The Guide to Healing Your Gut

Review of the Microbiome

In these series of articles on the Microbiome we have discussed its role in the immune system, its connection via the blood brain barrier and how the gut becomes ‘diseased’ which is more appropriately expressed as ‘imbalanced‘, a condition called Gut Dysbiosis

Diet plays a huge part in maintaining balance or causing imbalance as well as exogenous and endogenous toxins. In previous articles on the microbiome we discussed the composition of the gut flora ( microbiome, microbiota) consisting of Beneficial vs opportunistic or commensal bacteria. and Pathogenic bacteria,viruses and Fungi.  These are all constituent parts of our internal microbial eco system. In fact Fungi are considered a seperate eco system referred to as the Mycobiome.

Beneficial are micro-factories producing anti-biotic, anti-viral, anti-fungal substances to maintain health and balance in the gut. Bacteria give birth to many offspring to take the place of their parents who have for example have chelated heavy metals like mercury, arsenic, and aluminum that have found their way into the body from fish consumption.

Opportunistic can exist as either beneficial or opportunistic gut flora, dependent upon the healthy state of the beneficial bacteria since healthy gut flora keep the opportunistic flora in check. In some instances our beneficial flora inoculate or neutralize pathogens that populate the commensal flora colony.  These ‘micro-creatures protect us, the host.  

Pathogenic are by far the most dangerous of the

Some bacterial colonists bind these heavy metals to themselves to escort them out of the body, essentially sacrificing themselves to be eliminated in the stool of the host.  Despite government warnings to reduce fish consumption because of our polluted bodies of water ( rivers, the ocean ), it generally will not affect people with healthy gut floras.

80% of our immune system resides on the gut wall and our beneficial flora modulate this main defense system, and its modulation is achieved by our bacterial flora which is why it is so crucial that there is a working symbiotic relationship between the host and the gut bacteria as we mentioned in previous articles.  

The central command areas, the ‘Peyer’s patches’ that are attached to the epithelium, launch immune system responses recruiting T and B Lymphocyte cells, Macrophages and Dendrites. It is the beneficial bacteria species Bifidobacteria that activate the the T & B Lymphocyte cells using a secreted substance Muramil Depeptide.  

Furthermore, our gut flora assist in our protection by destroying potential harmful bacterial species, where some species of E.Coli produce protein based Bacteriocins to kill off competing species, thus controlling the growth of enterohemorrhagic E.Coli.  

The gut flora act as balancing agents for TH1 and TH2 responses preventing spurious allergic reactions that can happen any time in a persons life, if imbalance occurs, especially if the liver suffers toxic overload as explained below.

Microbiome and Digestion Review

In the article on digestion, we discussed the purpose of our digestive system and its function to digest/absorb food and nutrients, but it can only do so if the microbiota is functioning efficiently and the various microbial colonies are happy and fed well with nutritional food.

Efficient digestion and absorption is performed by our epithelial cells, the enterocytes that our bacteria help to orchestrate functionally.

If we have consumed insoluble fibers from plant sources, i.e lignans or some other indigestible fibre than our bacteria will break it down by fermentation, producing Short Chain Fatty Acids (SCFA) such as propionate, acetate and butyrate which are then ingested by other microbial species to achieve optimal energy for the host.

Our healthy gut consists of  3 dominant Bacterial Phyla : Bacteroidetes, Firmucutes and Actinobacteria.which will change depending on the health status of the host. ( e.g  Firmicutes  will dominate over Bacteroidetes in an obese person ).  

Nature in its infinite intelligence has provided for us certain beneficial bacterial strains that produce Vitamins K2, B1, B2, B6, B12 and others that synthesize nutrients such as Vitamins K2, B5, B1, B2, B3, B6, B12 and folic well as antibiotic substances called Colicins within the colon.

Even if food and nutrients are scarce and the gut is functioning our bodies will still be nourished with essential nutrients internally.  

However, if the gut is not functioning these nutrients are not synthesised, causing nutrient deficiency and individuals can look pale and pasty which are obvious signs of anemia because they are B12 deficient.

