Our immune system: the body’s healing and defense mechanism

30 Aug 2016 no comments HAB Extract Categories General Suppliments

Good digestion is an essential part of heart health, it helps us absorb nutrients that are important for our heart. If you are using the products from the ‘Healthy Hearts Club’, you may have noticed that they go right to work without requiring much digestion. This is important since digestive disorders and compromised immunity are becoming an increasing health challenge. In particular, it is the health of the universe of bacteria that live in our gut, known as microbiome, that is essential for digestion, absorption of nutrients and immunity. Healthy gut flora digests protein, ferments carbs, breaks down lipids and fiber. On the other hand, unhealthy gut flora compromises digestion, immunity and determines our food choices. If you think you are in control when it comes to food, it may surprise you to learn that the bacteria that live in your gut is choosing your menu for you.

In a recent article from the New York Times titled ‘Educate your immune system’ the author, Moises Velasquez-Manoff, asserts: “In the last half-century, the prevalence of autoimmune diseases — disorders in which the immune system attacks healthy tissue in the body — has increased sharply in the developed world. An estimated one in 13 Americans has one of these often debilitating, generally lifelong conditions….Many researchers are interested in how the human microbiome — the community of microbes that live mostly in the gut and are thought to calibrate our immune systems — may have contributed to the rise of these disorders.” The author quotes a study done by a team of scientists who began following 33 newborns genetically at risk of developing Type 1 diabetes, a condition in which the immune system destroys the insulin-producing cells of the pancreas. “After three years, four of the children developed the condition. The scientists had periodically sampled the children’s microbes, and when they looked back at this record, they discovered that the microbiome of children who developed the disease changed in predictable ways nearly a year before the disease appeared. Diversity had declined and inflammatory microbes bloomed.” (1)

This very interesting research points the role the microbiome has in our health, and confirms what Dr. Natasha Campbell-McBride concludes with her research: “We carry most of our future health problems right in our gut from birth”. Her work as a neurologist and nutritionist proves that it is the universe of bacteria that live in our gut that comprises our immune system almost in its entirety. According to her, the microbiome makes up 90% of who we are and it is the health of these bacteria that determine our immunity.

Do you experience uncontrollable cravings for some not so healthy foods? Or do you feel rapid heartbeat after eating certain foods? It might be that your gut bacteria is out of balance. How would you like to supercharge your heart health by improving your immunity? In what follows we will focus on the latest research on gut health as explained by Dr. Natasha Campbell-McBride MD, MMedSci (neurology), MMedSci (nutrition). In the revised and expanded edition of her classic book ‘Gut and Psychology Syndrome’ she shares her knowledge about what we could consider the foundation of our health, the gut. After her son was diagnosed with autism, and not being able to find answers in her field of expertise, neurology, she decided to continue her education in human nutrition. This is when she learned how several factors have contributed to the decline of immune health in the general population.

Where does our immune system start?

According to Dr. Natasha it all starts at the moment of birth. As a baby passes through the birth canal, his skin, eyes, mucous membranes in the mouth and nose acquire their first micro-flora from the mother’s gut (mainly the lactobacillus, lactobacillus acidophilus, lactobacillus casei and lactobacillus fermentum). Since a baby is born with an immature immune system, this is crucial for the child’s immunity. This, together with breast milk provides the child with the immunity needed for the rest of his life. As the baby is breast fed, his digestive tract is populated with healthy bacterial flora from the mother. This plays a crucial role in the maturation of their immune system to such extent that if this doesn’t happen in the first twenty days after being born, the baby will be left immune-compromised for life according to Dr. Natasha.

This is how our immune system is supposed to become strong from birth. However, in her research she has found that in just the last few generations the health of our gut bacteria has been dramatically affected, causing an alarming increase in the cases of autism, learning and behavioral disorders in children and adults as well as psychiatric conditions, due to what she calls ‘the gut-brain connection’. In particular, the last few generations of women have experienced a greatly altered microbiome due to several factors. This change in the mothers’ gut bacteria has had a cumulative effect resulting in the current generation of women with a high percentage of pathogenic bacteria in the gut. Children born to these women have acquired the pathogenic bacteria present in the mother. This is in her opinion what explains the alarming increase in the cases of autism in the last decades that have gone from 1 in every 10,000 kids a few years ago to 1 in every 150 kids, both in the UK and the USA. In her clinic, where she treats these children she often finds other symptoms overlap with autism: ADHD/ADD, dyslexia, dyspraxia, behavioral and learning problems, allergies, asthma, eczema. All of these are also reaching epidemic proportions. What do all these conditions have in common? According to her research, the health of the gut. It is possible, according to her, to turn each of these conditions around by detoxifying the child’s gut and allowing it to heal. In her clinic she has seen autistic kids start talking for the first time after a course of colonics. She coined the term ‘GAPS’ to refer to her patients, which stands for ‘Gut And Psychology Syndrome’ and which we will use here often.

