturation of the gut wall, gut flora, immune system, nervous system, and all other organs and systems in the child's body. There is of course so much more to say but I will leave it there and finally conclude the introduction to the gut microbiome. My next post will be about the GAPS diet disspelling alot of confusion about animal foods and vegetables. Here is a study from The center for Microbiome Study at Stanford that you may find interesting: https://www.cell.com/cell/fulltext/S0092-8674(23)00597-4

INTRODUCTION: PART 2A This blog is for educational purposes only and should not be construed as health or medical advice. This blog post is a continuation of Introduction Part 1, my first 'That Gut Feeling" post, in February, so If you have not done so please read it as it provides context for this post. I am excited to include the first Game Changer's Video: The making of GAPS Meat Stock (Very Different), so please check it out in the GAME CHANGERS section of the blog! POST A few years ago, I took an online physiology course at Duke University; there we studied all the systems of the human body including the digestive system. During the entirety of the course, the word "microbiome or microbes" was never mentioned! It was a bit of a surprise, as by then, being the new frontier in western science, it had been somewhat amply researched and some of its roles, which is the purpose of this post, known. I came to realize that new scientific information trickles into the curriculum of universities and medical schools, certainly in the west. This was not the case for this subject in the former Soviet Union, where microbes had been researched intensively for well over a hundred years, and the concept of a microbial community taught in their medical schools, after Ilya Metchnikoff the "radical scientist" of his time received in 1908 the Nobel Prize in Physiology for his work in immunology. Metchnikoff was a keen observer who made a number of invaluable discoveries throughout his lifetime. For example, During the 1892 cholera epidemic in France, he was surprised by the fact that the disease affected only some people but not others when they were equally exposed to the infection. To understand the differences in susceptibility to the disease, he drank a sample of cholera but never got sick. He tested on two volunteers of which one was not affected while the other almost died. He hypothesised that the difference in cholera infection was due to differences in intestinal microbes, speculating that those who have plenty of beneficial ones would be healthier. (1) He developed a theory that aging was due to pathogenic microbes in the gut and that lactic acid in probiotics could prolong life; he therefore drank sour milk everyday of his life. Honoured as the Father of the innate immune system, he would go on to receive a number of scientific awards and honorary recognitions for his work. The human digestive tract is a very long tube open to the external enviroment from its beginning to its end. According to some researchers, the absorptive surface of this tract is about the size of a tennis court, maybe even larger! This long tube is covered from beginning to end with a thick layer of microbes living as a complex community in their own biofilm, a sticky substance they produce to make homes for themselves. A major part of this biofilm is mucus which is produced by the gut wall itself. So this mucus forms the basis for what we can call the "soil" inside us, serving not only as a barrier between the gut wall and the microbes but also as a major habitat for those microbes. In her book Gut and Physiology Sydrome Dr. McBride writes: Mucus looks quite magical under the microscope; it contains large molecules shaped like bottlebrushes, each made out of a central protein backbone with strings of sugar coming from it. These molecules are called mucins; they give mucus its gel-like consistency. Between these bottlebrushes there is a whole 'soup' of nutrients for microbes to live on ... but only in the outer layers of the mucus cover. As we go deeper into the mucus, it contains chemicals and immune factors which do not allow microbes close; by the time we penetrate to the gut wall it looks almost sterile. Every mucus membrane in the body produces this magical cover ... whether it is our nose, throat, sinuses, lungs, digestive system, urinary tract or elsewhere. One of the major roles of the microbes in the digestive tract is to protect us from invaders and toxins. They have many tools with which to do this, one of them is by producing and excreting powerful antifungals, antivirals, antibacterials as well as many other substances, most of which have not yet been researched. This not only keeps their own community in order and balanced but protects the gut wall from any microbes and parasites that come from the outside. They work closely with the immune system engaging it to appropriately respond to invaders. They also protect us from damaging chemicals we may consume with food and drink or other harmful chemicals produced as by-products of digestion. They do so by neutralising those substances and if unable to, they chelate them; that is, they hold on to them until they are removed through stool. Comparing the usage of microbes in the bioremediation process of contaminated soil, from the same book Dr. McBride writes: ... If the gut flora cannot destroy the chemicals it will chelate them... Like the claw of a crab, chelators in your gut flora grab hold of toxins until they are taken out of the body...This happens to toxic metals (such as mercury, lead, cadmium, arsenic, and aluminum), carcinogens and many other chemicals....gut