GAPS patients have a long list of nutritional deficiencies due to abnormal 
digestion and absorption, so their immune system is not only unbalanced, 
but also malnourished. But as if all that is not enough, an immune system in a body with abnor­
mal bacterial flora is exposed to a whole host of extremely toxic sub­
stances, many of which have a direct damaging effect on immunity. These 
toxins come from all the opportunistic microbes, which happily overgrow 
in the gut and elsewhere in the body of a person with GAPS thanks to the 
absence of beneficial flora's control. We have already examined what happens to the digestive wall when the 
gut flora is abnormal: it becomes damaged and leaky. A constant stream of 
invaders and undigested food comes through the damaged epithelial 
barriers in the gut. The immune system has to deal with all that, 
while being malnourished, deficient, compromised, unbalanced and 
intoxicated. So, should it come as a surprise to us that GAPS children and adults have 
their immune system in such a poor state? 4. WHAT CAN 
DAMAGE GUT FLORA? We have looked in detail at the different roles our indigenous gut flora 
plays in the body. We have seen how important it is for us to keep this 
microscopic world inside us healthy and active. However, in our modern 
world this task has become extremely difficult if not impossible. Let us 
have a look at what dangers our gut flora has to face on a regular basis. Antibiotics 
We all have taken antibiotics in our lives. It is one of the most commonly 
prescribed medications in our modern world. Since the moment we are 
born we are likely to be exposed to this group of drugs on a regular basis 
not only through prescription, but also through food. Farm animals and 
poultry are routinely given antibiotics, so all the products we get from 
them (meat, milk, eggs) will provide us with a constant supply of anti­
biotics and antibiotic resistant bacteria, which these animals develop in 
their bodies and all the toxins which these bacteria produce.JFarmed fish 
like salmon has antibiotics routinely added to their tanks, A lot of fruit and 
vegetables are sprayed with antibiotics to control disease. The way things 
are in our sophisticated modern world we simply cannot avoid exposure to 
antibiotics. It has become such a "normal" part of life'that not many of us 
ask the question "What are they doing to us?" And as the production of 
antibiotics grew from hundreds of tons a year in the 1950s to tens of thou­
sands of tons a year in the 1990s, so grew the evidence and worried research 
into the harmful effects of this group of drugs on human health. Let us see 
what this research shows: 
• Antibiotics have a devastating effect on beneficial bacteria in the 
human body, not only in the gut but in other organs and tissues. • Antibiotics change benign bacteria, viruses and fungi into pathogenic, 
giving them an ability to invade tissues and cause disease. • Antibiotics change bacteria making it resistant to antibiotics, so the industry has to work on more and more powerful new antibiotics to 
attack these new changed bacteria. A good example is tuberculosis, 
where wide use of antibiotics has created new varieties of the 
Mycobacterium Tuberculosis resistant to all existing antibiotics. • Antibiotics have a direct damaging effect on the immune system, 
making us more vulnerable to infections, which leads to a vicious 
cycle of more antibiotics and more infections. Let us have a look at what different groups of antibiotics do to the gut flora. Penicillins 
In this group we have very widely used Amoxicillin, Ampicillin, 
Flucloxacillin and all other antibiotics with "-cillin" at the end of their 
name. These drugs have a damaging effect on two major groups of our 
beneficial resident bacteria: Lactobacilli and Bifidobacteria, while promot­
ing growth of pathogenic Proteus family, Streptococci and Staphylococci 
This particular group of antibiotics allow bacteria normally found only in 
the bowel to move up to the intestines, which predisposes the person to 
development of IBS (Irritable Bowel Syndrome) and other digestive 
disorders. Tetracyclines (Tetracycline, Doxycycline and other "-cyclines") 
This group of drugs is routinely prescribed to teenagers for acne as a long 
course, lasting from three months to two years. Tetracyclines have a partic­
ular toxic effect on the gut wall by altering protein structure in the mucous 
membranes. This in turn does two things. First, it makes the gut wall 
anatomically vulnerable to invasion by pathogenic microbes; second, it 
alerts the immune system to attack these changed proteins, starting an 
auto-immune reaction in the body against its own gut. In parallel tetracy­
clines stimulate growth of disease causing Candida fungus, Staphylococci 
and Clostridia in the digestive tract. Aminoglycosides (Gentamycin, Kanamycin), Macrolides (Erythromycin) 
and other "-mycins" 
These drugs have a particular devastating effect on colonies of such bene­
ficial bacteria in the gut as physiological E.coli and Enterococci. A pro­
longed 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 lead to selective stimulation of growth of the Proteus family 
and lactose-negative Exoli species, capable of causing serious disease. Combinations of antibiotics have stronger damaging effects on the gut 
flora than single drugs. The damage is worse when antibiotics are adminis­
tered orally and when the course of antibiotic is a lengthy one on a low 
dose, like the one prescribed for acne, chronic cystitis, chronic ear infec­
tion and other chronic infections. Medical personnel and workers in phar­
maceutical industry are at a particular risk of chronic exposure to low 
doses of antibiotics and indeed gut dysbiosis is very common among these 
people. When an antibiotic is prescribed in a high dose, it leaves the gut with a 
lot of empty niches to be populated by whatever bacteria, viruses or fungi 
would 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 the course of antibiotic is short and the dose 
is low, it takes different beneficial bacteria in the gut a long time to recover: 
physiological Exoli takes one to two weeks, Bifidobacteria and Veillonelli 
take two to three weeks, Bacteroids, Peptostreptococci take a month. If in 
this period the gut flora is subjected to another damaging factor(s), then 
gut dysbiosis may well start in earnest. The majority of GAPS patients I have seen have been exposed to numer­
ous courses of antibiotics during their life. The most common reasons in 
children are repeated ear infections, chest infections, impetigoand masti­
tis in the breast-feeding mother, when the baby would get antibiotics 
through the breast milk. Considering that many of these children had little 
chance to develop a healthy gut flora from the beginning, these courses of 
antibiotics would have a devastating effect on their fragile gut ecology. Other drugs 
Most drugs, particularly prescribed for long periods of time or perma­
nently, have a detrimental effect on gut flora. Pain killers or analgesics (aspirin, ibuprofen, etc.) are often prescribed 
for long periods of time to people with chronic pain. These drugs stimulate 
growth of haemolytic forms of bacteria and Campylobacterin the gut, all of 
which are capable of causing disease. Steroid drugs, like Prednisolone, Hydrocortisone, Betamethasone, 
Dexamethasone, etc. damage gut flora. In addition, they have a strong immunosuppressing ability, which makes the body vulnerable to all sorts 
of infection. For example, it is known that a course of steroids is almost 
invariably associated with fungal overgrowth in the body, particularly of 
Candida species. Contraceptive pills or The Pill is something many women take for many 
years, often from a very young age. This group of drugs has a devastating 
effect on the gut flora. By the time a woman is ready to have children, she 
has been on these drugs for a long period of time and has an abnormal gut 
flora. A human baby is born with a sterile gut and acquires most of its gut 
flora from the mother. So if the mother has an abnormal gut flora, that is 
what she will pass to her child, predisposing this child to eczema, asthma, 
other allergies and in severe cases to learning disabilities. Many other groups of drugs, including sleeping pills, "heartburn" pills, 
neuroleptics, cholinolytic drugs, cytotoxic drugs, etc., etc. cause different 
damage to the gut flora, digestive system and immune system. Drug-induced gut dysbiosis is usually the most severe and the most 
resistant to treatment. In the last 50 years we have seen a tremendous 
increase in drug use by western population. It almost became a normal 
part of life to take some sort of prescription or over-the-counter drug, 
something to talk about with your neighbours. Yet not many people think 
what these drugs are doing to their bodies, let alone to their gut flora. What other factors can have an effect on gut flora? Diet 
What we eat has a direct effect on the composition of the gut flora, A 
modern diet of convenience rather than nutrition, full of processed foods, 
has a serious detrimental effect on the gut flora. Too much sugary foods and processed carbohydrates increase numbers 
of different fungi, Candida species in particular, Streptococci, 
Staphylococci, some Clostridia species, Bacteroids and some aerobic 
opportunistic bacteria. Processed and sugary carbohydrates (white bread, 
cakes, biscuits, pastries and pasta) also promote population of the gut with 
worms and other parasites. A diet low on fibre from fresh fruit and vegetables has a profound nega­
tive effect on gut flora and general body metabolism, predisposing the 
person to bowel cancer, atherosclerosis, abnormalities in hormonal 
metabolism and many other problems. Bottle-fed babies develop completely different gut flora to the breast-fed 
babies. Breast-feeding is essential for appropriate population of baby's gut with 
balanced healthy gut flora. Babies are born with a sterile gut. Breast-feed­
ing is the one and only opportunity we have in our lives to populate the 
entire surface of our gut with a healthy mixture of bacteria to lay the veiy 
basis of our future health. Bottled~fed babies have their gut populated by a 
combination of different bacteria, which predisposes them later to many 
health problems. We have a whole generation of people, mainly born in the 
1960s and 1970s who were not breast fed because it was not fashionable. A 
whole host of medical problems that arose from that fashion have made it 
obvious to the medical profession and the rest of us how important breast­
feeding is. Thankfully, now, a majority of mothers do their best to breast 
feed their newborn babies. Prolonged fasting and starvation, overeating and parenteral feeding can 
seriously alter the composition of gut flora and start a chain of health prob­
lems, so supplementing beneficial bacteria in a form of probiotic would be 
a good idea in these situations. Generally, when gut dysbiosis is caused exclusively by poor diet it is 
usually fairly mild and can be corrected by better eating habits. Unfortunately, in our modern world it is rare not to be exposed to other 
factors which would also damage your gut flora, antibiotics for example. Disease 
Different infectious diseases, like typhoid, cholera, dysentery, salmonella 
and some viral infections can cause lasting damage to the gut flora. Repopulating the gut with beneficial bacteria has to he an important part 
of the treatment of patients with these serious infections. Different chronic illnesses are accompanied by serious defects in gut 
flora, like diabetes, autoimmune disease, endocrine disease, obesity and 
neurological conditions. It is a common after-effect of surgery, chemo­
therapy, hormone therapy and radiotherapy. Stress 
A short-term stress has a detrimental effect on the gutflora,but it usually recov­
ers well after the stressful situation is over. However, a long-term physical or 
psychological stress can do permanent damage to the indigenous flora. Other factors % 
Physical exertion, old age, alcoholism, pollution, exposure to toxic sub­
stances, seasonal factors, exposure to ionising radiation and extreme 
climates all have a profound effect on our friendly bacteria. Every one of us carries a unique mixture of microbes in the gut. Under 
the influence of drugs and other factors, listed above, this gut flora will be 
changed in a unique way in every one of us, predisposing us to different 
health problems. It is a completely unpredictable process and the science 
so far has not got very reliable methods of testing for the full range of 
microbes in the gut, let alone treating any abnormalities. This damage gets 
passed from generation to generation as a newborn child gets its gut flora 
from the mother. And as the damage gets passed through generations, it 