What factors have contributed to the decline in our beneficial bacteria?

In the world we live in, it is almost impossible to keep our gut flora healthy. We all face attacks on our gut flora on a daily basis:

1. Antibiotics: Probably one of the most commonly prescribed medications in our modern world. We are exposed to them not only through medication but also through foods. Farm animals and poultry, farmed fish and shellfish  are routinely given antibiotics so we get them when we eat these animals, plus the antibiotic resistant bacteria these animals produce in their bodies and the toxins these bacteria produce.

Research on antibiotics shows evidence that:

They have a devastating effect on human gut flora, as well as other organs.

Antibiotics change bacteria, viruses and fungi, from beneficial to pathogenic giving them the opportunity to invade organs and cause disease.

They make bacteria resistant to antibiotics. This translates into stronger antibiotics being needed and a new resistance to the these antibiotics.

Antibiotics have a direct damaging effect on the immune system, making us more vulnerable to infections, all of which leads to a vicious cycle.

What antibiotics do to the gut

When antibiotics are used on a high dose, they leave the gut with a lot of empty nitches to be populated by whatever bacteria, viruses or fungi get there first. This is a crucial time to administer a good probiotic to make sure that these niches get populated by friendly bacteria instead of pathogenic ones. Even when antibiotics are used for a short time and at a low dose it takes beneficial bacteria in the gut a long time to recover. E.coli takes 1-2 weeks, bifidobacteria and veillonelli 2-3 weeks, bacteroids and peptostreptococci 1 month. If in this period gut flora is subjected to another damaging factor gut dysbiosis may well start in earnest. Antibiotics have a deeper negative impact in children, breast feeding babies can get them through the breast milk if the mother is taking them. Combinations of antibiotic have stronger damaging effects on the gut flora than single drugs. Damage is worse when administered orally and for a long time on a low dose like the ones for acne or chronic conditions.

Among the most problematic we can find:

Penicillins: and all the ones that end with ‘cillin”. These damage two strains of good bacteria, the lactobacilli and bifidobacteria and allow the growth of the pathogenic proteus family, streptococci and staphylococci. These antibiotics allow bacteria only found in the bowel to move up the intestines, which predisposes the person for IBS (irritable bowel syndrome) and other digestive problems.

Tetracyclines: and all the ones ending in ‘cyclines’, usually prescribed for acne. They have a toxic effect on the gut wall by altering protein structure in many membranes. This does two things: makes the gut vulnerable to invasion by pathogenic microbes and alerts the immune system to attack these changed proteins, starting an auto-immune reaction in the body against its own gut. The cyclines stimulate the growth of the candida fungus, staphylococci and clostridia in the digestive tract.

Amino glycosides: Gentamycin, Kanamycin, Erythromycin and other ‘mycins’. These drugs have a devastating effect on colonies of beneficial bacteria in the gut such as physiological E. coli and Enterococci. A prolonged course of treatment can completely eliminate these bacteria from the digestive system, leaving it open to invasion by pathogenic species of E. coli and other microbes.

Antifungal antibiotics: Nystatin, Amphotericin, etc. These drugs cause a growth of the Proteus family and lactose-negative E. coli species, capable of causing serious disease.

Other drugs 

Most drugs when prescribed for long periods of time have a detrimental effect on gut flora:

Pain killers stimulate the growth of haemolytic forms of bacteria and campylobacter in the gut, capable of causing disease. Steroid drugs damage gut flora and shut down the immune system. Steroids in particular are linked with fungal overgrowth, specially candida.

Contraceptive pills have a devastating effect on the gut bacteria. Women on these medications will see a dramatic increase in pathogenic bacteria which will then be passed on to their children.

Many other drugs like sleeping pills, acid reducers, neuroleptics, etc also have a negative impact on gut bacteria.

Drug induced gut dysbiosis is the most severe and the most resistant to treatment.

What other factors can have an effect on gut flora?

2. Diet: processed food have a detrimental effect on gut flora. Sugar and processed carbohydrates (white bread, pasta, pastries, cake , biscuits, etc) increase the number of fungi, candida, bacteroids, worms and parasites. A diet high in fiber from grains (breakfast cereals specially) has a profound negative effect on gut flora, predisposing us for IBS, bowel cancer, nutritional deficiencies and many other problems. Fruit and vegetables are a better source of fiber and are not so harsh on the digestive system.

