Leaky Gut Update for the know-it-alls 
By Walter Sorochan

Posted February 20, 2016; updated Aril 27, 2023. Disclaimer  The information presented here is for informative and educational purposes only and is not intended as curative or prescriptive advice. The statements of this web-site have not been evaluated by the United States Food and Drug Administration (FDA). Nothing stated here should be considered as medical advice for dealing with a given problem, or to diagnose / treat / prevent / cure any disease.


Leaky gut is an imbalance between beneficial and harmful species of bacteria in your large intestine.  It was assumed to be a digestive disorder in a small number of the human population. But recent information points out that the majority of the population may have some degree of leaky gut and not be aware of it. Leaky gut is important because of the many diseases and disorders that are linked to it, like autism, Alzheimer's, diabetes, heart disorders, MS, Chronic Fatigue, arthritis, lupus, skin disorders, fibromyalgia and cancer.

Leaky gut occurs when the pores of the semi-permeable inner lining of the large intestinal wall become inflamed, causing the pores to enlarge. When this happens, the enlarged pores allow substances, that are normally block out .... bacteria, fecal material and toxins, to pass into the blood; thereby causing numerous organ disorders and diseases.

Leaky gut symptoms can vary widely from reflux or heartburn to bloating, gas, constipation, stomach pain and diarrhea.

Fixing leaky gut is complicated.  The best way to get rid of leaky gut syndrome is with a diet that feeds good bacteria and starves the bad bacteria. A leaky gut list of good to eat foods and bad foods to avoid is presented.

Author suggests seven steps to heal a leaky gut.

This article attempts to make some sense of the health-disease interrelationships with leaky gut. The author attempted to simplify medical research and make it easy for non-medical persons to understand.

It is only recently that we have become aware of the symbiotic lifestyle between bacteria and humans. 

I've got it!

Well, I have symptoms of digestive disorder. And yet, for most of my life, I lived in ignorance and did not realize that perhaps I did suffer from some form of leaky gut that may have  contributed to maladies, like GERD, itchy skin and constipation, that doctors were unable to successfully treat for whatever reason.  Putting it in another way, my digestive disorders occurred so often that these felt like these were part of my normal human landscape.

Researching about leaky gut not only informed me about this tragedy, but also made me aware that most  humans are probably suffering from leaky gut and they are not aware of it.

The trickle of what we do know is that our wellbeing is determined by the food we eat and not antibiotics.

In spite of the good research being done throughout the world, leaky gut still remains a human mystery.

I am most grateful to my friend who was diagnosed with a leaky gut and who asked me to find out more about her digestive disorder.

But this relationship is not controlled by the human body; instead it is bacteria in the large intestine that control the destiny of your well-being.  This may come a real shock for the majority of persons who have been raised to believe that human waste had nothing to do with good health.

The relationship between the composition of bacteria in the large intestine [ colon, gut] and human diseases has become front page news since 2000. Chey: Update IBS 2015  Galland: Leaku gut syndrome 2011    INRA-France: studying microbiota 2014

Researchers and medical doctors are beginning to pay attention to the kind and number of bacteria and their links to human diseases and disorders. No longer are they embarrassed to sample and talk about "dirty feces or poopoo!"   This is also true of leaky gut and how this disorder can affect most persons although most are not aware that their health problems may be related to leaky gut. Kresser: Leaky gut Pimentel 2015

leaky-gut-syndrome image

Leaky gut was assumed to be a disorder of a small number of the population.But recent information points out that the majority of the population may have some degree of leaky gut and not be aware of it. Making matters more confusing, the symptoms of leaky gut [ reflux, constipation, diarrhea, flatulence, bloating, inflammation ] are similar to other digestive disorders, primarily Irritable Bowel Syndrome [IBS] and Small Intestinal Bowel Overgrowth [SIBO].

Such a shared common denominator of symptoms linking all three disorders adds to medical confusion in the examination room.  Those experiencing these symptoms are likewise bewildered in seeking relief. A person may be living, by appearances, a healthy lifestyle but be afflicted by reflux, flatulence or constipation and not be aware that these symptoms may indicate some form of a leaky gut.