gets deeper and deeper. This process reflects in the severity of healthprob-
lems related to abnormal gut flora seen in generations. For example, this is 
quite a common scenario, which I see in my clinic: a grandmother has mild 
digestive problems as a result of low-key gut dysbiosis. She passes moder­
ately abnormal gut flora to her daughter. On top of that she decides not to 
breast feed, because it is not fashionable. As a result, her daughter suffers 
from allergies, migraines, PMS and digestive problems. Then she takes 
contraceptive pills from the age of 16 which deepens the damage to her gut 
flora, not to mention a few courses of antibiotics along the way for various 
infections and a diet of fast foods. After 10 years of being "on the pill" she 
has children, to whom she passes her seriously abnormal gut flora. Her 
children develop digestive and immune problems, which then lead to 
eczema, asthma, autism and other learning problems. Most of the factors, described here, are hard to escape in the modern 
world. Under the influence of these factors, the beneficial bacteria in the 
gut lose their ability to fulfil all the functions we have looked at in the pre­
vious chapters. They are unable to protect the digestive tract from oppor­
tunistic flora and transitional bacteria, viruses and fungi, which sets up a 
whole chain of pathology in the gut and the rest of the body. To gain more 
understanding of what happens in this situation, let us have a look at the 
opportunistic flora, which lives in our digestive system. 5. THE 
OPPORTUNISTIC FLORA 
We talked in detail about the essential flora (the good bacteria) of the gut 
and its multiple functions. Let's look at the second group of bacteria now -
the opportunistic flora. This is a large group of various microbes, the 
number and combinations of which can be quite unique. There are around 
500 different species of them found in the human gut. These are the most 
common: Bacteroids, Peptococci, Staphylococci, Streptococci, Bacilli, 
Clostridia, Yeasts, Enterobacteria {Proteus } Clebsielli Citrobacteria, etc. ), 
Puzobacteria, Eubacteria, Spirochaetaceae, Spirillaceae, Catenobacteria, 
different viruses and many others. Interestingly, many of these opportunis­
tic bacteria when in small numbers and under control actually fulfil some 
beneficial functions in the gut, like taking part in the digestion of food, 
breaking down lipids and bile acids. In a healthy gut their numbers are limited and tightly controlled by the 
beneficial flora. But when this beneficial flora is weakened and damaged, 
they get out of control. Each of these microbes is capable of causing 
various health problems. It is a fascinating area for future research, 
because it appears that it is the character of our individual opportunistic 
flora that may determine what disease we succumb to. Yes, we carry most 
of our future health problems in our own gut pretty much from birth. As 
long as we take good care of our defenders, the beneficial flora, those bad­
dies may never show their ugly faces. Unfortunately, our modern life-styles 
sooner or later damage our indigenous bodily flora and whatever oppor­
tunists were waiting for their turn become active. The best known is the fungus Candida albicans, which causes untold 
misery to millions of people. There is an abundance of literature published 
about Candida infection, so we will not concentrate on it here, However, I 
have to say that a lot of what is described as Candida Syndrome is in effect 
a result of gut dysbiosis (abnormal gut flora), which include the activity of 
lots of other opportunistic and pathogenic microbes. Candida albicans is 
never alone in a human body. Its activity and ability to survive and cause 
disease depend on the state of trillions of its neighbours - different bacteria, viruses, protozoa, other yeasts and many other micro-creatures. In a healthy body Candida and many other disease-causing microbes are 
very well controlled by the beneficial flora. Unfortunately, the era of anti­
biotics gave Candida albicans a. special opportunity. The usual broad-spec­
trum antibiotics kill a lot of different microbes in the body - the bad and 
the good. But they have no effect on Candida. So, after every course of 
antibiotics Candida is left without anything to control it, so it grows and 
thrives. At the dawn of the antibiotic era the medical profession recognised 
this phenomenon, so it used to be a rule to prescribe Nystatin (an anti-can-
dida antibiotic) every time a broad-spectrum antibiotic was administered. However, for whatever reason, doctors stopped this practise decades ago 
and now we are paying the price for it - Candida infection has become 
extremely common. Apart from antibiotics another factor in our modern 
world plays a major role in Candida overgrowth - our diet. Candida flour­
ishes on sugar and processed carbohydrates and these are the foods, which 
nowadays dominate our western eating habits. Some opportunists, listed above, when out of control get through the gut 
wall barrier into the lymph and bloodstream and cause problems in 
various organs in the body. But of course, the first place to suffer will be the 
digestive system. Holding an abnormal bacterial mass, it is no surprise that 
the digestive system cannot function well. The most common result of gut 
dysbiosis is the infamous Irritable Bowel Syndrome (IBS), where a whole 
host of opportunistic bacteria populate the intestines, causing the 
unpleasant symptoms of IBS. More and more research is coming out link­
ing Crohn's disease and ulcerative colitis with the activity of opportunistic 
gut flora getting out of control. Certain opportunists, when not controlled by damaged good bacteria, 
get access to the gut wall and damage its integrity, making it "leaky". For 
example, microbiologists have observed how common opportunistic 
gut bacteria from the families Spirochaetaceae and Spirillaceae have an 
ability due to their spiral shape to push apart intestinal cells, breaking 
down the integrity of the intestinal wall and allowing through substances 
which normally should 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 gets 
through this leaky gut wall into the blood stream, where the immune 
system recognises them as foreign and attacks them. This is how food aller­
gies or intolerances develop. What is happening is that foods do not get a 
chance to be digested properly before they are absorbed through the damaged gut wall. In many cases, when the gut wall is healed food allergies 
disappear. Opportunistic flora constantly produces toxic substances, which are the 
by-products of their metabolism. In a healthy situation many of these by­
products can be physiological because in the process of evolution they got 
included in the normal functioning of the human body. For instance, a 
well-known group of toxins, produced by gut bacteria are amines - the 
metabolites of amino acids. Many of them have some important roles to 
play in the normal physiology of the body. A good example is histamine -
an important neurotransmitter in the body. Certain cells in the body nor­
mally produce histamine. However, it is also produced by Proteus family, E. 
coli family, Staphylococci and many other bacteria in the gut. In a situation 
where these opportunistic bacteria overgrow due to the lack of control 
from the beneficial flora, they start producing too much histamine. As his­
tamine takes part in many different functions in the body, all these func­
tions go wrong with the excess of histamine coming into the blood. These 
are the common symptoms of this condition: allergies, constantly low 
blood pressure, excessive production of body fluids, like saliva, dysfunc­
tion of hypothalamus with hormonal changes (PMS is a common result), 
emotional instability, sleep abnormalities, addictions and many others. An 
excess of histamine in the body is called histadelia. This condition was 
found by Dr Carl Pfeiffer in many people with depression, schizophrenia, 
addictions and autism. Antihistamine drugs are used by psychiatrists to 
treat schizophrenia. Nobody has yet looked at correcting the gut flora 
in order to normalise histamine production in the body and remedy 
symptoms of histadelia. Other well studied amines: dimethylamine, piperidine, pyrrolidine, tyra-
mine, octopamine, which are produced by bacterial activity in the gut from 
amino acids choline, lecithin, methylamine, lysine, arginine, ornithine and 
tyrosine, are also known to cause cerebral depression with symptoms of with­
drawal, intellectual regression, behavioural and emotional abnormalities. GAPS children and adults routinely show overgrowth of opportunistic 
microbes in their stool tests (the ones we can test for). The most commonly 
seen are Candida albicans, Bacteroids, Clostridia spp., Proteus family, 
Streptococci and Staphylococci. Invariably, this overgrowth is combined 
with either the absence or greatly reduced numbers of beneficial bacteria. Unfortunately, stool testing so far available to us is quite primitive. There 
has not been a lot of money put into this research. There is a debate going 
on between professionals about the validity of stool analysis, as it only shows what microbes may be in the lumen of the bowel. It gives no informa­
tion on the most important inhabitants of the gut - the ones that live on the 
gut wall, the mural bacteria. These are the bacteria, which maintain gut 
integrity and its ability to digest and absorb food and which play such an 
important role in our immunity. There are limited studies done with biopsy of 
the gut wall and following microbiological analysis, which show that the mural 
bacteria can be quite different from the ones, which live in the lumen of the 
gut. Apart from that, stool analysis only reflects the microbial population of 
the bowel and does not reflect what lives higher in the intestines where the 
very important digestion and absorption happens. Unfortunately, we are still 
in the very early stages when it comes to testing for gut flora. Nevertheless, 
there is a large amount of information available now about what the bacterial 
population of a normal healthy person's stool should look like and compared 
to that information GAPS people have very abnormal results. A group of opportunistic gut bacteria, called Bacteroids, routinely found 
in GAPS stool analysis, deserves some attention. It is the most ubiquitous 
opportunistic bacteria in the gut of adult population in the western world 
which may be explained by what these bacteria like to eat - sugar, starch, 
lactose - the backbone of the western diet. There are in excess of 22 differ­
ent members of this family identified so far in the human body, the most 
common Bacteroides fragilis and Bacteroides melaninogenicus. These bac­
teria are almost always found in infected tissues of the digestive tract, 
abscesses, ulcers, urinary infections, lung infections, peritonitis, infected 
heart valves, blood infections, mouth infections, teeth and gum disease, 
gangrene and post-operative infections. They are opportunists always 
hanging around in every mucous membrane of the body waiting for their 
opportunity to cause trouble. However, they usually do not cause trouble 
alone but join some bigger bully on the playground and in that company 
really show their ability to cause disease. For example, they are usually 
found in company with Clostridia. They appear to be good friends with the 
Clostridia family, which is considered to be more dangerous than 
Bacteroids. But Bacteroids seem to show their ability to cause disease 
better in the company of Clostridia, at the same time assisting Clostridiain 
its activity. Members of Clostridia family are almost always detected in the stool 
analysis of autistic children and adults. There are about a hundred of dif­
ferent Clostridia species known so far. Apart from autism they are present 
in the stools of people with schizophrenia, psychosis, severe depression, 
muscle paralysis and muscle tonus abnormalities and some other neurological and psychiatric conditions. Many Clostridia species are 
normal inhabitants of a human gut. For example Clostridium tetani is rou­
tinely found in the gut of healthy humans and animals. Spores of this bac­
terium are passed through faeces into soils, where they can survive for 
years. Most soils in the world test positive for tetanus spores. Everybody 
knows that tetanus is a deadly disease, due to an extremely powerful 
neurotoxin Clostridium tetani produces. Anybody who gets a wound or 
even a scratch contaminated by soil is immediately advised to have a shot 
of anti-tetanus vaccine. But we contract tetanus only when the bacterium 
gets directly into our tissues or blood. Clostridium tetani which lives in the 
gut, normally does not do us any harm because its toxin cannot get 