The Most Vulnerable – The Newborn Infant

In terms of gut health versus gut dysbiosis the most vulnerable are new born infants.  

If the child is born naturally through the birth canal the baby will swallow the bacterial content of the mother’s vagina which contains part of the fathers gut flora.  

Both bacterial flora in this area comes from the bowel, which is combined with the baby’s immature microbiome developed while in the womb (despite current thinking that the infant is not sterile prior to birth, since some bacterial strains get through the placenta to the embryo).  

If the mother’s gut flora is dysbiotic than the baby will have a compromised gut flora as well as a compromised immune system (it is the first 20 days of life that defines the microbiome prior to its maturation stage). If the baby is breastfed, and despite its mother having gut dysbiosis, she will produce some antibodies that gives the baby some protection (it is easy to see why, from the rich content of nutrition contained in breast milk as seen below).  

However, a compromised gut flora infant in its first year of life may contract ear infections and chest infections which are ignorantly treated with antibiotics doing further damage.

Once the breast feeding stage is over, the gut damaged child is vulnerable, and if the child is quackzenated the child’s compromised immune system can’t handle the potential harmful substances like animal proteins and powerful adjuvants used to trigger an immune response.

Dr Natasha Campbell Mcbride believes that quackzenes per se do not cause Autism, but they are a ‘last straw’ trigger on an already compromised host in terms of their gut flora and ultimately their immune system.  She relates to us that children that she sees in her clinic that are autistic, some have never been quackzenated.  

The Nutrient Richness of Breast Milk

It cannot be stressed enough that breast milk is the most nutritious substances that exists.  It contains :

Carbohydrates: Lactose and oligosaccharide (many simple sugars that make up fibre in plants,many vegetables, healthy dietary fibre digested by our bacteria).

Carboxylic acids including Alpha hydroxy acid ( a natural exfoliant that supports skin cell replacement) and lactic acid.

Proteins: (Whey, Alpha Lactalbumin ( contains 123 amino acids for nutrition), Lactoferrin (used as an anti-inflammatory and antioxidant), Casein, Serum albumin (for cell health)

Nitrogenous compounds: Creatine (muscle growth)

Amino acids: 

Alanine (helps convert glucose into energy and helps liver excrete toxins),

Arginine (E) (used to support muscle health and immune system support),

Aspartate (used to support metabolism),

Glycine (used to create muscle tissue and convert glucose into energy),

Cystine (used for skin,hair,bone and connective tissue health and the production of Glutathione),

Glutamate (support for efficient neurotransmission),

Histidine (E) (used to support healthy tissue throughout the body including Myelin sheath neuron insulation),

Isoleucine (E) ( used to boost energy and recover from strenuous exercise),

Leucine (E) used for muscle repair, blood sugar regulation and energy production)

Lysine (E) (Antiviral support)

Methionine (E) (used to eliminate fat tissue and is used to produce Glutathione),

Phenylalanine (E) (used to support the central nervous system ) ,

Proline (used for the production of collagen and cartilage),

Serine (overall health incl brain and CNS function) ,

Taurine (E) (regulation of the nervous system and muscles, brain and heart health)

Threonine (E) (maintains protein balance in the body)

Tyrosine (E) (supports mood regulation and nervous system stimulation, metabolism booster)

Valine (E) (promotes normal growth, tissue repair,blood sugar regulation, works together with Isoleucine and leucine)

Carnitine (fatty acid transporter to cell mitochondria for acid to energy conversion)

(E = Essential amino acids) These cannot be made in the body.  There are 11 essential amino acids.  Arginine is used to prevent cancer and hypertension, Taurine is used to prevent macular degeneration and Tyrosine to prevent goiter.

Nucleotides: 13 are contained in breast milk, these are the building blocks for nucleic acids used for DNA synthesis

Fatty Acids (Polyunsaturated):

ALA (E) (Alpha Linolenic acid) an omega 3 fatty acid derived from plants and seeds like flax and hemp seeds. It is the most essential acid for health even more than DHA/EPA. Its derivatives are normally DHA/EPA but these are also a constituent part of breast milk

LA (E) (Linoleic acid) an essential omega 6 fatty acid.