Dr. Mark Hyman, MD, has made an easy to understand video that explains Irritable Bowel Syndrome [IBS] leaky gut and other digestive disorders -- length 9:07 mns:  Hyman: fixing IBS 2013


The healthy body gets its wellbeing from the bacteria in the large intestine or colon. This is illustrated in the diagram below:

Gut-health good-bad

Since this author pointed out the similar inter-relationships between leaky gut, IBS and SIBO, it is appropriate to point out the commonly [shared] symptoms as well. Healers reporting symptoms of these digestive disorders include: Axe: Getting rid of leaky gut    Carnahan: signs IBS 2014  Chey: Update IBS 2015  Kresser: Leaky gut & Fibromyalgia 2014  Longstreth: Functional bowel disorders 2006  Article by Pimentel: :IBS linked to gut bacteria is no longer active.

It is not uncommon to have both SIBO and leaky gut simultaneously. And very often if you have SIBO for a long period of time, you will develop a leaky gut. Studies show that over 50% of patients diagnosed with IBS actually have an underlying imbalance called SIBO, or small intestinal bacterial overgrowth. The majority of our gut bacteria should be in the colon. When the bacteria migrate backwards into the small bowel or when there is low stomach acid or poor pancreatic enzyme production, bacteria in the small bowel can overgrow and cause symptoms, such as diarrhea, gas, or bloating.  Carnahan: signs IBS 2014

Bad breath: An obvious consequence of bacterial fermentation is production of gas. A variety of gases that develop in the gut expand the diameter of the gut and are absorbed through the mucosa, travel in the bloodstream and then are excreted through the pulmonary system and come out of the mouth. Researcher   Hughes' explanation partially tells us that bad breath can come from not just bacteria in the mouth but also from the colon.

What is Leaky Gut:

To understand what leaky gut is we need to understand how the large healthy intestine works.

The intestine wall is semi-permeable. This means the pores [small holes] only allow certain things to enter the bloodstream and block other things from entering the bloodstream. For example, the intestinal wall reabsorbs liquid back into the blood stream. Specific molecules and nutrients are also allowed to pass through but toxins and large undigested food particles are blocked. With leaky gut, your pores can continue to widen [ like getting a larger hole torn in a fishing net ] and get bigger.

And as pores widen, the undigested food particles and other “bad stuff” [ yeast, toxins, proteins like gluten, bad bacteria and all other forms of waste ] that are supposed to be kept out, pass through into the bloodstream and then flow freely in the bloodstream.  This causes systemic inflammation inside the wall of the colon, leading to an immune reaction. Often times the body will begin to recognize certain foods as toxic and will facilitate an immune reaction [ allergy ] whenever one eats that food. If this problem continues, leaky gut can then progress to an autoimmune disease. Axe: Getting rid of leaky gut

Leaky gut is related to bacteria.  There are several reasons for thinking this way.  Firstly, bacteria in the large intestine get their food from the same food we ingest to sustain our energy and wellbeing. Secondly, a bad diet feeds the bad bacteria, that in turn, give off excessive toxic wastes, which, in turn, tend to plug up the intestinal pores. Thirdly, the accumulation of excessive wastes causes a reaction in the intestinal lining, causing inflammation and the pores to widen. As the larger pores widen and allow toxic wastes to pass into the blood stream, the toxic wastes trigger auto immune disorders and diseases in different parts of the body. The process of toxic wastes leading up to auto-immune disorders centers around an excess of bad bacteria in the large intestine.  Wiki: gut flora

Thus, to understand leaky gut, we need to understand that the colon or large intestine has good and bad bacteria. Somewhere between 300 and 1000 different species live in the gut, with most estimates at about 500. However, it is probable that 99% of the bacteria come from about 30 or 40 species. Fungi, protozoa, and archaea also make up a part of the gut flora, but little is known about their activities.

It is estimated that 100,000 billion bacteria populate the gut of each individual [ or 10 to 100 times more than the number of cells in the human body ], and their diversity is considerable. However, because only 15% of these bacteria were previously isolated and characterized by genome sequencing, an immense number of the microbial genes previously identified still need to be assigned to a given species.  NRA-France: studying microbiota 2014  Studying colon bacteria is difficult because most cannot be studied outside their colon.

The problem of bad bacteria in the colon causing leaky gut is that the bacteria can invade the small intestine and cause problems in the small intestine referred to as Small intestinal bacterial overgrowth [ SIBO]. This can be important for healthy persons — as up to at least 20% of the population can have SIBO, an over-colonization of specific bacteria, usually the colon bacteria, into the small intestine, where they don’t belong. SIBO, at least according to breath tests or other testing methods, may be linked many of our autoimmune disorders and this linkage has not been recognized as yet by the medical establishment.  So what do we make of that? Is it possible to have SIBO and be completely asymptomatic? The answer is 'YES.'