through the healthy gut wall. GAPS patients do not have a healthy gut wall, 
which would allow toxins to get into the body. Many other species of Clostridia {perfringens, novyi, septicum, his-
tolyticum, sordelli taerofoetidum f tertium, sporogenes, etc. ), routinely found 
in the human gut, produce toxins similar to tetanus toxin as well as many 
other toxins. So how can we have these deadly bacteria in our gut and be 
healthy? Because, they are controlled by our friendly bacteria, which will 
not allow them to flourish and, most importantly does not allow their 
toxins through the gut lining into the bloodstream. However, in the GAPS gut where the person hasn't got the beneficial bac­
teria to protect the gut wall and control Clostridia, neurotoxins have a good 
chance of getting into the bloodstream and into the brain and the rest of 
the nervous system, affecting its development and functioning. Sensitivity 
to light and noises is a typical symptom of tetanus infection and GAPS con­
ditions, like autism, schizophrenia, psychosis, dyslexia, so it seems plausi­
ble that the two may be connected. Most GAPS children and adults, whom 
I see in my clinic, have got abnormalities of muscle tonus similar to low 
exposure to tetanus neurotoxin. A typical picture is where extensor mus­
cles have higher tonus than contractor muscles. Maybe that is the reason 
why autistic children and adults walk on tiptoes and often self-stimulate by 
stretching their arms, fingers and legs in odd positions. In these cases 
where the patient's stool has been tested almost without exception an 
overgrowth of Clostridia spp. is observed. Recent research at the University 
of Reading in the UK by a microbiological team led by Professor Glenn 
Gibson has found very high levels of Clostridia in the gut of 150 autistic 
children and a second research programme found similarly high levels in 
the gut of another 80 autistic children, which were not present in their 
non-autistic siblings. Just like Candida albicans, the Clostridia family was given a special 
opportunity by the era of antibiotics, because Clostridia are also resistant 
to them. So, every course of broad-spectrum antibiotics removes good 
bacteria, which leaves Clostridia uncontrolled and allows it to grow. Different species of Clostridia cause severe inflammation of the digestive 
system, for example Clostridium difficile causes a potentially fatal pseudo­
membranous colitis. Some species of Clostridia have been linked to such 
debilitating digestive disorders as Crohn's disease and ulcerative colitis. I 
have no doubt that the Clostridia family plays an important role in the 
development of autistic enterocolitis as well. Future research will show. However, there are some facts already which support this thought. For 
example, William Shaw at Great Plains Laboratories reports a number of 
cases where a course of anti-clostridia drugs Metronidazole (Flagyl) and 
Vancomycin reduced autistic symptoms and improved digestion and the 
biochemical picture in autistic children. However, in almost all cases as 
soon as the drug was stopped, all the symptoms and biochemical abnor­
malities returned. Unfortunately, anti-clostridia drugs are toxic, they have 
serious side effects, so we can not prescribe them for long periods of time 
to children or adults. Clostridia are spore-forming bacteria, which makes 
them impossible to eradicate. We can only control them and the best way 
to do it is Nature's way - with beneficial bacteria. Another large group of bacteria, which commonly overgrow in the gut 
dysbiosis situation are sulphate-reducing bacteria. There are many 
species of sulphate-reducing microbes. To mention just a few: 
Proteobacteria, Thiobacilli, Chromatiaceae, Desufotomaculum spp., some 
gram-positive bacteria, some fungi and Bacteroids. These microbes 
metabolise sulphate coming from food into sulphites, many of which are 
toxic. Severe deficiency in sulphates has been found in 95% of autistic chil­
dren. Undoubtedly, sulphate-reducing bacteria play an important role in 
causing this deficiency. Sulphates are needed in the body for many func­
tions, some of which are detoxification and normal metabolism of brain 
neurotransmitters. An overgrowth of sulphate-reducing bacteria would 
make sulphur unavailable for the body to use, turning it into toxic sub­
stances like hydrogen sulphide, which is the gas with a rotten egg smell. Many parents of autistic children tell me that their child's stool and flatus 
has this characteristic smell. Here we have looked at some pathogens found in the gut of GAPS 
patients. To their happy company we can add the measles virus found by 
Dr A. Wakefield's research group. This is only one virus, which received such detailed attention. There are some indications in literature that mem­
bers of the herpes virus family are also very active in these patients. How 
many other viruses may there be in the GAPS gut, which have never been 
studied? How many other pathogenic bacteria, fungi, protozoa and other 
microbes are there, which we have no methods to detect or study yet? I 
have no doubt that sooner or later science will catch up with them and we 
will learn what they are and how to deal with them. In the meantime, what 
should we do to help our GAPS children and adults now? As always, Nature 
has a good answer - the beneficial flora. Having good bacteria in the gut is 
the best way to keep Clostridia, Candida, Bacteroids, viruses and many 
many other microbes under control. Well-functioning healthy gut flora 
would not only keep those pathogens down but would maintain the 
integrity of the gut wall so it does not let through the toxins from those 
pathogenic microbes. This is Nature's way of dealing with them and the 
smart thing for us is to try and copy it. Due to the absence or greatly reduced numbers of beneficial bacteria, 
the GAPS digestive system gets taken over by opportunistic and pathogenic 
microbial flora, constantly producing a river of toxicity flowing from the 
gut to the brain. This is the toxicity, which is probably making these chil­
dren and adults autistic, schizophrenic, hyperactive, dyspraxic, dyslexic, 
psychotic, depressed, obsessed, etc., etc. We have already looked at some of these toxins. Let us have a look at 
more. 6. THE GUT-BRAIN 
CONNECTION 
One only sees what one looks for, 
one only looks for what one knows. Goethe 
Modern medicine has divided us, human beings, into different systems 
and areas: cardio-vascular system, digestive system, nervous system, etc. According to this division different medical specialities have been created, 
each concentrating on a particular bit of the human body: cardiology 
gastroenterology gynaecology neurology, psychiatry etc., etc. There is a 
reason for that. Medical science over the years has accumulated an enor­
mous amount of knowledge. No doctor in the world can possibly know it 
all in detail, so specialising allows doctors to concentrate on a particular 
area of knowledge, to learn it thoroughly and to become an expert in that 
area. However, from the early years of this specialisation many doctors have 
recognised a problem developing. A specialist in a particular area tends to 
pay attention to the organs, which he or she knows best, ignoring the rest 
of the body. The fact that every organ in the body exists and works in con­
tact with the rest gets forgotten. The body lives and functions^as a whole, 
where every system, organ, tissue and even cell depend on each other, 
affect each other and communicate with each other. One should not look 
at, let alone treat, any organ without taking the rest of the body into 
account, f 
One area of medicine is particularly prone to look at its organ separately 
from the rest of the body. That area is psychiatry. Mental problems are 
examined from all sorts of angles: genetics, childhood experiences and 
psychological influences. The last thing that would be considered is look­
ing at the patient's digestive system. Modern psychiatry just does not do 
that. And yet medical history has plenty of examples, where severe psychi­
atric conditions were cured by simply "cleaning out" the patient's gut. A 
renowned Japanese Professor Kazudzo Nishi has estimated that at least 
one in ten psychiatric conditions are due to self-intoxication coming from 
the bowel. The vast majority of psychiatric patients suffer from digestive problems, which are largely ignored by their doctors. The gut-brain connection is 
something which, for some reason, many modern doctors do not under­
stand. As they give out millions of prescriptions for antidepressants, sleep­
ing pills and other drugs, which the patients have to place into their diges­
tive systems in order to affect their brains, they still fail to see the 
connection between the digestive system and the brain. Everybody knows 
what effect alcohol has on our brains. Where do we place alcoholic drinks? Into our digestive systems of course. However, we don't have to consume 
toxic substances to affect our brains. Having particular microbes in the 
digestive system can provide us with our own permanent source of toxicity. As discussed in the previous chapters, a GAPS (Gut And Psychology 
Syndrome) person's digestive system becomes a major source of toxicity in 
the body. An unknown number of various neurotoxins are produced by 
abnormal flora in the gut of these children and adults, which get absorbed 
through the damaged gut wall into the blood and taken to the brain. The 
mixture of toxins can be very individual and this is one of the reasons why 
all GAPS patients are so different. As I mentioned, the number of different 
toxins is unknown. However, we have accumulated a considerable knowl­
edge of some of the neurotoxins, commonly found in GAPS children and 
adults. These are the kind of toxins, which can make anybody mentally ill. In the previous chapter we looked at some of them. Unfortunately, there 
are more to examine. Ethanol and acetaldehyde 
Thinking about autism, ADHD, schizophrenia, dyslexia, dyspraxia and 
other psychological problems, not many people would think about alco­
holism. And yet there is a very serious connection. We know that due to 
various factors GAPS children and adults develop an overgrowth of patho­
logical flora in their bodies. One group of these pathogens, almost without 
exception, are yeasts, including Candida species. Yeast requires glucose as 
food. Glucose comes from the digestion of carbohydrates. In healthy 
people dietary glucose gets converted into lactic acid, water and energy 
through a biochemical process called glycolysis. In people with yeast over­
growth Candida highjacks the glucose and digests it in a different way, 
called alcoholic fermentation. In this biochemical process Candida and 
other yeasts convert dietary glucose into alcohol (ethanol) and its by­
product acetaldehyde. This phenomenon was first described in adults, 
who appeared to be drunk without consuming any alcohol. Later on it was found that these adults had an overgrowth of yeast in their gut, which 
produced alcohol and made them permanently "drunk". These people 
were particularly "drunk" after a carbohydrate meal, because carbohy­
drates get consumed by Candida with the production of alcohol. Despite 
the fact that these people did not consume alcohol, they developed some 
typical symptoms of alcoholism. Alcohol and its by-products have a small molecular weight, which makes 
it very easy for them to cross any barrier in the body. They get absorbed 
into the blood very quickly and have a very good ability to get through 
placenta to a developing foetus. Pregnancy is a natural state of immune 
suppression. If a woman already has Candida overgrowth in her body, 
pregnancy would make this problem worse. Overgrowing yeast in a preg­
nant woman would produce alcohol and its by-products, affecting the 
child's development. After the child is born it will continue to get alcohol 
and its by-products through breast milk, which usually contains the same 
amount as the woman's blood. Then as the child inherits the mother's 
bodily flora, overrun by yeast, the child starts producing its own alcohol 
and many other toxins. Alcohol consumption and yeast overgrowth in 
fathers also has an effect on the child's development, so fathers with yeast 
overgrowth contribute to the problem as well. Indeed in my clinic more 
than 50% of fathers of autistic children suffer from abnormal gut flora and 
related health problems. So what does alcohol and its by-products do to us? Everybody knows 
that alcohol is very toxic, particularly for a child. There is no^part of the 
body that will not suffer from the constant supply of alcohol even in tiny 
amounts. Here are just a few influences of chronic presence of alcohol in 
the body: 
• Reduced ability of the stomach wall to produce stomach acid. • Pancreas degeneration with reduced ability to produce pancreatic 