EPA (Eicosapentaenoic acid) Fish derived omega 3 fatty acid used anti-inflammatory agents

DHA (Docosahexaenoic acid) Fish derived omega 3 fatty acid used anti-inflammatory agents

CLA (E) (Conjugated Linoleic acid) is an essential omega 6 fatty acid that supports metabolism and immune system

Fatty Acids (Monounsaturated ):

Oleic acid is an omega 9 fatty acid that controls blood pressure, cell protection from free radical damage, it also generates brain myelin

Palmitoleic acid is a rare omega 7 fatty acid that is used as a signaling molecule providing fat and muscle tissue communication

Heptadecenoic acid supports metabolism

Fatty Acids ( Saturated ):

Stearic, Palmitic acid, Lauric acid, and Myristic acid

Phospholipids there are 6 varieties in breast milk and used to support cell membranes

Sphingolipids there are 11 varieties in breast milk that support cell membranes of the brain and nervous tissue.

Sterols: 15 types are naturally found in breast milk including Cholesterol, Vitamin D3 metabolite ( 7-dehydrocholesterol – precursor for Vitamin D3 sulphate ), squalene an omega 2 oil ( found in abundance in shark liver to protect deep dives with very little oxygen) but for humans it is an anti-cancer and anti-cardiovascular disease.  It supports extreme sportsman during high intensity exercise and lack of oxygen but this substance diminishes rapidly in the body over between the ages of 30-40.

Nutrients: Vitamin A,Beta carotene,Vitamin B6,Vitamin B8 (Inositol),Vitamin B12 Vitamin C,Vitamin D,Vitamin E,a-Tocopherol,Vitamin,K,Thiamine,Riboflavin,NiacinFolicacid,Pantothenic acid,Biotin,Calcium,Sodium,Potassium,Iron,Zinc,Chloride, Phosphorus,Magnesium,Copper,Manganese,Iodine,Selenium,Choline,Sulpher, Chromium,Cobalt,Fluorine,Nickel,Molybdenum

Growth Factors: used to mature the intestinal lining, and there are 22 in total including Tumor necrosis factor-α,Interferon-γ,Epithelial growth factor (EGF), Transforming growth factor-α (TGF-α).TGF β1,TGF-β2,Insulin-like growth factor-I (IGF-I), Insulin-like growth factor- II and Cytokines  IL-2,IL-4,IL-6,IL-8,IL-10, Granulocyte-colony stimulating factor (G-CSF), Macrophage-colony stimulating factor (M-CSF), and Platelet derived growth factors (PDGF)

Peptides: there are 14 types that are used for muscle growth including Parathyroid hormone (PTH), Parathyroid hormone-related peptide (PTHrP), β-defensin-1,Calcitonin, Gastrin, Motilin

Hormones: 24 in total including Cortisol, Triiodothyronine (T3), Thyroxine (T4), Thyroid stimulating hormone (TSH) (also known as thyrotropin), Thyroid releasing hormone (TRH), Prolactin, Oxytocin Insulin, Corticosterone, Thrombopoietin, Gonadotropin-releasing hormone (GnRH)

Enzymes: Amylase, Arysulfatase, Catalase, Histaminase, Lipase, Lysozyme, PAF-acetylhydrolase, Phosphatase, Xanthine oxidase

Antiproteases: used to prevent allergic reaction : a-1-antitrypsin,a-1-antichymotrypsin

Antimicrobial factors: 38 in total including  Leukocytes (white blood cells), Phagocytes, Basophils, Neutrophils, Eosinophils, Macrophages, Lymphocytes, B lymphocytes (also known as B cells), T lymphocytes (also known as C cells), sIgA (Secretory immunoglobulin A), , Ribonuclease, Haemagglutinin inhibitors, Bifidus Factor (increases growth of Lactobacillus bifidus), Lactoferrin (binds to iron which prevents harmful bacteria from using the iron to grow), Lactoperoxidase, B12 binding protein.
As you can see from the above list Breast milk is an extremely powerful substance to protect the newborn infant.