Starvation and overeating can critically change the composition of the gut flora and start a chain of health problems.

3. Serious infectious diseases like typhoid, cholera, dysentery, salmonella can cause lasting damage to the gut flora.

4. Surgery, chemotherapy, hormone therapy, and radiotherapy can also affect our gut flora.

5. Stress: Long term physical or psychological stress can damage our gut flora too.

6. Other factors: physical exertion, old age, alcoholism, pollution, toxic substances, radiation and extreme climates all have a profound effect on our friendly bacteria.

In all of these cases supplementing with a probiotic is a good treatment. Each of us has a unique mixture of bacteria, so under the influence of the factors listed above each of us will be predisposed to different health problems, completely unpredictable. Science has not developed reliable methods to test the full range of bacteria in the gut, much less treating any abnormalities. This damage is passed from generation to generation and as it does it gets deeper showing up in the severity of the health problems related to abnormal gut flora: digestive problems, immune problems, asthma, etc.

Where is our immune system?

A very important part of our immune system is located in the ileum, which is the last three fifths of the small intestine. The walls of the ileum are full of lymph nodes called Peyer’s patches. They have two major functions:

They filter the lymph removing bacteria, viruses, fungi, dead cells, toxins and even cancer cells. If the lymph nodes cannot destroy these bacteria they trap them.

These lymph nodes make lymphocytes, the most important group of immune cells that fight infections. When there is an infection they produce a lot of lymphocytes to fight infection, which makes lymph nodes large and inflamed sometimes painful–this is called lymphoid nodular hyperplasia.

What is more, the epithelial surface of the digestive system is the cradle of the immune system. This is where the beneficial bacteria live and where they play a major role in our immune system in a number of ways:

Bifidobacteria is the good bacteria mostly found in the human colon. It has a substance called ‘muramil dipeptide’ which activates lymphocytes. A healthy gut wall is literally packed with lymphocytes that protect the body from any offender. Scientific research shows that in people with poor gut flora there are few lymphocytes in the gut wall.

Lymphocytes in the gut produce immunoglobulins, the most important of which is ‘secretory immunoglobulin A (IgA)’. This one is secreted in body fluids so it can be found in the nose, throat, bladder, urethra, vagina, saliva, tears, sweat, colostrum, breast milk and the mucous membranes of the digestive system. Its job is to protect mucous membranes by killing bacteria, viruses, fungi and parasites that would come in from food and/or drink. Beneficial bacteria also slows down the degradation of IgA so it has more time to do its job. Due to abnormal gut flora, IgA is deficient in GAPS individuals and people with deficiency of good bacteria, making them defenseless against fungi, viruses, bacteria and parasites.

Apart from lymphocytes, other immune cells called neutrophils and macrophages are lacking when there is a deficiency of gut bacteria. These two literally swallow viruses, toxins, bacteria and cellular debris. Around 126 billion neutrophils pass through the wall of the gastrointestinal tract. In people with abnormal gut flora this destruction of pathogens doesn’t happen as effectively, allowing these viruses to survive inside the neutrophills and macrophages, the very cells that are supposed to destroy them.

Healthy gut flora also produce interferons, cytokines and many other regulators of immune system response, especially important in fighting viral infections. On GAPS people, these viruses have a good chance of surviving.

Another fascinating way in which the beneficial bacteria work with the immune system is called ‘mimicking phenomenon’. The bacteria on the surface of the gut epithelium swap antigens, improving efficiency of a large number of various immune responses.

Gut flora’s influence of the immune system reaches far beyond the gut itself. When gut flora is damaged the levels of IgA, lymphocytes, macrophages, interferons, cytokines, etc drop in the digestive system, but also in the whole body, getting out of balance. The result is a person that is immune compromised.

The two armies of the immune system 

Our immune system comprises two types of ‘armies’. On the one hand we have the Th1 (T-cell helper type 1). It promotes a so called cell-mediated immunity which is located everywhere in the body that is in contact with the outside world. Its role is to fight infection in the mucous membranes, skin and inside cells. It is the first and most effective barrier to any invasion into the body. Secretory immuno globulin A, interleukin-2 (IL-2), interleukin 12 (IL-12) , gamma interferon, etc belong to this system. Healthy gut flora has a very important role in keeping this part of the immune system healthy. When the flora is damaged it starts allowing microbes and toxins which activates the other part of the immune system, the less effective one, the Th2 immunity (T-cell helper type 2). This other part of our immune system is responsible for immunity in the liquids of the body. To this belongs interleukins 4, 5, 6 and 10. Alpha interferon and IgE (Immunoglobulin E)are activated in allergic reactions in the body. They are very active in people with asthma, eczema, hay fever and other allergies. In someone with abnormal gut, Th1 becomes low and Th2 becomes overactive, meaning the person is prone to allergies, chronic inflammation, auto-immunity, chronic viral infections, chronic fatigue syndrome, candidiasis, asthma, eczema, autism, etc. We need both Th1 and Th2 in the right balance. The reason behind this is that all these conditions share dysbiosis.