Recent evidence linking colon bacteria to leaky gut and other diseases and disorders:

"Emerging evidence suggests that intestinal permeability is impaired in patients with IBS, lending possible credence to the concept of the “leaky gut."  Multiple studies have also shown an association between IBS and small intestinal bacterial overgrowth [SIBO]. Chey: Update IBS 2015

One condition that plays a huge part in Leaky Gut is Irritable Bowel Syndrome or IBS. Longstreth uses Rome II diagnostic criteria to define "IBS as a functional bowel disorder in which abdominal pain or discomfort is associated with defecation or a change in bowel habit, and with features of disordered defecation." Throughout the world, about 10%–20% of adults and adolescents have symptoms consistent with IBS, and most studies find more females than males have it. Only a fraction of affected individuals—between 25% and 50%—seek medical care for their symptoms. Chey: Update IBS 2015  IBS symptoms come and go over time, often overlap with other functional disorders, symptoms impair quality of life, and result in high health care costs. Article by Longstreth: Functional bowel disorders is no longer active.

This interconnected condition is in itself, very complex with multiple symptoms and multiple potential causes. Many people suffer with IBS without necessarily realizing it. And, even if they were aware of it, they would not always know what it means. The pathophysiology of IBS is not fully understood. Chey: Update IBS 2015   Many people don’t realize that this connection between IBS and Leaky Gut exists.

So how are the two related? Well, it’s a tricky one because, on the one hand, IBS can cause Leaky Gut but on the other, Leaky Gut can also cause IBS! The inflammation and digestive disturbances associated with IBS can damage the intestinal lining, and a less-than-healthy intestinal lining makes it harder for the digestion to work properly. This causes a confusing ‘chicken and egg’ situation where it’s hard to tell where the problem started. This in turn, makes it difficult to diagnose and treat the root cause of the problem.

The prevalence of Irritable Bowel Syndrome or IBS varies by countryIBS world pop and by age range examined. The bar graph at left shows the percentage of the population reporting symptoms of IBS in studies from various geographic regions. Wiki: IBS

Healthy persons — up to 20% can have Small intestinal bacterial overgrowth [SIBO] and not be aware of it, at least according to breath tests or other testing methods.

One can conclude that the number of suspected persons suffering from leaky gut, or IBS, as mentioned by conflicting quotes, is unknown.

Here is additional supporting information that colon bacteria are linked to leaky gut, IBS, SIBO and other disorders:

1.  Leaky gut Syndrome is a very common condition affecting a high percentage of the population today. The medical profession has no protocol or 'gold standard' to diagnose or treat leaky gut syndrome; many do not acknowledge it even exists. As a result many people go undiagnosed and are unaware that they may suffer from a leaky gut. Pretty much every chronic degenerative disorder stems from a leaky gut from arthritis, and digestive problems to ME, MS, Chronic Fatigue Syndrome, Irritable Bowel Syndrome (IBS), Fibromialgia [ FM], diabetes1, and neurological disorders to name a few.

2. 10-15% of the US population has Irritable Bowel Syndrome [IBS].  Kresser: Leaky gut & Fibromyalgia 2014  This estimate is on the low side  and it is probably close to 80% or more of the population. IBS can occur anywhere in the digestive tract from the mouth to the anus. Therefore, the symptoms can vary widely from reflux and heartburn to bloating, gas, constipation, stomach pain and diarrhea. The majority of people experience at least one or more of these symptoms almost every day and do not report these to their doctor.  Most doctors find IBS a mystery and are unable to help those unwittingly suffering from IBS.

3. Irritable Bowel Syndrome (IBS) is present in 30–70% of fibromyalgia patients. Kresser: Leaky gut & Fibromyalgia 2014

4. Up to 50% of patients with fibromyalgia have functional dyspepsia, which is a fancy term for “indigestion” with no known cause. Kresser: Leaky gut & Fibromyalgia 2014

 Folks, we have a real silent health problem that is incubating while we sleep!

What Causes Leaky Gut?