enzymes, which would impair digestion. • Direct damage to gut lining, causing malabsorption. • Nutritional deficiencies through malabsorption of most vitamins, 
minerals and amino acids. Deficiencies in B and A vitamins are partic­
ularly common. • Damage to the immune system. • Liver damage with reduced ability to detoxify drugs, pollutants and 
other toxins. • Inability of the liver to dispose of old neurotransmitters, hormones and other by-products of normal metabolism. As a result these sub­
stances accumulate in the body, causing behavioural abnormalities 
and many other problems. • Brain damage with lack of self-control, impaired co-ordination, 
impaired speech development, aggression, mental retardation, loss of 
memory and stupor. • 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 other toxins. • Alteration of metabolism of proteins, carbohydrates and lipids in the 
body. Acetaldehyde is considered to be the most toxic of alcohol by-products. One of the most devastating influences of this chemical is its ability to alter 
the structure of proteins. We are largely made up of proteins; a myriad of 
various active substances from hormones to enzymes are proteins. When 
they are changed by acetaldehyde they can not do their jobs properly. Acetaldehyde-altered proteins are thought to be responsible for many 
autoimmune reactions, which means that the immune system starts 
attacking its own body. Antibodies against these acetaldehyde-altered pro­
teins, which the immune system makes to destroy them, may also attack 
the normal proteins in the body with similar structure. Autistic children 
and schizophrenic patients are commonly found to have antibodies 
against their own tissues. One of the commonest is an antibody against a 
protein in a substance called myelin. Myelin is an integral part of the brain 
anatomy and the rest of the nervous system, coating brain cells and their 
branches, the nerve fibres. When myelin is damaged in adults it manifests 
itself as multiple sclerosis. There are some similarities in the neurological 
picture of autistic and dyspraxic children and patients with multiple scle­
rosis which may be due to acetaldehyde produced by the yeast overgrowth 
in these children. Alcohol and acetaldehyde render a lot of essential nutrients useless in 
the body. For example, binding to proteins acetaldehyde causes functional 
deficiency of vitamin B6, which is a co-factor in production of neurotrans­
mitters, fatty acid metabolism and many other functions in the body What 
is a functional deficiency? It means that the child may get plenty of vitamin 
B6 in the diet, but because acetaldehyde occupied the working sites of this vitamin on proteins, it cannot do its job. So, it floats around the body in a 
rather useless fashion and eventually gets excreted. This may not happen 
just to vitamin B6 but to many other active substances in the body which 
have to bind to proteins in order to fulfil their purposes. So, we talked about alcoholism in connection with children and young 
adults. Shocking, isn't it? What next?... Well, next we are going to talk about 
drug addiction. Opiates from gluten and casein 
Opiates are drugs, like opium, morphine and heroin, which are commonly 
used by drug addicts. What have they got to do with GAPS children and 
adults? Gluten is a protein present in grains, mainly wheat, rye, oats and barley. Casein is a milk protein, present in cow, goat, sheep, human and all other 
milk and milk products. In the bodies of GAPS people these proteins do not 
get digested properly and turn into substances with similar chemical struc­
tures to opiates, like morphine and heroin. There has been quite a substan­
tial amount of research done in this area by Dohan, Reichelt, Shattock, 
Cade and others, where gluten and casein peptides, called gluteo-
morphins and casomorphins, were detected in the urine of patients with 
schizophrenia, autism, ADHD, post-partum psychosis, epilepsy, Downs 
syndrome, depression and some autoimmune problems, like rheumatoid 
arthritis. These opiates from grains and milk are thought to get through the 
blood-brain barrier and block certain areas of the brain, just like morphine 
or heroin would do. Why does this happen? The explanation is undoubtedly hidden in the 
person's digestive system. * 
As we saw earlier GAPS patient's digestive system is in a poor state. The 
digestion of proteins starts in the stomach with the action of pepsin, a pro­
tein-digesting enzyme produced by the stomach wall. Stomach acid is 
essential for protein digestion, as it provides normal conditions for pepsin 
to do its work of breaking down proteins into shorter peptide chains. GAPS 
people commonly have low stomach acidity due to abnormal gut flora and 
overgrowth of pathogenic flora. For example, Candida alone can make 
toxins which have a strong suppressing ability on stomach acid produc­
tion. These toxins would be excreted with breast milk in a mother with 
Candida overgrowth in her gut. It is possible that, while being breast fed, 
GAPS children receive these toxins from the mother through the breast milk, which impair production of stomach acid from the very beginning of 
the child's life. As the breast milk requires virtually no digestion the child 
does not need much stomach acid while exclusively breast fed. But when 
other foods get introduced, the child's low stomach acidity becomes a 
problem. By the time the breast feeding stops the child's digestive system 
would probably have grown enough of its own Candida and other 
pathogens to produce toxins, which would carry on reducing the stomach 
acidity. The most usual weaning proteins first introduced to the child's 
digestive system are casein from formula milk and gluten from wheat. In a 
stomach with low acidity the first steps in the digestion of these and many 
other proteins would not go well. Then these maldigested proteins would 
be passed into the intestines, where pancreatic digestive enzymes are sup­
posed to carry on breaking down proteins. Low stomach acidity would 
impair production of pancreatic enzymes, so the next step in protein 
digestion would also go askew. Next these maldigested proteins reach the 
final stage of their digestion - the intestinal wall. The intestinal wall is lined 
by highly sophisticated cells, called enterocytes which on their surface 
have got a whole host of different digestive enzymes to complete the final 
step s in the digestion of various nutrients. As we have already discovered in 
the chapter on the gut flora, in GAPS people these cells are in poor shape 
due abnormal gut flora. They are not able to accomplish these final steps in 
the digestion of casein, gluten and many other nutrients. As Dr J. Robert 
Cade from the University of Florida said in his interview with Health 
Science Centre in March 1999 "We think that with autism and schizophre­
nia, the basic disorder is in the intestine, and these individuals are absorb­
ing beta-casomorphin-7 that they normally should break down in the body 
as amino acids, rather than peptide chains up to 12 amino acids long". There has been some research published on one of the protein-digesting 
enzymes which sit on the enterocytes. It is called dipeptidyl peptidase IV 
(DPP IV) and it is supposed to brake down casomorphin and gliadomor-
phin into smaller peptides. GAPS children show deficiency in this enzyme. Interestingly, people, who suffer from alcoholism, schizophrenia, depres­
sion or autoimmune disease also have low levels of this enzyme due to the 
fact that in these conditions the patient's enterocytes are also damaged. Based on this research DPP IV is now added to some digestive enzyme for­
mulations which can be supplemented to GAPS patients. The problem is 
that this is only one enzyme, which we have studied and know something 
about. How many more enzymes are there on the surface of enterocytes, 
which we know nothing or very little about at present? With the lack of beneficial bacteria, which normally live on these cells, feed them, look 
after them and protect them, these cells fall ill and become unable to func­
tion properly As a result maldigestion and malabsorption set the scene In 
the GAPS gut. At the same time pathogenic bacteria, fungi and viruses 
damage the gut wall and allow maldigested proteins, like casomorphin and 
gliadomorphin, and other substances to be absorbed into the blood and 
carried to the person's brain. There is another aspect to this problem. Normally proteins should be 
broken down into amino acids before they are absorbed in the gut. Apparently we all absorb some of our proteins in the form of peptides (par­
tially broken down proteins) or even unchanged. These dietary peptides 
act as inhibitors of a special group of enzymes in the body, called pepti­
dases, responsible for breaking down our neurotransmitters, hormones 
and many other active substances after they have performed their jobs. In 
GAPS patients these peptidases get severely suppressed by too many 
dietary peptides coming in, which floods the body with debris of our own 
inner peptides, which themselves can cause damage and psychological 
symptoms. Based on the research into gluteomorphin and casomorphin a gluten-
and casein-free diet (GFCF diet) was developed. Some autistic children 
show dramatic improvement on this diet. However, many children do not. The reason for that is that diere is much more to GAP Syndrome than 
gluteomorphins and casomorphins. So, for the majority of affected 
patients the diet has to take into account many other aspects of GAPS. Other toxins 
In the previous chapter we have talked about the Clostridia family and 
their toxins. Clostridia are difficult to study due to the fact that they are 
strict anaerobes. However, in his book Dr William Shaw describes in detail 
a number of autistic children who showed significant improvements in 
their development and biochemical tests while on anti-clostridia medica­
tion. Unfortunately, as soon as the medication was stopped the children 
slipped back into autism. As we have mentioned in the previous chapter, 
the best way to deal with Clostridia and many other pathogens in the gut is 
establishing proper healthy gut flora, as the beneficial bacteria are the 
natural way of controlling Clostridia. Other frightening toxic substances have been found in autistic children 
by a biochemist Dr Alan Friedman. These chemicals are called deltorphin and dermorphin. They were first found on the skin of poison dart frogs in 
South America where native people used to dip their darts into the mucous 
on these frogs in order to paralyse their enemy, because deltorphin and 
dermorphin are extremely potent neurotoxins. Dr Friedman believes that 
it is not the frog that produces these neurotoxins, but a fungus, which 
grows on the skin of this frog. It is possible that this fungus grows in the gut 
of autistic children. Hopefully, future research will elucidate this issue for 
us. A number of other potent toxins have been identified and studied in 
GAPS people. To look at all of them is beyond the scope of this book. The 
important point is that GAPS children and adults are very toxic people. This toxicity comes from their digestive systems. So it is the person's diges­
tive system we have to concentrate on first and foremost in order to treat 
the condition. 7. THE FAMILIES 
Being a mother of an autistic child, I am very familiar with the feeling of 
guilt, which so many parents experience. We feel that we have done or 
haven't done something which caused our child's condition. It is a perfectly 
natural feeling and as parents we have to learn to deal with it as well as 
everything else our GAPS children bring into our lives. Whenwestartread-
ing and learning about what could have caused our child's condition on 
biochemical and physiological levels, we start feeling even guiltier. If only 
we could have avoided this and that and if only we could have done things 
differently, our child might have been different! In this chapter I am going 
to talk about the health of parents of GAPS children and how it could con­
tribute to your child's condition. In no way do I want to make anybody feel 
guilty about it. We are what we are! Our children are physically made by us 
from whatever we are made of. Some of these things, like genetics, we are 
born with and there is nothing we can do about them. Some were given to 
us by our parents, like our bodily microbial flora and our eating habits. Some were created by our life-styles and choices. Some were imposed on 
us by our modern society and the world we live in. Most parents of GAPS 
children, I have met, rather than concentrating on their feeling of guilt, 
find a way of learning as much as possible about their children's condition 
and concentrating on what can be done about it 