All of this points to an important fact: around 80% of our immune system is located in our gut wall with its bacterial layer. GAPS people and people with dysbiosis in general, because of abnormal digestion and absorption have unbalanced immune system. On top of that, someone with abnormal bacterial flora is exposed to extremely toxic substances, which damage immunity even more. Because of the absence of beneficial flora all the opportunistic microbes grow out of control. When this happens, the gut wall gets damaged and leaky, which causes a constant stream of invaders and undigested food to come through those holes compromising immunity further. People with GAPS have a compromised immune system, they lack some immunoglobulins, while others are out of proportion. Deficiencies in enzymes are also common. The most scary thing is that their immune system starts making antibodies that attack the body’s own tissues, including the brain and the nervous system, all because of the poorly functioning digestive system.

Many patients with compromised immune system have typical symptoms of IBS (Irritable Bowel Syndrome): abdominal pain, bloating, stool abnormalities and flatulence. A small percentage have normal stools but have malnutrition, reflux, heartburn and abdominal pain.

The roots of a tree

We could compare our body to a tree, with the roots being our digestive system and gut bacteria. A tree without healthy roots cannot be strong. Similarly our body cannot be strong without a healthy digestive system and good bacteria.

Of extreme importance is the kind of bacteria we have living in our gut. Our body lives in coexistence with trillions of highly organized invisible micro-organisms, with some predominating over others. The largest colonies of microbes live in our digestive system, where a healthy adult carries around 3-4 pounds of them. Their functions are so important that without them we would not survive. We can divide them as follows:

Essential/beneficial flora. The most important and numerous in a healthy person. To this belong bifidobacteria, lactobacteria, propionobacteria, e. coli, peptostreptococci and enterococci.

Opportunistic flora. There are around 500 various species of microbes that have been found so far in the human gut. In a healthy person their numbers are limited and controlled tightly by the beneficial flora. Each of these microbes are capable of causing various health problems when they get out of control. Among them we can find: yeasts, bacteroids, peptococci, staphylococci, streptococci, bacilli, clostridia, enterobacteria, fuzobacteria, eubacteria, catenobacteria, etc.

Transitional flora. These are microbes from the environment swallowed daily with food and drink. When the gut is well protected these microbes go through the digestive tract and do no harm, but if we have damaged flora they can cause disease.

Health and the integrity of the gut. The ‘sacred’ gut wall

The human digestive system is a long tube open at both ends. Harmful organisms from the outside world can enter it. We actually eat and drink micro-organisms, chemicals and toxins everyday. How do we survive? In healthy people there is a thick layer of indigenous bacteria that coats the whole digestive tract providing a natural barrier against invaders, undigested food, toxins and parasites. In inflammatory bowel disease, on the contrary, different pathogenic bacteria are found which allow the pathogens to reach the gut wall.

Apart from being a physical barrier, these protective bacteria produce antibiotic-like, anti-fungal, anti-viral substances, including interferon, lizocym and surfactins that dissolve the membranes of viruses and bacteria. The beneficial bacteria also reduce the pH near the wall of the gut to 4.0-5.0 making it acidic, which makes it almost impossible for bad microbes to survive because they require an alkaline environment to survive.

This is all important because pathogenic microbes produce a lot of very potent toxins, plus the toxins from the food we ingest. Healthy gut flora can neutralize nitrates, indoles, phenols, etc as well as inactivate histamine and chelate heavy metals. They also absorb carcinogenic substances making them inactive. However, if the beneficial gut bacteria are not present, all these invasions will cause disease. A pathogen like candida, and other viruses, bacteria, parasites, can then cause chronic inflammation in the gut. To this we need to add the opportunistic flora which live in the gut, they are always ready to cause trouble if their guardians, the good bacteria, get weak.