Gut Dysbiosis and the Young Adult

If the gut dysbiosis is not fixed in infancy, the growing child will continue to have digestive problems and prefer to eat nutritionless food that is starchy and contain excessive sugar.

The child can develop social ,and/or behavioural problems as well as learning difficulties (Dyslexia) or developmental coordination disorder (Dyspraxia ) at school, making the young adult a potential outcast who is yearning to ‘fit in’.  

The parent sees their offspring depressed and introverted because their gut is unbalanced causing this ‘shape shifting’ of their character. Some even turn to substance abuse which can have devastating effects.  

Dr Natasha Campbell-Mcbride refers to these young people as GAPS (Gut and Psychology/Physiology Syndrome) individuals.

A normal teenager that smokes Cannabis generally is perfectly okay, but a GAPS individual with gut dysbiosis runs the risk of having a psychotic episode which may even develop into Schizophrenia. If the child is taken to a Psychiatrist, OMG, problems will escalate if he is prescribed a mind altering psychotic substance. The only way to heal these individuals is the administration of the GAPS diet which can be a long journey but a worthwhile one to normalize the individual for the rest of their lives.

Gut Dysbiosis Review

I cannot stress enough that mothers milk is remarkably nutritious and no infant formula is going to come close to the same nutrient density.  

So young mothers, seriously, seriously consider breastfeeding; your baby will thank you for it and so will you in the long run.  

If the child’s gut flora is dysbiotic, than once the breast feeding ceases, problems could start to appear emanating in autism, hyperactivity or some other behavioural and learning dysfunction, as well as digestive issues.

We have discussed the epithelium, the enterocytes and their digestive enzymes and the tight junctions that glue the epithelium together with zonulin protein in previous articles.  

The only way that nutrients can pass the gut barrier is by the epithelial cells (enterocytes) that take the nutrients into the cells, examined and released into the bloodstream.

However, with gut dysbiosis, pathogenic bacteria can break the tight junctions by chemically dissolving the zonulin proteins thus destroying the enterocyte security and all substances like bacteria, undigested food particles pass through unheeded, straight into the bloodstream.

This is labeled Leaky gut syndrome – I don’t know why this is called ‘syndrome’ because we know what it is, and we know what causes it but allopathic medicine is still looking for the gene that causes it.

The enterocytes themselves become damaged, the microvilli or brush border becomes damaged and they are unable to break down food substances because the enzymes that sit on the brush border become inactive.

When undigested food particles leak through into the bloodstream it is attacked by the immune system causing auto-immune conditions, allergies and food intolerances.

Under normal circumstances all substances are filtered via the enterocyte/TJ security barrier, and then released into the bloodstream which then flow into the liver.  

The blood is collected and sent through to the lower portal vein to the right side of the heart which pumps it straight into the lungs, since the lung is the secondary detox organ to the liver.

Both water soluble and fat soluble nutrients end up in the lung, water soluble via the liver, fat soluble via the lymph system.

In the compromised gut, the liver can get overloaded with toxins, bacteria and food particles and the liver becomes congested and blocked and these substances that should be processed by the liver get rejected and they flow back into the bloodstream.  

What can make things worse, is, if anything is put on the skin such as sunscreen or makeup, this ends up in the bloodstream along with the previously rejected substances causing a toxic storm.

This is an ideal scenario for allergic reactions to erupt, and suddenly individuals are allergic to makeup, grass, pollen, moisturising cream, fruit, almost anything because the liver has been compromised.

Since the gut when in a dysbiotic condition some valuable nutrients may not get absorbed which include some of the nutrients that the liver needs to detox, which are B vitamins, Folic acid, Glutathione, Carotenoids, Vitamin E & C (Phase I detox), Selenium, Sulphur, Amino acids – Glutamine,Glycine,Taurine,Cysteine (Phase II detox).