So, let's carry on learning! As far as the science knows an unborn baby is sterile. Its body has no 
bacteria, viruses or fungi living in it. When the time of birth comes, as the 
baby goes through the birth canal, it gets its first dose of microbes. Its skin, 
eyes, mucous membranes in the mouth and nose acquire their first micro­
flora. Through swallowing liquids in the mother's vagina the baby's diges­
tive system gets its first population of bacteria, viruses and fungi. So, what­
ever lives in the vagina of the mother is what the baby would get. Now, let's have a look at what lives in a mother's vagina. A healthy 
woman has a very large population of microbes in her vagina, called vagi­
nal flora. Normally it is dominated by Lactobacillus species, namely 
Lactobacillus acidophilus, Lactobacillus Casei, Lactobacillus Fermentum and others. These good bacteria keep the pH in the vagina quite acid, 
around 4-7, which does not allow other bacteria to take hold and grow. This 
normal flora in the vagina is absolutely vital for the woman's health. It pro­
tects her from infections, keeps the mucous membrane of the vagina and 
other organs in that area healthy, stimulates the production of large num­
bers of immune cells and immunoglobulins in the walls of the vagina to 
keep it well defended from any invaders. But when these good bacteria are 
damaged the problems start. Let's see what can have a damaging effect on vaginal flora. Antibiotics and other systemic antibacterial drugs have a direct effect on 
the composition of vaginal flora, because they destroy the beneficial bacte­
ria in the vagina as well as everywhere else in the body. If the beneficial 
bacteria in the vagina are not there then the coast is clear for any invading 
bacteria, fungus, virus or parasite to take hold and grow. The pH in the 
vagina goes up and various aerobic, anaerobic and micro-aerophilic 
species start populating the woman's vagina, such as Gardnerella vaginalis, 
Prevotella spp., Peptostreptococcus spp., Mycoplasma hominis, Ureaplasma 
urealyticum and Mobilincus spp. causing inflammation with many very 
unpleasant symptoms. A well-known family of fungi, called Candida albi­
cans, is a very common inhabitant of an unhealthy vagina, causing thrush. This fungus cannot live in a vagina with a good population of healthy 
bacteria. The contraceptive pill has the same damaging influence on vaginal flora 
as antibiotics. Steroids in the pill have an ability to suppress the immune 
system and change the composition of bodily flora. Unfortunately, in our 
modem society women are put on the pill at a very early age and by the 
time they are ready to have children they have been taking these drugs on a 
regular basis for years, which would have a profound effect on the compo­
sition of their bodily micro-flora. Many other drugs have a damaging effect on vaginal flora particularly 
steroids, sulphonamides, some non-steroid anti-inflammatory prepara­
tions and others. Apart from drugs there are some other influences, which can change the 
composition of vaginal flora, for example poor diet, infections, personal 
care products and prolonged stress. But here we have to talk about the 
most important question: where does the vaginal flora come from? The medical science shows that the flora in the vagina comes from the 
gut. What lives in the woman's bowel will live in her vagina. For example, in 
women with recurrent thrush, no matter how many powerful anti-fungal topical preparations are used, the thrush always comes back. It comes back 
because the fungus, which causes it, called Candida albicans, lives in this 
woman's bowel. Until she gets rid of it in the bowel, she is not going to be 
free from vaginal thrush. But why does this woman have an overgrowth of 
fungi in her bowel? Because she does not have a healthy gut flora to protect 
her from this fungus and many other microbial invaders. This woman has a 
condition, called Gut Dysbiosis. She will not only have an overgrowth of 
Candida albicans in her gut but lots of other pathogenic microbes, causing 
many other health problems. Amongst all the parents of GAPS children I have met, the mother always 
invariably has signs of chronic gut dysbiosis. Most mothers have been 
taking the contraceptive pill for years before having children. Many moth­
ers have had numerous courses of antibiotics. Many of them have not been 
breast fed as babies and their mothers show typical symptoms of gut dys­
biosis. Almost every one of them has one or more health conditions which 
are typically associated with abnormal gut flora. The most common health 
problems, which mothers of GAPS children suffer from are: digestive disor­
ders, asthma, eczema, hay fever and other allergies, migraines, PMS, 
arthritis, skin problems, chronic cystitis and vaginal thrush. These condi­
tions seem to be unrelated, but they are all children of one parent - Gut 
Dysbiosis. What about fathers? In many cases fathers of GAPS children also suffer 
from digestive problems, asthma, eczema, migraines and skin problems 
which indicates that they do not have a normal gut flora. Of course the 
father is a great contributor to a mother's vaginal flora through regular 
sexual contact. In fact in those rare cases when the mother did not show 
any signs of gut dysbiosis the father was severely affected by it. Having 
abnormal gut flora the father would have abnormal flora in the groin, 
which he would regularly share with his wife. Then the wife would pass that 
flora to the baby at the time of birth. So, what happens after the baby is born? The most important thing that 
should happen is breastfeeding. Breast milk, particularly colostrum in the 
first days after birth, is vital for appropriate population of the baby's diges­
tive system with healthy microbial flora. It is known that bottle-fed babies 
develop completely different gut flora to the breast-fed babies. That flora 
later on predisposes bottle-fed babies to asthma, eczema, different other 
allergies and other health problems. We all know that breast is the best! However, most things that are floating in a mother's blood will be in her 
breast milk. A mother with abnormal gut flora would have a whole host of toxic substances, which are produced by pathogenic microbes in her gut 
andmaldigested foods absorbed into her bloodstream. These toxins will be 
excreted in her breast milk and fed to her baby. In particularly severe cases 
mothers of GAPS children could not breastfeed their babies because the 
baby would refuse the breast or just fall asleep after the first few mouthfuls 
of the breast milk. We know that some of the toxins, which are produced by 
abnormal gut flora, have the chemical structure of opiates, like morphine 
and heroin. If the baby gets these opiates in the breast milk then it is quite 
understandable why the baby falls asleep after the first few mouthfuls. Another reason for the baby to refuse breast is milk allergy. In a woman 
with gut dysbiosis the gut lining is damaged and leaky. It allows through 
partially digested proteins and antigens. Milk antigens have been detected 
in breast milk. I have seen a few cases when the baby took to the breast 
after the mother removed dairy foods from her diet. A lot of cases of severe 
eczema in babies can also be relieved by this measure. On the positive side, however, the mother would also develop antibodies 
to her pathogenic flora in the gut. These antibodies too will be excreted 
through her milk and fed to her baby. So, if the baby has inherited abnor­
mal gut flora from the mother, this flora will be controlled by antibodies in 
the breast milk while the baby is breastfed. When the breastfeeding stops, 
however, this protection stops as well. A lot of parents of GAPS children can 
time the start of health problems in their child to the time of stopping 
breastfeeding: ear infections, digestive problems, eczema, etc. It is possible 
that the baby has developed an abnormal gut flora, which was controlled 
by antibodies in breast milk, so its own immune system has not developed 
any protection against this abnormal gut flora. On the contrary, there is a 
lot of evidence to suggest that the baby's immune system accepts these 
pathogenic microbes in the gut as something normal because that is all it 
has known from the beginning and it does not recognise these microbes as 
foreign and does not attack them As a result after the breast feeding stops 
there is an explosion of growth of abnormal bacteria, viruses and fungi in 
the baby's digestive system. In different children it takes a different length 
of time, depending on the individual composition of the gut flora, severity 
of gut dysbiosis and the diet of the child. Coming back to the health of the parents of GAPS children, when I ask 
questions about the health of their child's grandparents, particularly on the 
mother's side, it becomes obvious that we have generations of people with 
compromised gut flora. This damage becomes deeper in every generation. The era of antibiotics, contraceptive pill, breast feeding going out of fashion arid drastic changes in diet have all contributed to this phe­
nomenon. Doctors have known for centuries that unhealthy parents pro­
duce unhealthy children. Mother's body is a home for the growing baby for 
nine months and a source of nourishment and care for months after the 
birth. So, mother's health is particularly important for the health of the 
baby. In our modern society we have generations of women, whose health 
has been compromised by our modern life-styles. Should it, therefore 
come as a surprise to us that we have epidemics of autism, ADHD, dys­
praxia, dyslexia, asthma, eczema, allergies, diabetes and many other health 
problems in our children? There is another important factor, which makes children vulnerable -
the toxic load which the child is born with. What is it? For years we believed 
that the placenta in a pregnant woman protects the foetus from any toxins 
which the woman might have in her body. Recent studies show that we 
were wrong. The foetus accumulates most toxins, which the mother is 
exposed to. Mercury from amalgam fillings, toxins coming from food and 
environment and toxins produced by abnormal gut flora in the mother 
have a good chance of accumulating in the foetus. Depending on how toxic 
the mother is during pregnancy different babies are born with a different 
toxic load. A baby with a high toxic load will start its life at a disadvantage 
being more vulnerable to various environmental influences: vaccinations, 
infections, food, drugs, etc. That is why the old wisdom of treating preg­
nancy with respect is so important. A pregnant woman has to be extremely 
careful what she puts into her mouth and on her skin. A good quality diet, 
plenty of rest, plenty of clean, fresh air and gentle physical activity in the 
fresh air are all vitally important. Protecting pregnant woman from expo­
sure to any man-made chemicals, tobacco smoke, radiation, drugs, etc., 
will help her produce a child with a low toxic load in its little body, which 
will give it a good start in life. What about other children in the family? In my clinical experience the 
siblings of autistic, hyperactive and other GAPS children are almost invari­
ably affected by abnormal bodily flora and conditions, which are caused by 
it. The most common ones are eczema, asthma, digestive problems and 
anaemia. Less common are attention deficit with or without hyperactivity, 
dyspraxia, dyslexia and autism. Of course, these children have inherited 
the same flora as their GAPS sibling. But due to genetic differences, a dif­
ferent toxic load at birth and various other factors, their bodily dysbiosis 
and toxicity, which it produces, manifests itself differently. Well-function­
ing gut flora is the major regulator and housekeeper of our immune system. Allergies, like eczema and asthma are the result of a malfunction­
ing immune system and the most common conditions I see in the siblings 
of autistic children, for example. Different digestive problems are usually not as severe in the siblings, as 
in their GAPS brother or sister. Nevertheless, they are quite common, 
which is not surprising considering that they got their gut flora from the 
same mother as their more severely affected sibling. Anaemia is something that is not readily recognised in connection with 
autism, eczema, asthma, ADHD, schizophrenia and other GAPS disorders. And yet the majority of GAPS children, I have seen, look pale and pasty and 
their blood tests show typical for anaemia changes. However, when you 
look at mothers and siblings of these children, they almost without excep­
tion look just as pale and pasty. The reason for that is that most people with 
abnormal gut flora have various stages of anaemia. We have already dis­
cussed why it happens in the previous chapters.