The gut lining is also coated with finger-like protusions called villi with deep crypts between them. These villi are coated by cells called enterocytes, they are of key importance because they digest and absorb the food we eat and convert it into food for the gut lining. The good bacteria in our gut work very hard to keep these enterocytes young. The enterocytes are constantly dying and being replaced by new ones, which means that the epithelium of the intestines is constantly being renewed. The problem comes when there is no good bacteria. Without good flora, the gut wall also becomes malnourished. This is because good flora are a source of energy for the enterocytes. When good bacteria are not present, this process of renewal gets out of order and can cause these enterocytes to become cancerous so fewer cells are born. When they are malnourished, degenerative changes start in the digestive wall, which further impairs its ability to absorb nutrients. All this is so important to understand, without good bacteria the cells that digest our food start dying, compromising absorption of nutrients, causing nutritional deficiencies and food intolerances.  What is more, holes start forming in the gut, which allow food particles to make it into the blood stream, causing auto-immune diseases and thickening the blood. This is all to say that the gut flora is the ‘housekeeper’ of the digestive system.

To make matters worse, the absence of good bacteria always coincides with bad bacteria getting out of control, which now are going to create havoc, release toxins and compound health problems even more.

Nourishment of the body

Healthy gut flora is essential for good digestion, it digests protein, ferments carbs, breaks down lipids and fiber. Byproducts of bacterial activity in the gut transport minerals, vitamins, water, gases, and other nutrients through the gut wall into the bloodstream. If the gut flora is damaged, the best foods and supplements in the world may not have a chance of being broken down and absorbed.

Apart from E. coli, other beneficial bacteria in the healthy gut flora will not only ensure appropriate absorption of nutrients from foods but will also synthesize nutrients like vitamin K 2, B 5, folic acid, B 1, B 2, B 3, B 6 and B 12. Healthy gut flora are our own factory for these vitamins. When healthy flora is damaged, despite adequate nutrition, we develop vitamin deficiencies. This is because many vitamins have a short life in the body, so a person without good gut flora is unable to provide a constant steady stream of vitamins and other active substances for the body to use. Every GAPS patient and person with dysbiosis is deficient in these vitamins that their gut flora is supposed to produce. Restoring the beneficial bacteria in their gut is the best way to deal with those deficiencies.

People with abnormal gut flora have multiple nutritional deficiencies, the very minerals, vitamins, essential fats, amino acids that are necessary for the brain, immune system and rest of the body: magnesium, zinc, selenium, copper, calcium, manganese, sulphur, phosphorus, iron, potassium, sodium, vitamins B 1, B 2, B 3, B 6, B 12, C, A, D, folic acid, pantothenic acid, omega 3, 6, 9 fatty acids, taurine, alpha keto glutaric acid, glutathione, etc.

Fiber for your heart

Certain foods like fiber are impossible to digest without beneficial bacteria. In a healthy gut, fiber gets broken down into oligosaccharides, amino-acids, minerals, etc that feed the gut wall and the rest of the body. The beneficial bacteria feed on fiber, producing a whole host of good nutrition for the gut wall and the whole body. Good bacteria also engage fiber in:

Absorbing toxins.

Water and electrolytes metabolism.

Recycling of bile acids and cholesterol, etc.

It is the bacteria acting on fiber that allows it to perform all of these good functions in the body. When gut bacteria is damaged, they are not able to work on the fiber, so fiber can become dangerous for the digestive system, providing a good habitat for the pathogenic bacteria to grow and aggravating the inflammation in the gut wall.

The opportunistic flora

The opportunistic flora is a large group of around 500 various microbes living in our gut in a unique number and combination. The most common are: bacteroids, peptococci, staphylococci, streptococci, bacilli, clostridia, yeasts, enterobacteria (proteus, clebsielli, citrobacteria, etc), fuzobacteria, eubacteria, spirochaetaceae, spirillaceae, catenobacteria, different viruses and many others. In a healthy gut their number is limited and tightly controlled by the beneficial flora with which they live in balance. When this is the case, these opportunistic bacteria fulfill some beneficial functions in the gut like digesting foods, breaking down lipids and bile acids.

However, when the good bacteria get weak, the opportunistic bacteria get out of control. Each of these microbes is capable of causing various health problems. Because each of us have a unique microbiome, the character of our individual opportunistic flora will determine what disease we succumb to. According to Dr. Natasha “We carry most of our future health problems right in our gut from birth”. The best known of these pathogens is candida albicans. The problem with candida is that it never acts alone in the human body. What many times is described as candida is actually dysbiosis, which includes lots of other opportunistic and pathogenic microbes. Candida’s ability to survive and cause disease depends on the state of trillions of its neighbors: bacteria, viruses, protozoa, other yeasts, etc. In a healthy body, candida is well controlled by beneficial bacteria. However, the usually prescribed broad spectrum antibiotics kill the different microbes in the body but have no effect on candida. What this means is that after a course of antibiotics, candida is left alone to thrive. In her years of experience, Dr. Natasha has observed that when antibiotics started being used doctors would prescribe Nystatin (an anti-candida antibiotic) as part of the antibiotic treatment, but that practice has been abandoned, which has caused an epidemic of candida infections in the general population. Apart for antibiotics, she has observed that our diet high in sugar and processed carbs has also contributed to the increase in candida overgrowth.