Cell to cell communication afforded by neurotransmitters are recycled in the liver which is not happening because of liver congestion, causing nervous system dysfunction leading to neurological disorders.  

Toxins that the liver should have been broken down get sent to the lungs unprocessed, which in turn could damage part of the bronchial system in the lungs causing the individual to start ‘wheezing’ and displaying an atopic asthmatic condition.  

Dr Campbell-Mcbride informs us that Asthma was a benign condition in the 50s and doctors of the day would advise parents of children suffering from an asthmatic attack to make the child comfortable, make sure they are calm and give them some tea or maybe a bath with epsom salts, and wait for the body to fix the problem in the bronchial tract in the lung which will take about 20 minutes to repair.

Today the child is given inhalers and other drugs that block the body’s natural repair process, which if allowed to continue could convert asthma from a benign condition to a life threatening condition.

Dr. Campbell-Mcbride goes on to say that every 6 minutes in the UK a child suffers from a near fatal asthma attack. With the liver congested, toxins begin to be eliminated through the skin causing an array of various continuous skin rashes, eczema, etc in addition to allergies and asthma.  

Toxins contaminate the urine and when it sits in the bladder, it begins to damage the bladder lining so the body wants to expel it as fast as possible to prevent further damage and the person, child or adult if they are sleeping can cause bed-wetting because bladder control is lost.  

As this continues, cystitis sets in and other chronic conditions occur, due to membrane and mucous damage to the elimination organs from the acid urine as well as a flip/flop scenario between diarrhea and constipation.  

This myriad of physiological and psychological problems all caused by liver congestion baffles the physician (who wants to remove the blockage by cutting out the liver…lol).

We discussed the immune system and the microbiome, specifically ‘adaptive immunity’ where the particular cells of the immune system are our floating ‘memory sticks’. During the plague of Athens in 430 BC Thucydides, an Athenian general and historian indicated that people who survived the plague can only be the only ones to tend the sick since the infected could not be infected a second time. This phenomena are a result of our ‘memory’ cells that are mediated Lymphocyte T and B cells where the B cell is the antigen producing cell and the T cell the memory cell.  

We also discussed in the Cancer Part 2 article ‘Major Histocompatibility Complex’ (MHC , a unique identifier ‘fingerprint’ which is expressed in all mammalian cell membranes that is read by our immune system to distinguish self from invader.  

But this intelligence becomes ‘screwed’ when the gut is dysbiotic and the immune system becomes confused and non-functional.

This situation coupled with a breach in the gut barrier causes the host to begin attacking its own tissues because the amino acid sequence of the unprocessed substances in the bloodstream could be similar to the amino acid sequence on a body tissue, a condition called ‘molecular mimicry’.  

This is referred to as an ‘Autoimmune condition’.  

The body can also attack the amino acid sequence for Collagen, the substance that our tissue and skin are made of, because some toxins prefer to attach themselves to the Collagen substance and as a consequence changes the molecular structure.  

The immune system does not recognise our collagen anymore since the toxins have distorted their composition, and considers it a foreign invader and launches an attack, resulting in arthritic pain that can occur any way in the body.  

The body heals the inflammatory response and the pain disappears only for the pain to appear somewhere else.

I can again refer to the great medical profession that are expert in labeling disease but very little else.

This condition is called Migratory Neuralgia.

The result of the toxic load, undigested food particles, non-recycled neurotransmitters, toxic substances crossing the BBB and their accumulation in the brain creates a myriad of Psychological and Physiological disorders.

A partial list is shown below which are all caused by Gut dysbiosis (Imbalanced microbiome) :

Allergy, Asthma, Skin conditions: Eczema, Psoriasis, leaky gut syndrome, liver dysfunction, multiple sclerosis, Type 1 Diabetes, Hashimoto’s Thyroiditis, Hepatitis, Systemic lupus erythematosus, Thyroiditis, Rheumatoid arthritis, Scleroderma, Celiac disease, Graves Disease, Sjogren’s syndrome, Addison’s disease, Fibromyalgia, Crohn’s disease, Dyslexia, Dyspraxia, Depression, Autism, Schizophrenia, Epilepsy, Obsessive compulsive disorder, Rasmussens Encephalitis, Bipolar disorder and others.