Gut_and_Psychology_Syndrome.txt
Summarize the following text section accurately and concisely. Maintain specific details and numerical information, and use anti-repetition mechanisms:

        GAPS patients have a long list of nutritional deficiencies due to abnormal 
digestion and absorption, so their immune system is not only unbalanced, 
but also malnourished. But as if all that is not enough, an immune system in a body with abnor­
mal bacterial flora is exposed to a whole host of extremely toxic sub­
stances, many of which have a direct damaging effect on immunity. These 
toxins come from all the opportunistic microbes, which happily overgrow 
in the gut and elsewhere in the body of a person with GAPS thanks to the 
absence of beneficial flora's control. We have already examined what happens to the digestive wall when the 
gut flora is abnormal: it becomes damaged and leaky. A constant stream of 
invaders and undigested food comes through the damaged epithelial 
barriers in the gut. The immune system has to deal with all that, 
while being malnourished, deficient, compromised, unbalanced and 
intoxicated. So, should it come as a surprise to us that GAPS children and adults have 
their immune system in such a poor state. 4. WHAT CAN 
DAMAGE GUT FLORA. We have looked in detail at the different roles our indigenous gut flora 
plays in the body. We have seen how important it is for us to keep this 
microscopic world inside us healthy and active. However, in our modern 
world this task has become extremely difficult if not impossible. Let us 
have a look at what dangers our gut flora has to face on a regular basis. Antibiotics 
We all have taken antibiotics in our lives. It is one of the most commonly 
prescribed medications in our modern world. Since the moment we are 
born we are likely to be exposed to this group of drugs on a regular basis 
not only through prescription, but also through food. Farm animals and 
poultry are routinely given antibiotics, so all the products we get from 
them (meat, milk, eggs) will provide us with a constant supply of anti­
biotics and antibiotic resistant bacteria, which these animals develop in 
their bodies and all the toxins which these bacteria produce. JFarmed fish 
like salmon has antibiotics routinely added to their tanks, A lot of fruit and 
vegetables are sprayed with antibiotics to control disease. The way things 
are in our sophisticated modern world we simply cannot avoid exposure to 
antibiotics. It has become such a "normal" part of life'that not many of us 
ask the question "What are they doing to us. " And as the production of 
antibiotics grew from hundreds of tons a year in the 1950s to tens of thou­
sands of tons a year in the 1990s, so grew the evidence and worried research 
into the harmful effects of this group of drugs on human health. Let us see 
what this research shows: 
• Antibiotics have a devastating effect on beneficial bacteria in the 
human body, not only in the gut but in other organs and tissues. • Antibiotics change benign bacteria, viruses and fungi into pathogenic, 
giving them an ability to invade tissues and cause disease. • Antibiotics change bacteria making it resistant to antibiotics, so the industry has to work on more and more powerful new antibiotics to 
attack these new changed bacteria. A good example is tuberculosis, 
where wide use of antibiotics has created new varieties of the 
Mycobacterium Tuberculosis resistant to all existing antibiotics. • Antibiotics have a direct damaging effect on the immune system, 
making us more vulnerable to infections, which leads to a vicious 
cycle of more antibiotics and more infections. Let us have a look at what different groups of antibiotics do to the gut flora. Penicillins 
In this group we have very widely used Amoxicillin, Ampicillin, 
Flucloxacillin and all other antibiotics with "-cillin" at the end of their 
name. These drugs have a damaging effect on two major groups of our 
beneficial resident bacteria: Lactobacilli and Bifidobacteria, while promot­
ing growth of pathogenic Proteus family, Streptococci and Staphylococci 
This particular group of antibiotics allow bacteria normally found only in 
the bowel to move up to the intestines, which predisposes the person to 
development of IBS (Irritable Bowel Syndrome) and other digestive 
disorders. Tetracyclines (Tetracycline, Doxycycline and other "-cyclines") 
This group of drugs is routinely prescribed to teenagers for acne as a long 
course, lasting from three months to two years. Tetracyclines have a partic­
ular toxic effect on the gut wall by altering protein structure in the mucous 
membranes. This in turn does two things. First, it makes the gut wall 
anatomically vulnerable to invasion by pathogenic microbes; second, it 
alerts the immune system to attack these changed proteins, starting an 
auto-immune reaction in the body against its own gut. In parallel tetracy­
clines stimulate growth of disease causing Candida fungus, Staphylococci 
and Clostridia in the digestive tract. Aminoglycosides (Gentamycin, Kanamycin), Macrolides (Erythromycin) 
and other "-mycins" 
These drugs have a particular devastating effect on colonies of such bene­
ficial bacteria in the gut as physiological E. coli and Enterococci. A pro­
longed 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 lead to selective stimulation of growth of the Proteus family 
and lactose-negative Exoli species, capable of causing serious disease. Combinations of antibiotics have stronger damaging effects on the gut 
flora than single drugs. The damage is worse when antibiotics are adminis­
tered orally and when the course of antibiotic is a lengthy one on a low 
dose, like the one prescribed for acne, chronic cystitis, chronic ear infec­
tion and other chronic infections. Medical personnel and workers in phar­
maceutical industry are at a particular risk of chronic exposure to low 
doses of antibiotics and indeed gut dysbiosis is very common among these 
people. When an antibiotic is prescribed in a high dose, it leaves the gut with a 
lot of empty niches to be populated by whatever bacteria, viruses or fungi 
would 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 the course of antibiotic is short and the dose 
is low, it takes different beneficial bacteria in the gut a long time to recover: 
physiological Exoli takes one to two weeks, Bifidobacteria and Veillonelli 
take two to three weeks, Bacteroids, Peptostreptococci take a month. If in 
this period the gut flora is subjected to another damaging factor(s), then 
gut dysbiosis may well start in earnest. The majority of GAPS patients I have seen have been exposed to numer­
ous courses of antibiotics during their life. The most common reasons in 
children are repeated ear infections, chest infections, impetigoand masti­
tis in the breast-feeding mother, when the baby would get antibiotics 
through the breast milk. Considering that many of these children had little 
chance to develop a healthy gut flora from the beginning, these courses of 
antibiotics would have a devastating effect on their fragile gut ecology. Other drugs 
Most drugs, particularly prescribed for long periods of time or perma­
nently, have a detrimental effect on gut flora. Pain killers or analgesics (aspirin, ibuprofen, etc. ) are often prescribed 
for long periods of time to people with chronic pain. These drugs stimulate 
growth of haemolytic forms of bacteria and Campylobacterin the gut, all of 
which are capable of causing disease. Steroid drugs, like Prednisolone, Hydrocortisone, Betamethasone, 
Dexamethasone, etc. damage gut flora. In addition, they have a strong immunosuppressing ability, which makes the body vulnerable to all sorts 
of infection. For example, it is known that a course of steroids is almost 
invariably associated with fungal overgrowth in the body, particularly of 
Candida species. Contraceptive pills or The Pill is something many women take for many 
years, often from a very young age. This group of drugs has a devastating 
effect on the gut flora. By the time a woman is ready to have children, she 
has been on these drugs for a long period of time and has an abnormal gut 
flora. A human baby is born with a sterile gut and acquires most of its gut 
flora from the mother. So if the mother has an abnormal gut flora, that is 
what she will pass to her child, predisposing this child to eczema, asthma, 
other allergies and in severe cases to learning disabilities. Many other groups of drugs, including sleeping pills, "heartburn" pills, 
neuroleptics, cholinolytic drugs, cytotoxic drugs, etc. , etc. cause different 
damage to the gut flora, digestive system and immune system. Drug-induced gut dysbiosis is usually the most severe and the most 
resistant to treatment. In the last 50 years we have seen a tremendous 
increase in drug use by western population. It almost became a normal 
part of life to take some sort of prescription or over-the-counter drug, 
something to talk about with your neighbours. Yet not many people think 
what these drugs are doing to their bodies, let alone to their gut flora. What other factors can have an effect on gut flora. Diet 
What we eat has a direct effect on the composition of the gut flora, A 
modern diet of convenience rather than nutrition, full of processed foods, 
has a serious detrimental effect on the gut flora. Too much sugary foods and processed carbohydrates increase numbers 
of different fungi, Candida species in particular, Streptococci, 
Staphylococci, some Clostridia species, Bacteroids and some aerobic 
opportunistic bacteria. Processed and sugary carbohydrates (white bread, 
cakes, biscuits, pastries and pasta) also promote population of the gut with 
worms and other parasites. A diet low on fibre from fresh fruit and vegetables has a profound nega­
tive effect on gut flora and general body metabolism, predisposing the 
person to bowel cancer, atherosclerosis, abnormalities in hormonal 
metabolism and many other problems. Bottle-fed babies develop completely different gut flora to the breast-fed 
babies. Breast-feeding is essential for appropriate population of baby's gut with 
balanced healthy gut flora. Babies are born with a sterile gut. Breast-feed­
ing is the one and only opportunity we have in our lives to populate the 
entire surface of our gut with a healthy mixture of bacteria to lay the veiy 
basis of our future health. Bottled~fed babies have their gut populated by a 
combination of different bacteria, which predisposes them later to many 
health problems. We have a whole generation of people, mainly born in the 
1960s and 1970s who were not breast fed because it was not fashionable. A 
whole host of medical problems that arose from that fashion have made it 
obvious to the medical profession and the rest of us how important breast­
feeding is. Thankfully, now, a majority of mothers do their best to breast 
feed their newborn babies. Prolonged fasting and starvation, overeating and parenteral feeding can 
seriously alter the composition of gut flora and start a chain of health prob­