How do these pathogenic bacteria affect us?

The pathogenic bacteria listed above, when they get out of control can make it through the gut wall barrier into the bloodstream affecting different organs of the body, but first and foremost the digestive system. The most common result of dysbiosis is IBS (Irritable Bowel Syndrome) caused by these opportunistic bacteria populating the intestines. More and more research is coming out linking Crohn’s disease and ulcerative colitis with these opportunistic bacteria getting out of control.

Some of these opportunists, when not controlled by good bacteria, can reach the gut wall and damage it, making it ‘leaky’. The spirochaetaceae and spirillaceae for example, because of their spiral shape can push apart intestinal cells, breaking down the integrity of the intestinal wall and allowing through substances which would normally not get through. Candida albicans has this ability as well, its cells attach themselves to the gut lining, literally putting ‘roots’ through it and making it leaky. Partially digested foods then make it into the blood stream, where the immune system attacks these ‘foreign’ substances. This is how food allergies or intolerances develop. In many cases when the gut wall is healed food allergies disappear.

Another way in which opportunistic flora affect us is that they are constantly releasing toxic substances. An example are the proteus family, E. coli family, staphylococci and other bacteria. All of these pathogens in the gut make histamine. Histamine is an important neurotransmitter in the body and many cells in the body naturally produce histamine, the problem is when these bacteria get out of control and there is no good bacteria to stop them. If this is the case, they produce too much histamine. Since histamine has many different functions in the body, when these bacteria start producing too much histamine it travels through the blood and affects all these functions in the body. This can manifest as: allergies, low blood pressure, excessive body fluids like saliva, dysfunction of the hypothalamus with hormonal changes like PMS, emotional instability, sleep abnormalities, addictions, etc. According to Dr. Jockers, histamines can effect the gut, lungs, skin, brain and the entire cardiovascular system. He asserts: “This is why there are such a wide array of health problems associated with histamine and it is quite challenging to pinpoint and diagnose if you are not aware of the condition.”. (2) Signs of histamine intolerance are:


Difficulty falling asleep, easily arousal


Vertigo or Dizziness

Arrhythmia, or accelerated heart rate 

Difficulty regulating body temperature


Nausea, Vomiting

Abdominal cramps


Nasal Congestion, Sneezing, Difficulty Breathing

Abnormal menstrual cycle



Tissue swelling

Unexplained cravings?

A group of opportunistic gut bacteria, the bacteroids, is found in abundance in adult population in the western world. This bacteria like to eat sugar, starch and lactose. So far 22 different members of this family have been identified in the human gut. The most common are ‘bacteroides fragilis’ and ‘bacteroides melaninogenicus’. These bacteria are almost always found in infected tissues of the digestive tract, abscesses, ulcers, lung infections, peritonitis, infected heart valves, blood infections, urinary infections, mouth infections, teeth and gum disease, gangrene and post-operative infections. These bacteria are opportunists which means they are always present in every mucous membrane of the body waiting for their opportunity to cause trouble. However, they never act alone and always need other bacteria to really cause damage, like clostridia, which is even more dangerous than bacteroids.

There are around 100 different clostridia known so far. Many clostridia members are normal inhabitants in the human gut. For example, ‘clostridium tetani’ is found in the gut of healthy animals and humans. Spores of these bacteria are passed from the stools to the soils, where they can survive for years. Most soils in the world have spores of this bacteria. ‘Clostridium tetani’ normally lives in the gut where it causes no harm, even though it can produce a very powerful neurotoxin. What keeps it from being harmful? The health of our gut wall, which is always maintained by good flora. When this gut wall becomes vulnerable, it allows clostridia to make it through the gut wall. Dr. Natasha has observed that her GAPS patients, because they do not have a healthy gut wall, have this toxin in their blood. In her patients these neurotoxins produced by clostridia can cause nervous system and brain problems. Just like candida, clostridia has been allowed to grow out of control with every single course of broad spectrum antibiotics. Different species of clostridia cause severe inflammation of the digestive system, for example ‘Clostridium difficile’ can cause fatal colitis, others cause crohn’s disease and ulcerative colitis. Anti-clostridia drugs like ‘Metronidazole’ (Flagyl) and ‘Vancomycin’ have been shown to reduce autistic symptoms and improve digestion in autistic kids, but as soon as the drug is stopped the symptoms come back. What is more, anti-clostridia drugs are toxic and have serious side effects so they cannot be prescribed for long. Clostridia are spore forming bacteria, because of this they are impossible to eradicate, we can only keep them under control with good bacteria.