There is a full list at

All the above conditions are DIGESTIVE PROBLEMS and an appropriate diet is the only cure. Don’t forget “ALL DISEASE STARTS IN THE GUT”.  Do not ‘Pass GO’, Do not collect $200, and do not take any pharmaceutical drugs like antidepressants or cognitive-behavioural therapies for problems like Obsessive Compulsive Disorder.

Why Drugs Can’t be used to Heal the Gut

To combat these symptoms, Allopathic medicine prescribe various drugs like Antibiotics that do further damage to the gut flora, or corticosteroid medications like Prednisone.  

This drug is prescribed to open up the bronchial airways for breathing problems and for Leaky gut syndrome, Irritable Bowel syndrome and Crohn’s disease. WHY ?  Prednisone is an immunodepressant poison.

Why would you want to suppress an immune system that is already compromised?  Because in the allopathic mindset, since the immune system is on the attack, we must suppress it, leaving the body completely defensive, a completely psychotic, unscientific modality. 

The immune system is attacking our own tissues because IT IS IN CHAOS, because the regulatory mechanism, our own beneficial bacterial ecosystem is compromised.  Read the signs, uncover the clues and THINK critically.

Furthermore, Prednisone also blocks Osteogenesis (natural bone formation), and stimulates the release of Cortisol our own natural anti- inflammatory, which over time can damage the gut barrier.  

Dr Olree states that this drug annihilates no less than 200 amino connectors and alters some 200 genes.  He had a woman patient that had been over-medicated with this drug to help her breathe (Did we not talk about bronchial damage caused by liver congestion, when the gut flora is damaged and unbalanced).

After 4 years the woman had no bone structure that was visible on an X-ray and she died within 30 days. Another patient of Olree, an 82 year old woman came to see him complaining of backache,muscle ache and extreme fatigue. He took an X-ray and could barely see a trace of her skeletal system, and what he did see had multiple fractures. She had been taking prednisone for 5 years for a lung inflammation SYMPTOM.

She nor her family had no idea how destructive this drug was and she died soon after.

Epilepsy (1% of all children under the age of 20 suffer from this condition), and we have all seen a poor child suffering an epileptic fit and is given a pen to bite on so he/she does not bite his/her tongue off.

Because of the ignorance of the parent, perpetuated by the Psychologist the child or teenager is turned into a Zombie from taking prescribed anti-epileptic drugs, when all that is required is a GAPS type of nutritional protocol to heal the gut.  

Dr Natasha Campbell-Mcbride’s explains her hypothesis on Epilepsy. This condition occurs when the toxic load in the brain reaches an overload level, the brain sends an electrical signal to burn out the toxins to ‘reset’ the brain to normal.  

This ‘electrical reset’ causes the epileptic seizure (‘fit’), but the sufferer is more lucid after, until the next toxic build up which can be avoided once the gut is healed. The only sure solution to cure these many conditions is through diet; the GAPS nutritional protocol diet

The Gaps Diet

Throughout my articles I mention certain heroes of mine and Dr Natasha Campbell-Mcbride is certainly one of those selfless natural physicians that has helped hundreds of GAPS families in her clinic in Cambridge UK.  

To finalise this last article on the microbiome, I would like to summarize the GAPS diet developed by this doctor and to reference her website where anybody can self administer the GAPS nutritional protocol :  or

This GAPS type diet was first used by an American pediatrician Dr. Sidney Valentine Haas (1870-1964) who devised this Specific Carbohydrate Diet (SCD) to heal gut related problems.

However, this story of healing the gut by nutritional means goes back even further to a Dr. Samuel Gee’s (1839-1911) 1888 report “On the Coeliac Affection” in which he noted that if the patient is to be cured it must be from diet, ensuring that milk and starch should not be included.  