lems, so supplementing beneficial bacteria in a form of probiotic would be 
a good idea in these situations. Generally, when gut dysbiosis is caused exclusively by poor diet it is 
usually fairly mild and can be corrected by better eating habits. Unfortunately, in our modern world it is rare not to be exposed to other 
factors which would also damage your gut flora, antibiotics for example. Disease 
Different infectious diseases, like typhoid, cholera, dysentery, salmonella 
and some viral infections can cause lasting damage to the gut flora. Repopulating the gut with beneficial bacteria has to he an important part 
of the treatment of patients with these serious infections. Different chronic illnesses are accompanied by serious defects in gut 
flora, like diabetes, autoimmune disease, endocrine disease, obesity and 
neurological conditions. It is a common after-effect of surgery, chemo­
therapy, hormone therapy and radiotherapy. Stress 
A short-term stress has a detrimental effect on the gutflora,but it usually recov­
ers well after the stressful situation is over. However, a long-term physical or 
psychological stress can do permanent damage to the indigenous flora. Other factors % 
Physical exertion, old age, alcoholism, pollution, exposure to toxic sub­
stances, seasonal factors, exposure to ionising radiation and extreme 
climates all have a profound effect on our friendly bacteria. Every one of us carries a unique mixture of microbes in the gut. Under 
the influence of drugs and other factors, listed above, this gut flora will be 
changed in a unique way in every one of us, predisposing us to different 
health problems. It is a completely unpredictable process and the science 
so far has not got very reliable methods of testing for the full range of 
microbes in the gut, let alone treating any abnormalities. This damage gets 
passed from generation to generation as a newborn child gets its gut flora 
from the mother. And as the damage gets passed through generations, it 
gets deeper and deeper. This process reflects in the severity of healthprob-
lems related to abnormal gut flora seen in generations. For example, this is 
quite a common scenario, which I see in my clinic: a grandmother has mild 
digestive problems as a result of low-key gut dysbiosis. She passes moder­
ately abnormal gut flora to her daughter. On top of that she decides not to 
breast feed, because it is not fashionable. As a result, her daughter suffers 
from allergies, migraines, PMS and digestive problems. Then she takes 
contraceptive pills from the age of 16 which deepens the damage to her gut 
flora, not to mention a few courses of antibiotics along the way for various 
infections and a diet of fast foods. After 10 years of being "on the pill" she 
has children, to whom she passes her seriously abnormal gut flora. Her 
children develop digestive and immune problems, which then lead to 
eczema, asthma, autism and other learning problems. Most of the factors, described here, are hard to escape in the modern 
world. Under the influence of these factors, the beneficial bacteria in the 
gut lose their ability to fulfil all the functions we have looked at in the pre­
vious chapters. They are unable to protect the digestive tract from oppor­
tunistic flora and transitional bacteria, viruses and fungi, which sets up a 
whole chain of pathology in the gut and the rest of the body. To gain more 
understanding of what happens in this situation, let us have a look at the 
opportunistic flora, which lives in our digestive system. 5. THE 
OPPORTUNISTIC FLORA 
We talked in detail about the essential flora (the good bacteria) of the gut 
and its multiple functions. Let's look at the second group of bacteria now -
the opportunistic flora. This is a large group of various microbes, the 
number and combinations of which can be quite unique. There are around 
500 different species of them found in the human gut. These are the most 
common: Bacteroids, Peptococci, Staphylococci, Streptococci, Bacilli, 
Clostridia, Yeasts, Enterobacteria {Proteus } Clebsielli Citrobacteria, etc. ), 
Puzobacteria, Eubacteria, Spirochaetaceae, Spirillaceae, Catenobacteria, 
different viruses and many others. Interestingly, many of these opportunis­
tic bacteria when in small numbers and under control actually fulfil some 
beneficial functions in the gut, like taking part in the digestion of food, 
breaking down lipids and bile acids. In a healthy gut their numbers are limited and tightly controlled by the 
beneficial flora. But when this beneficial flora is weakened and damaged, 
they get out of control. Each of these microbes is capable of causing 
various health problems. It is a fascinating area for future research, 
because it appears that it is the character of our individual opportunistic 
flora that may determine what disease we succumb to. Yes, we carry most 
of our future health problems in our own gut pretty much from birth. As 
long as we take good care of our defenders, the beneficial flora, those bad­
dies may never show their ugly faces. Unfortunately, our modern life-styles 
sooner or later damage our indigenous bodily flora and whatever oppor­
tunists were waiting for their turn become active. The best known is the fungus Candida albicans, which causes untold 
misery to millions of people. There is an abundance of literature published 
about Candida infection, so we will not concentrate on it here, However, I 
have to say that a lot of what is described as Candida Syndrome is in effect 
a result of gut dysbiosis (abnormal gut flora), which include the activity of 
lots of other opportunistic and pathogenic microbes. Candida albicans is 
never alone in a human body. Its activity and ability to survive and cause 
disease depend on the state of trillions of its neighbours - different bacteria, viruses, protozoa, other yeasts and many other micro-creatures. In a healthy body Candida and many other disease-causing microbes are 
very well controlled by the beneficial flora. Unfortunately, the era of anti­
biotics gave Candida albicans a. special opportunity. The usual broad-spec­
trum antibiotics kill a lot of different microbes in the body - the bad and 
the good. But they have no effect on Candida. So, after every course of 
antibiotics Candida is left without anything to control it, so it grows and 
thrives. At the dawn of the antibiotic era the medical profession recognised 
this phenomenon, so it used to be a rule to prescribe Nystatin (an anti-can-
dida antibiotic) every time a broad-spectrum antibiotic was administered. However, for whatever reason, doctors stopped this practise decades ago 
and now we are paying the price for it - Candida infection has become 
extremely common. Apart from antibiotics another factor in our modern 
world plays a major role in Candida overgrowth - our diet. Candida flour­
ishes on sugar and processed carbohydrates and these are the foods, which 
nowadays dominate our western eating habits. Some opportunists, listed above, when out of control get through the gut 
wall barrier into the lymph and bloodstream and cause problems in 
various organs in the body. But of course, the first place to suffer will be the 
digestive system. Holding an abnormal bacterial mass, it is no surprise that 
the digestive system cannot function well. The most common result of gut 
dysbiosis is the infamous Irritable Bowel Syndrome (IBS), where a whole 
host of opportunistic bacteria populate the intestines, causing the 
unpleasant symptoms of IBS. More and more research is coming out link­
ing Crohn's disease and ulcerative colitis with the activity of opportunistic 
gut flora getting out of control. Certain opportunists, when not controlled by damaged good bacteria, 
get access to the gut wall and damage its integrity, making it "leaky". For 
example, microbiologists have observed how common opportunistic 
gut bacteria from the families Spirochaetaceae and Spirillaceae have an 
ability due to their spiral shape to push apart intestinal cells, breaking 
down the integrity of the intestinal wall and allowing through substances 
which normally should 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 gets 
through this leaky gut wall into the blood stream, where the immune 
system recognises them as foreign and attacks them. This is how food aller­
gies or intolerances develop. What is happening is that foods do not get a 
chance to be digested properly before they are absorbed through the damaged gut wall. In many cases, when the gut wall is healed food allergies 
disappear. Opportunistic flora constantly produces toxic substances, which are the 
by-products of their metabolism. In a healthy situation many of these by­
products can be physiological because in the process of evolution they got 
included in the normal functioning of the human body. For instance, a 
well-known group of toxins, produced by gut bacteria are amines - the 
metabolites of amino acids. Many of them have some important roles to 
play in the normal physiology of the body. A good example is histamine -
an important neurotransmitter in the body. Certain cells in the body nor­
mally produce histamine. However, it is also produced by Proteus family, E. coli family, Staphylococci and many other bacteria in the gut. In a situation 
where these opportunistic bacteria overgrow due to the lack of control 
from the beneficial flora, they start producing too much histamine. As his­
tamine takes part in many different functions in the body, all these func­
tions go wrong with the excess of histamine coming into the blood. These 
are the common symptoms of this condition: allergies, constantly low 
blood pressure, excessive production of body fluids, like saliva, dysfunc­
tion of hypothalamus with hormonal changes (PMS is a common result), 
emotional instability, sleep abnormalities, addictions and many others. An 
excess of histamine in the body is called histadelia. This condition was 
found by Dr Carl Pfeiffer in many people with depression, schizophrenia, 
addictions and autism. Antihistamine drugs are used by psychiatrists to 
treat schizophrenia. Nobody has yet looked at correcting the gut flora 
in order to normalise histamine production in the body and remedy 
symptoms of histadelia. Other well studied amines: dimethylamine, piperidine, pyrrolidine, tyra-
mine, octopamine, which are produced by bacterial activity in the gut from 
amino acids choline, lecithin, methylamine, lysine, arginine, ornithine and 
tyrosine, are also known to cause cerebral depression with symptoms of with­
drawal, intellectual regression, behavioural and emotional abnormalities. GAPS children and adults routinely show overgrowth of opportunistic 
microbes in their stool tests (the ones we can test for). The most commonly 
seen are Candida albicans, Bacteroids, Clostridia spp. , Proteus family, 
Streptococci and Staphylococci. Invariably, this overgrowth is combined 
with either the absence or greatly reduced numbers of beneficial bacteria. Unfortunately, stool testing so far available to us is quite primitive. There 
has not been a lot of money put into this research. There is a debate going 