Other opportunistic bacteria are the ‘sulphate reducing bacteria’. They break down sulphate from food into sulphites, many of which are toxic. Sulphates are needed by the body for the detoxification of brain neurotransmitters. An abundance of these bacteria make sulphate unavailable to the body. It will also make sulphur unavailable and will turn it into toxic substances like hydrogen sulphide (rotten egg gas). For this reason GAPS people’s feces have a characteristic smell.

Other viruses active in GAPS people are the ‘measles virus’ and the ‘herpes virus’. There are many others that haven’t been studied yet. In the meantime, the only way to protect ourselves from candida, clostridia, and bacteroids is with good bacteria.

The gut-brain connection

Because every organ in the body exists and works in contact with the rest, one should not look at, let alone treat any organ, without taking the rest of the body into account. The usual treatment with antidepressants, sleeping pills, etc end up affecting the brain too. According to Dr. Natasha, psychiatry likes to look at the brain alone separated from the rest of the body and never looks at the gut for a solution, but research is showing how severe psychiatric conditions can be cured by simply “cleaning out’ the patient’s gut. Most psychiatric patients she has seen suffer from digestive problems. In these patients, the gut is a constant source of neurotoxins coming from abnormal flora which are absorbed through the gut wall into the blood and then the brain. The mixture of toxins is very individual and this is why GAPS patients are all different. The number of toxins is unknown, but research has accumulated a lot of information on what kind of neurotoxins are found in GAPS patients:

1. Ethanol and acetaldehyde:

Yeasts including candida eat sugar and glucose. These two come from the digestion of carbohydrates from our diet. In a healthy person glucose is converted into lactic acid, water and energy through a process called glycolisis. In people with candida, this fungus highjacks glucose and digests it in a different way. This is what is called alcoholic fermentation. By this process candida converts glucose into alcohol (ethanol) and its byproduct acetaldehyde. This makes the person ‘drunk’ after consumption of carbohydrates even when they didn’t drink any alcohol. Alcohol is absorbed into the blood stream very quickly. In the case of pregnant women, this alcohol can make it into the placenta and affect the fetus and its development directly. When the baby is born, breastfeeding will affect the baby too because the alcohol is in the blood and can make it into the breast milk. Then because the baby inherits the mother’s flora, overrun by yeast, the child will start producing its own alcohol and other toxins. Chronic presence of alcohol in the body have these effects:

Reduced ability of the stomach to make acid.

Pancreatic degeneration which reduces the ability of this organ to make enzymes, impairing digestion.

Direct damage to gut lining, causing malabsorption.

Vitamin, mineral and aminoacids deficiencies due to malabsorption, specially vitamin A and D.

Damage to immune system.

Liver damage with decreased ability to detoxify toxins, drugs, pollutants and poisons.

Inability for the liver to dispose of old neurotransmitters, hormones and other by-products of normal metabolism. All these accumulate in the body causing behavioral and other problems.

Brain damage with loss of self-control, impaired coordination, speech development, mental retardation, loss of memory,etc.

Peripheral nerve damage with altered senses and muscle weakness.

Direct muscle tissue damage with altered ability to contract and relax and muscle weakness.

Alcohol has an ability to enhance toxicity of most common drugs , pollutants and toxins.

Alteration of metabolism of proteins, carbohydrates and lipids in the body.

Acetaldehyde is one of the most toxic of alcohol by-products, it can alter the structure of proteins in the body. This is significant because we are mostly protein (from hormones to enzymes). When these proteins in our body are changed by acetaldehyde, they cannot do their job. This is when many auto-immune diseases start. One of the parts of our body that can be attacked is the ‘myelin’ that coats nerve and brain cells, resulting in multiple esclerosis in adults. In children this will show up as neurological problems like autism.

Acetaldehyde also makes many essential nutrients useless in the body, like is the case of B 6, which is a cofactor in the production of neurotransmitters, fatty acid metabolism, etc. Even if the person is consuming B 6 rich foods, acetaldehyde keeps this vitamin from being where it can be used, so B 6 floats around in the body and eventually gets excreted. This also happens to other vitamins in the body that usually bind to proteins to do their job.