Dr Gee was a pediatrician who worked at the Sick Children’s Hospital Great Ormond street, UK, and at St Bartholomew’s medical school.

Dr Gee was familiar with the Greek physician Aretaeus of Cappadocia who wrote about Celiac disease 8000 years ago.

Dr Haas in 1923 presented a paper entitled  “The Value of Banana in the Treatment of Celiac Disease,” which included 8 patients who had been cured of Celiac disease using a high protein diet of meat and carbohydrate diet consisting of fruit and vegetables

Wait a minute, this is just a normal healthy balanced diet that can cure Celiac why has the food industry manufactured all these gluten free products?

Dr Hass published a book in 1951 called the Management of Celiac disease’ outlining the full version of SCD.  Just before the death of Dr. Haas, he treated a patient in 1958 named Judy Gottschall who was suffering with ulcerative colitis and conventional medicine failed to improve her condition so she was put on the SCD which healed her.  

She went on to study the treatment of digestive disorders using diet and published a book in 1987 called ‘Breaking the cycle: Intestinal health through diet’.  

When I looked up celiac disease on an allopathic medicine website they explained that only about 20% of people get a proper diagnosis, since the damage to the intestine is very slow and it could be years before a proper diagnosis is made (at least they admit that).

There are no drugs to treat the disease but you have to follow a gluten free diet eliminating bread, cake, beer, etc from the diet. It is written that Celiac disease runs in families because it is a genetic disorder and you have a 1 in 10 chance of contracting it if your parent,brother or sister has it.  

However, even if you have the gene it is not necessary that you will get it ( is this serious??, the only inheritance associated with Celiac is from your mother’s dysbiotic microbiome.

This gene theory is another failed medical theory, as proven by the enormous waste of money and resouces sequencing the human genome, looking for disease causing genes and in the words of James Watson ( Watson and Crick who mapped out the double helix stucture of DNA) on May 2013 at the Salk Institute “ gene sequencing is not the answer to solving the problems of human health, and much of the research currently being conducted ( the human genome project) is irrelevant.

Human society has an experience with Celiac disease dating back 8000 years, and even today Harvard’s medical school is aware of the diet-celiac connection and its history. We must visit our past before we can progress into the future (I’m sure somebody else said that..maybe Spock ).

Some Problems with the GAPS Patients

The problem with GAPS children in particular, is that having inherited a damaged gut flora there are only a small subset of foods they can eat without feeling pain or sickness.  

These foods tend to be starchy or sugary foods because the overgrowth of commensal bacteria like Clostridia, and Staphylococcus etc prefer to feast on these types of food and when they do, their by products (Metabolites) are toxins that creep into the brain providing it with a pleasure signal as well as causing psychological problems as listed above.

Furthermore, GAPS individuals are trapped in an ever decreasing spiral of craving and dependence on the very food that is damaging their gut.  

Basically this is fast food and processed food (On the website referenced above, there is a section on ‘Fussy eaters’) so these foods have to be slowly eliminated from the diet, which requires a lifestyle change, which is difficult when you are a teenager who should be able to eat anything, (but what is worse is the 50 year old who thinks he can eat like a teenager).

The key to the GAPS diet is for the GAPS patient to consume easily digestible food which makes sense since he/she has a digestive problem.  

You don’t need to be a rocket scientist but you do need to be patient because you’re administering a solution for the child’s whole life so he/she can get on with their life and not worry about what they eat within moderation of course.  

Once the treatment is over try to limit your intake of ‘poisonous food’ so you can treat it like a treat.  For example, once a month you can eat your favorite pizza, no strings attached.  This nutritional regimen to heal the gut will take approximately 2 years to balance the bacterial ecosystem, so you can have a healthy well groomed internal garden when it’s all over. 