on between professionals about the validity of stool analysis, as it only shows what microbes may be in the lumen of the bowel. It gives no informa­
tion on the most important inhabitants of the gut - the ones that live on the 
gut wall, the mural bacteria. These are the bacteria, which maintain gut 
integrity and its ability to digest and absorb food and which play such an 
important role in our immunity. There are limited studies done with biopsy of 
the gut wall and following microbiological analysis, which show that the mural 
bacteria can be quite different from the ones, which live in the lumen of the 
gut. Apart from that, stool analysis only reflects the microbial population of 
the bowel and does not reflect what lives higher in the intestines where the 
very important digestion and absorption happens. Unfortunately, we are still 
in the very early stages when it comes to testing for gut flora. Nevertheless, 
there is a large amount of information available now about what the bacterial 
population of a normal healthy person's stool should look like and compared 
to that information GAPS people have very abnormal results. A group of opportunistic gut bacteria, called Bacteroids, routinely found 
in GAPS stool analysis, deserves some attention. It is the most ubiquitous 
opportunistic bacteria in the gut of adult population in the western world 
which may be explained by what these bacteria like to eat - sugar, starch, 
lactose - the backbone of the western diet. There are in excess of 22 differ­
ent members of this family identified so far in the human body, the most 
common Bacteroides fragilis and Bacteroides melaninogenicus. These bac­
teria are almost always found in infected tissues of the digestive tract, 
abscesses, ulcers, urinary infections, lung infections, peritonitis, infected 
heart valves, blood infections, mouth infections, teeth and gum disease, 
gangrene and post-operative infections. They are opportunists always 
hanging around in every mucous membrane of the body waiting for their 
opportunity to cause trouble. However, they usually do not cause trouble 
alone but join some bigger bully on the playground and in that company 
really show their ability to cause disease. For example, they are usually 
found in company with Clostridia. They appear to be good friends with the 
Clostridia family, which is considered to be more dangerous than 
Bacteroids. But Bacteroids seem to show their ability to cause disease 
better in the company of Clostridia, at the same time assisting Clostridiain 
its activity. Members of Clostridia family are almost always detected in the stool 
analysis of autistic children and adults. There are about a hundred of dif­
ferent Clostridia species known so far. Apart from autism they are present 
in the stools of people with schizophrenia, psychosis, severe depression, 
muscle paralysis and muscle tonus abnormalities and some other neurological and psychiatric conditions. Many Clostridia species are 
normal inhabitants of a human gut. For example Clostridium tetani is rou­
tinely found in the gut of healthy humans and animals. Spores of this bac­
terium are passed through faeces into soils, where they can survive for 
years. Most soils in the world test positive for tetanus spores. Everybody 
knows that tetanus is a deadly disease, due to an extremely powerful 
neurotoxin Clostridium tetani produces. Anybody who gets a wound or 
even a scratch contaminated by soil is immediately advised to have a shot 
of anti-tetanus vaccine. But we contract tetanus only when the bacterium 
gets directly into our tissues or blood. Clostridium tetani which lives in the 
gut, normally does not do us any harm because its toxin cannot get 
through the healthy gut wall. GAPS patients do not have a healthy gut wall, 
which would allow toxins to get into the body. Many other species of Clostridia {perfringens, novyi, septicum, his-
tolyticum, sordelli taerofoetidum f tertium, sporogenes, etc. ), routinely found 
in the human gut, produce toxins similar to tetanus toxin as well as many 
other toxins. So how can we have these deadly bacteria in our gut and be 
healthy. Because, they are controlled by our friendly bacteria, which will 
not allow them to flourish and, most importantly does not allow their 
toxins through the gut lining into the bloodstream. However, in the GAPS gut where the person hasn't got the beneficial bac­
teria to protect the gut wall and control Clostridia, neurotoxins have a good 
chance of getting into the bloodstream and into the brain and the rest of 
the nervous system, affecting its development and functioning. Sensitivity 
to light and noises is a typical symptom of tetanus infection and GAPS con­
ditions, like autism, schizophrenia, psychosis, dyslexia, so it seems plausi­
ble that the two may be connected. Most GAPS children and adults, whom 
I see in my clinic, have got abnormalities of muscle tonus similar to low 
exposure to tetanus neurotoxin. A typical picture is where extensor mus­
cles have higher tonus than contractor muscles. Maybe that is the reason 
why autistic children and adults walk on tiptoes and often self-stimulate by 
stretching their arms, fingers and legs in odd positions. In these cases 
where the patient's stool has been tested almost without exception an 
overgrowth of Clostridia spp. is observed. Recent research at the University 
of Reading in the UK by a microbiological team led by Professor Glenn 
Gibson has found very high levels of Clostridia in the gut of 150 autistic 
children and a second research programme found similarly high levels in 
the gut of another 80 autistic children, which were not present in their 
non-autistic siblings. Just like Candida albicans, the Clostridia family was given a special 
opportunity by the era of antibiotics, because Clostridia are also resistant 
to them. So, every course of broad-spectrum antibiotics removes good 
bacteria, which leaves Clostridia uncontrolled and allows it to grow. Different species of Clostridia cause severe inflammation of the digestive 
system, for example Clostridium difficile causes a potentially fatal pseudo­
membranous colitis. Some species of Clostridia have been linked to such 
debilitating digestive disorders as Crohn's disease and ulcerative colitis. I 
have no doubt that the Clostridia family plays an important role in the 
development of autistic enterocolitis as well. Future research will show. However, there are some facts already which support this thought. For 
example, William Shaw at Great Plains Laboratories reports a number of 
cases where a course of anti-clostridia drugs Metronidazole (Flagyl) and 
Vancomycin reduced autistic symptoms and improved digestion and the 
biochemical picture in autistic children. However, in almost all cases as 
soon as the drug was stopped, all the symptoms and biochemical abnor­
malities returned. Unfortunately, anti-clostridia drugs are toxic, they have 
serious side effects, so we can not prescribe them for long periods of time 
to children or adults. Clostridia are spore-forming bacteria, which makes 
them impossible to eradicate. We can only control them and the best way 
to do it is Nature's way - with beneficial bacteria. Another large group of bacteria, which commonly overgrow in the gut 
dysbiosis situation are sulphate-reducing bacteria. There are many 
species of sulphate-reducing microbes. To mention just a few: 
Proteobacteria, Thiobacilli, Chromatiaceae, Desufotomaculum spp. , some 
gram-positive bacteria, some fungi and Bacteroids. These microbes 
metabolise sulphate coming from food into sulphites, many of which are 
toxic. Severe deficiency in sulphates has been found in 95% of autistic chil­
dren. Undoubtedly, sulphate-reducing bacteria play an important role in 
causing this deficiency. Sulphates are needed in the body for many func­
tions, some of which are detoxification and normal metabolism of brain 
neurotransmitters. An overgrowth of sulphate-reducing bacteria would 
make sulphur unavailable for the body to use, turning it into toxic sub­
stances like hydrogen sulphide, which is the gas with a rotten egg smell. Many parents of autistic children tell me that their child's stool and flatus 
has this characteristic smell. Here we have looked at some pathogens found in the gut of GAPS 
patients. To their happy company we can add the measles virus found by 
Dr A. Wakefield's research group. This is only one virus, which received such detailed attention. There are some indications in literature that mem­
bers of the herpes virus family are also very active in these patients. How 
many other viruses may there be in the GAPS gut, which have never been 
studied. How many other pathogenic bacteria, fungi, protozoa and other 
microbes are there, which we have no methods to detect or study yet. I 
have no doubt that sooner or later science will catch up with them and we 
will learn what they are and how to deal with them. In the meantime, what 
should we do to help our GAPS children and adults now. As always, Nature 
has a good answer - the beneficial flora. Having good bacteria in the gut is 
the best way to keep Clostridia, Candida, Bacteroids, viruses and many 
many other microbes under control. Well-functioning healthy gut flora 
would not only keep those pathogens down but would maintain the 
integrity of the gut wall so it does not let through the toxins from those 
pathogenic microbes. This is Nature's way of dealing with them and the 
smart thing for us is to try and copy it. Due to the absence or greatly reduced numbers of beneficial bacteria, 
the GAPS digestive system gets taken over by opportunistic and pathogenic 
microbial flora, constantly producing a river of toxicity flowing from the 
gut to the brain. This is the toxicity, which is probably making these chil­
dren and adults autistic, schizophrenic, hyperactive, dyspraxic, dyslexic, 
psychotic, depressed, obsessed, etc.
The text mentions several factors that can damage the gut flora, including antibiotics, poor diet, stress, and other environmental toxins.
What are some common factors that can damage the gut flora?
According to the text, well-functioning gut flora is the major regulator and housekeeper of the immune system.
What is the main regulator of the immune system?
The text states that breast-fed babies develop a healthy gut flora, whereas bottle-fed babies do not.
What is the main difference between breast-fed and bottle-fed babies in terms of gut flora?
The text suggests that the development of autistic symptoms may be linked to the mother's abnormal gut flora, which is then passed on to the child, potentially leading to an overgrowth of Candida and other pathogenic microbes.
What is the main reason for the development of autistic symptoms in some children?
The text emphasizes the importance of restoring a healthy gut flora through the administration of beneficial bacteria (probiotics) and a healthy diet, as well as avoiding factors that can damage the gut flora.
What is the key to correcting the gut flora and treating GAPS patients?