Another organ that acetaldehyde affects is the thyroid. The thyroid gland may be producing plenty of hormones but their working sites are occupied by acetaldehyde and other toxins, causing thyroid dysfunction: depression, lethargy, fatigue, weight gain, poor body temperature control, poor immunity, etc.

2. Opiates from gluten and casein

Gluten is a protein found in grains like wheat, rye, oats and barley. Casein is a milk protein in cow’s, goat’s, sheep’s, human’s and all other milk products. In GAPS people these proteins don’t get digested properly and turn into substances similar to opiates, such as morphine and heroin. These substances called gluteomorphins and casomorphins have been detected in the urine of patients with schizophrenia, autism, ADHD, post-partum psychosis, epilepsy, down’s syndrome, depression, and some autoimmune diseases like rheumatoid arthritis. These opiates from wheat and milk are thought to cross the blood brain barrier and block certain parts of the brain, just like morphine and heroin would do. Why does this happen? It all starts with digestion, the digestion of proteins starts in the stomach with the action of pepsin, a protein digesting enzyme produced in the stomach. Stomach acid is essential for the digestion of protein, as it produces the right conditions for pepsin to do its work of breaking down proteins. GAPS people commonly have low stomach acid due to abnormal gut flora and pathogen overgrowth. For example, candida alone can make toxins that have a strong suppressing ability on stomach acid production. A pregnant woman can have these toxins from candida in her breast milk and it is possible that children that are being breastfed can get these toxins and have their stomach acid reduced early in life. While being breastfed, since breast milk doesn’t require much digestion, symptoms may not show up, but they will when other foods are introduced. By the time breastfeeding stops, the child’s body will have produced enough on his own candida and other toxins to keep reducing his stomach acid. Usually the first weaning foods after breastfeeding are milk and wheat. If the child is not making enough stomach acid, the first steps in digestion will already be compromised, so proteins will not be able to be broken down. These undigested proteins will go into the intestines where the pancreas is supposed to release enzymes to break down food further, however, without stomach acid, the pancreas is not going to release enzymes, so the next step in digestion is also compromised. Next, these undigested proteins reach the final stage, the intestinal wall, which is lined up with highly sophisticated cells, the enterocytes, which on their surface have a whole host of different digestive enzymes to complete the breakdown of food. Because in GAPS people these cells are in poor shape due to abnormal gut flora, they are not able to digest gluten, casein etc. Some research done on one of the enzymes found on the enterocytes, known as dipeptidyl peptidase IV (DPP IV), has shown that GAPS children, alcoholics, schizophrenics, depression sufferers and people with auto-immune diseases are deficient in this enzyme. Some enzyme products in the market incorporate this enzyme. The problem is that there are so many more enzymes we haven’t researched that digestive problems continue to be an health problem.

With the lack of beneficial bacteria the enterocyte cells fall sick, the result is indigestion and malabsorption. What is more, pathogenic bacteria, fungi and viruses damage the gut wall and allow undigested food to end up in the bloodstream where they can reach the brain. While some GAPS patients do well on a gluten and milk restricted diet (GFCF DIET), others do not, this is because there are many other aspects in these patients to take into consideration.

Research has shown a direct link between the consumption of grains and milk and the increase in the cases of schizophrenia and mental diseases. Mainstream medicine never considers the root cause to be the gut, instead they prescribe drugs that cause dependency and in the long term shrink the brain. Dr. Natasha recommends to slowly wean the patient off those drugs, while healing the gut and repopulating the good bacteria.


Dr. Natasha’s treatment for digestive disorders consists on detoxifying the person and lifting the toxic fog off their brain to allow it to fully function. To achieve this first the gut has to be cleaned up and the digestive system healed, so it stops being the first source of toxicity and becomes a source of nourishment as it is intended to be. Second, to remove toxicity that is already stored in the tissues of the body. This is what she called the GAPS program, which she developed from her personal experience with her own son, and the many children and adults she has personally treated in her clinic. Her program has three parts: diet, supplementation and detoxification. In our next blogs, we will look with detail at the diet.

Thanks for reading.


(1) http://www.nytimes.com/2016/06/05/opinion/sunday/educate-your-immune-system.html

(2) http://drjockers.com/suffering-histamine-intolerance/

(3) http://drjockers.com/is-your-brain-making-enough-gaba/

(4) http://drjockers.com/7-reasons-to-use-carminative-herbs/
(5) http://drjockers.com/10-ways-ginger-enhances-digestion/