bacteria are some of the strongest chelating agents we know protecting us from the most harmful chemicals in existence ... bacteria can neutralise and chelate chemicals even when they are dead;...research shows that when the gut flora is damaged and cannot neutralise and chelate toxins, our digestive system absorb large amounts of toxic metals and other damaging chemicals ... Cell regeneration is a marvelous process in the human body whereby our hard working cells die and are replaced by newly born cells. It is an ongoing process through out our lifetime which allows our body to regenerate, rejuvenate and to heal from damage. For example, in three to four months you will  have a "new" liver as most of your liver cells will shed and be replaced by newly born cells. Animal research has shown that the whole process of cell regeneration is controlled by our microbes; so the health of your newly born cells will be predetermined by the health of your microbial community. Cell regeneration is quite rapid in the gut lining where special epithelial cells called enterocytes work extremely hard to complete the digestion and absorption of nutrients from food; the cell regeneration process is about two to four days for these cells. Microbes in this process not only act as protectors of these cells but they also produce substances which nourish them and provide them with energy. If the microbial community is imbalanced the cell regeneration process goes wrong: amongst other things, the maturation of the enterocyte cells goes well beyond two to four days, the cell cycle activity in the crypts (the birth place so to speak of these cells) gets significantly suppressed leading to the birth of less cells and of unhealthy cells. The state of the cells themselves will be abnormal making them unfit to properly digest and absorb food leading to malnutrition. As this degenerative cycle repeats the ground is laid for disease as the gut wall becomes increasingly porous and leaky. One of the ways we use the GAPS diet is to specifically target the rapid cell regeneration process of enterocyte cells in the gut lining. We take advantage of this process to repair the lining by providing it with the most appropriate "building materials' (nutrients) with which to rebuild healthy enterocyte cells. At the same time we introduce probiotic foods to re-establish microbial balance to the orchestrators of this process and by so doing, we will "heal and seal" that porous/leaky gut wall. Those "building materials" are high fat animal foods as they are not only biochemically similar to our cells but they are also the only foods the human stomach can fully digest: meat, fish, eggs, raw or fermented dairy. Only foods which are properly digested are absorbed as nutrients to feed our very hard working, hungry organs ensuring they are not malnourished. A little known fact is that plants, for the most part, are "Indigestible" to the human stomach and so are unable to nourish us to any extent! They do have a role in the human body as cleansers/ detoxifiers, keeping us clean on the inside and are very much a part of the GAPS diet which allow them. The role of the microbes as well as GAPS foods will continue in next blog post. References 1) Lewis Danny (7 May 2015). "Probiotics Exist Thanks to a Man Who Drank Cholera" . Smithsonian Magazine . Retrieved 21 June2022

This blog is solely for educational purposes only and should not be construed as health advice. PART 1: INTRODUCTION While performing colonoscopies on patients with severe inflammatory bowel diseases, Dr. Robynne Chutkan, inflammatory bowel disease expert then at Georgetown University, observed complete healing from those diseases amongst certain patients who had made dietary changes. In an interview, she gave the example of the first patient in whom she saw this healing, a woman with severe Crohn's disease who had left the state for 2 years and who upon returning described herself as feeling better than ever after adopting the "Specific Carbohydrate Diet' "SCD". Upon performing her colonoscopy, Dr. Chutkan was amazed and shocked to see this woman's inflamed, ulcerated, bleeding, colon completely healed. She would go on to see this sort of healing amongst several of her patients who adopted this or similar type paleo diets. In the early 1990s Dr. Natasha Campbell McBride, a Soviet trained medical doctor, neurologist and neurosurgeon's first child was diagnosed severely autistic at the age of three. As there was no known existing treatment for this disability, she undertook to find a solution herself. After much research, she implemented a revised SCD diet as baseline treatment for her son's sickness, her son completely recovered.   In order to better understand the power of food on the human body, Dr. McBride returned to university for what she has described as her most profound education: a Masters of Science degree in Human Nutrition. Upon completing her degree  she opened a nutritional clinic first focusing on treating autism, learning disabilities and mental illnesses; she eventually branched out to other physiological illnesses upon her realization that poor health was also impacting other members within the families of those diagnosed with these illnesses/disabilities. After years of clinical practice she further modified the SCD diet to include amongst other things gelatinous meat stocks and fermented foods as key foundational foods for treating those illnesses.  