Below is a summarized list of food that can and cannot be consumed by GAPS patients.  There are more detail and recipes on the web site:

What Gaps Individuals Can Eat :

  • Cooked food at home – Organic grass fed meats
  • Organ meats like liver (every day which is essential, since liver contains many nutrients including Heme iron that our body absorbs the most,compared to the low absorption rate of non-heme iron from plant food): generally kids do not eat this but you can process the meat and make a stock with the ground up meat and freeze it in ice cube form and then add it to a meal each day (so you hide it)
  • Fresh or frozen Fish (no farmed fish since they are fed with grains)
  • Organic eggs
  • All Vegetables except for the starchy variety (as outlined below)
  • All ripe fruit (it must be ripe since unripe fruit contain starches that are double sugar molecules that cannot get through the gut barrier so they need to be broken down into single sugar molecules which is difficult if the gut is compromised)
  • Nuts and seeds
  • Fermented Dairy (not the commercial variety, ideally they should be home made)  i.e Probiotics Kefir. Yoghurt (be careful if an allergy exists which is possible with a damaged gut ), Also GAPS individuals need potent forms of probiotics which may need to be prepared at home. Commercially produced probiotic dairy like yoghurt, Kefir is too weak for GAPS. Kombucha, a fermented tea is also a possibility to use (it’s like pop so it’s a healthy substitute to coca-cola)
  • Fermented vegetables provide the highest amount of Probiotic bacterial species.
  • Honey (the allowed sweetener)
  • Natural fats: cream and butter and animal fats

What Gaps individuals cannot eat :

  • All grains (oatmeal, rice etc)
  • All starchy vegetables and legumes ( Peas, Potatoes.Parsnips, Beans ( yes that includes baked beans ) of all types including Soy ( if you never eat another soy bean unless it is fermented you will not go wrong)
  • All refined sugars and artificial sweeteners
  • Milk
  • All processed and fast food
  • No restaurant food

Part I: The Miracle of Birth

Obstetrician 1: Get the EEG, the BP monitor, and the AVV.

Obstetrician 2: And get the machine that goes ‘ping!’.

Obstetrician 1: And get the most expensive machine – in case the Administrator comes.

Patient: What do I do?

Obstetrician: Nothing, dear, you’re not qualified.

Hospital Administrator: Ah, I see you have the machine that goes ‘ping!’. This is my favourite. You see, we lease this back from the company we sold it to – that way it comes under the monthly current budget and not the capital account.

[The doctors and onlookers applaud.]

Hospital Administrator: Thank you, thank you. We try to do our best. Well, do carry on.

[As the doctors drop the baby into an incubator, the mother looks up.]

Patient: Is it a boy or a girl?

Obstetrician: Now, I think it’s a little early to start imposing roles on it, don’t you? Now, a word of advice. You may find that you suffer for some time a totally irrational feeling of depression. PND is what we doctors call it. So it’s lots of happy pills for you, and you can find out all about the birth when you get home. It’s available on Betamax, VHS, and Super 8.

Quote from the Monty Python’s movie ‘The Meaning of Life’ 1983

Check out the Previous Article in this series:

Microbiome and Digestion

Microbiome and Disease Part 1

Microbiome and Disease Part 2

Microbiome and the Immune system

Microbiome and the Gut-Brain Connection Part 1

Microbiome and the Gut-Brain Connection Part 2

Microbiome and the Gut-Brain Connection Part 3


  1. Gut and Psychology syndrome ( 2015 Book) Dr Natasha Campbell-Mcbride
  2. ‘Minerals for the genetic code’ (Book 2013) Charles Water, Dr Olree
  3. What’s in Breast milk & what’s in formulae Kelley Winder Feb 2016 BellyBelley website
  4. Amino acids section
  5. The SCD is backed by 124 years of Research & Testing SCD Lifestyle website
  6. Celiac Disease WebMD Website
  7. ‘Samual Gee/Aretaeus of Coppadocia/Prednisone/Thucydides Wikipedia
  8. Wise traditions ( Weston A Price ) presentation Dr Natasha Campbell-Mcbride
  9. Gaps Diet
  10. List of Autoimmune diseases  American Autoimmune website

Author: Eric Malouin ( Jan 2017)