In 2004 after many years of clinical practice and having helped thousands of people heal from disease she published her seminal book: "Gut and Psychology Syndrome: Natural Treatment for Autism, ADD/ADHD, Dyslexia, Dyspraxia, Depression, Schizophrenia" (acronym GAPS by her patients and followers). In this book which has been translated into 25 languages she outlined her hypotheses linking the state and health of the gut with the state and health of the mind introducing us to the concept of "microbes" as major orchestrators in this process. In it she writes:  "The human body is like a planet inhabited by huge number of micro-creatures. The diversity and richness of this life on every one of us is probably as amazing as the life on Earth itself! Our digestive system, skin, eyes, respiratory and excretory organs are happily coexisting with trillions of invisible lodgers, making one ecosystem of macro- and micro- life, living together in harmony. It is a symbiotic relationship, where neither party can live without the other...The largest colonies of microbes live in our digestive system...All these microbes are not just a chaotic microbial mass, but a highly organised micro-world with certain species predominating and controlling others. The number of functions they fulfil in the body is so vital to us, that if our gut got sterilised, we would probably not survive..."  Today more than 20 years after her hypothesis and the publication of her book, science has caught up and the microbiome is the new frontier in science with with well over 450,000 papers looking at the impact of the gut on all aspects of health. This ecosystem of trillions of micro organisms consisting of species of bacteria, fungi, viruses, protozoa, worms and many other creatures outnumber human cells by about 10 to 1 according to the NIH's "Human Microbiome Project".  In addition to that, some evolutionary biologists are hypothesising that a large percentage of human genes are of of microbial origin and they now speak of a holobiome or a hologenome which is the collection of human and microbial cells making one ecosystem of mixed genetics.  In her latest book published in 2020, called: "Gut and Physiology Syndrome: Natural Treatment for Autoimmune Illnesses, Arthritis, Gut Problems, Fatigue, Hormonal Problems, Neurological Disease" and which she describes as closing the GAPS concept by not only linking the state and health of the gut to the brain/mind but also to the state and health of the entire body, she writes:    "Healthy soil is nature's co-operative where every little thing is contributing and benefitting from the whole. Remove one of these elements and the balance is gone. Suddenly species, that used to be perfectly benign as part of the whole, start overgrowing and causing trouble...as a result, the soil stops supporting plants well and they become malnourished and sick...We have been doing the same to the soil inside us, to our gut flora, for decades...When the 'soil' in your digestive system gets damaged, instead of being your friend, it becomes a major enemy. Every microbe in the gut, even those deemed "beneficial", can start producing a plethora of toxic substances. These toxins absorb through the damaged gut wall and get distributed around the body.... There is no end to the microbes that can overgrow when the diversity of our gut flora is gone...Microbes take part in disease in the digestive system and any where else in the body, including mental and neurological illness, diabetes, obesity, cancer, allergies and autoimmunity...All we need to know is that unhealthy, unbalanced gut flora creates a river of toxicity, flowing from the gut into your body, and that the mixture of toxins is likely to be individual... In short, instead of being a source of nourishment, which is what our digestive system is supposed to be, it becomes a major source of toxicity in the body causing disease. Hippocrates, the father of modern medicines, stated almost 2 thousand years ago: 'All diseases begin in the gut!" No matter whether the disease is a chronic,  physical or mental disorder, he was absolutely right! Your digestive system holds the roots of your health! So, no matter what chronic illness we may suffer from we have to start treating it from the roots- the digestive system with its gut flora. It does not matter if you have digestive symptoms or not, the roots of your chronic illness is likely to be found in your gut." According to Dr. McBride, food is the most powerful influence on any microbial community in the body as it instantly changes the microbial composition causing certain species to die off and others to proliferate. Therefore, in order to change the microbial community in the human body, we must feed our body wisely. This is the GAPS diet, a high fat animal based diet with a strong emphasis on meat stocks and homemade probiotic fermented foods. Understanding the uniqueness of every individual, as no gut is the same, the diet offers many variations depending on ones health, cultural heritage, geographical region and area. All versions of the diet originate from the Original GAPS diet, they iclude: the original GAPS diet, the more- plant GAPS diet, the no-plant GAPS diet, the GAPS ketogenic diet and for those interested in fasting the GAPS liquid fast. GAPS describes health conditions and the solution Dr. McBride has designed is the GAPS nutritional protocol that encompasses not only diet but detoxification, minimal supplementation and healthy lifestyle changes like creating chemical free living enviroments. It's a demanding protocol but it has been designed in stages so as to be eased into gently if necessary. All of the above is described in her fully referenced books which she describes as self help books as she also includes plenty of recipes. This is probably enough to digest, stay tuned for Introduction Part 2 in about 2 weeks.