Four main causes of leaky gut have been proposed:  Axe: Getting rid of leaky gut

• Poor diet
• Chronic stress
• Toxin overload
• Bacterial imbalance

Leaky gut syndrome: The syndrome is a collection of symptoms that collectively define leaky gut. Illustration below:   Axe: Getting rid of leaky gut

2 Leaky gut symptoms Axe   

Reversing-Autoimmune-Disease Axe

There is some controversy about tests to identify leaky gut. For example Dr. Axe has evolved his own version of such a test. You can go on his web-site for more information: Article by Axe test for leaky gut is no longer active.

Dr. Pimentel has also created an inexpensive 3-minute paper quiz to help you find out if you may be suffering from the #1 problem missed by modern medicine. Yet, 10,000+ research papers link it to symptoms like fatigue, acne, brain fog, digestive complaints, depression, anxiety, allergies, and more…

Breath test for leaky gut:  If you suspect you may have some degree or form of leaky gut, then you should go to a specialist who can give you a breath test. The breath test is to confirm that you have a leaky gut and not that you have bad oral breath.  The authority on leaky gut, Dr. Mark Pimentel of Cedar Sinai Medical Center, has invented a breath test to identify leaky gut.  When the breath test has the gas, methane in it — that is a super accurate confirmation. If the methane is present on the breath test at greater than 3 parts per million at any part during the test, the association to constipation is over 90%. The other very interesting aspect of methane is that methane is proportional. So the higher the area under the curve on the breath test for methane, the greater the patient’s constipation severity is. And we know from animal studies that giving methane to animal subjects, just the gas itself, constipation or feces transit slows remarkably by about 60%; so getting rid of the methane is key. The breath test is very accurate at picking up methane. There’s almost no argument that methane breath test can confirm leaky gut.

Hybrids and the future: Leaky gut is not easy to identify and most difficult to fix. Since leaky gut is a linked relative of IBS, SIBO, other digestive disorders and bacteria in the colon, we should suspect that there are probably also hybrid leaky guts as well. If you do your simple math, then the number of such hybrid-bacterial combinations becomes astounding. Each hybrid may really be causing a specific and unique health problem. Medical science has not explored such a possibility. But if this is true, then, on the one hand, helping leaky gut patients becomes even more difficult. But on the other hand, such hybrid linkage narrows down finding healing processes for many diseases that really work.

Up to now, the focus has been on digestive disorders in a general manner. Overlooked is information about bacteria in the large intestine that may be good or bad and how to fix digestive disorders like leaky gut.

Fixing leaky gut and other digestive disorders:

gut-populationThere is no gold standard to deal with leaky gut. This is like the wild west of the 1880's shooting wars at the 'OKAY coral' with weak enforcement of the law. Medicine today is the okay corral.  Fixing the digestive disorders is similar to settling disputes in the 1880's, there is weak agreement upon therapeutic guidance.  Medical doctors are scrambling to find a therapy that works for some of their patients but not all.  It should not be surprising that the war here is to control the bad bacteria in the colon.  Most doctors agree that the best way to get rid of leaky gut syndrome is with diet.  Avoid eating foods that feed the bad bacteria! Replace the bad foods with good foods! Inoculate, if needed, the colon with probiotic bacteria to generate 80% good and 20% bad bacteria as a norm.  Drink lots of water to help your liver flush out the toxins. And finally stabilize the bacteria in the colon!  Axe: Getting rid of leaky gut  Walker: Cure for Crohns Disease  Ewers: Inflammation

"You don’t need to get rid of the bugs. Just stop them from producing methane is one such approach.

Unfortunately, fixing the diet does not always heal most of those afflicted with leaky gut. There are several reasons for this:

Fixing the diet, that is, eliminating bad foods and replacing these with good foods, may seem simple, but this is a most complex issue. Making informed and wise food choices is a most difficult one in lieu of processed foods and that most foods have some form of sweeteners added to them. Our food industry is designed for consumption and profit and not good health.

Compounding the choice of good foods is an uninformed general population about nutrition.  The body needs appropriate nutrients like vitamins, minerals, amino acids [proteins], carbohydrates and fats that are needed for normal body metabolism.  Null: Vit D triggers immunity  The body needs ALL essential nutrients [ co-factors ] to be present as a package to enhance good gastrointestinal tract health. Several of these include much overlooked vitamins A, B-complex, C, D, and E; and micro and macro minerals.  Vitamin D and magnesium act as turn on/off switches in many body processes, including DNA-RNA metabolic processes.  Null: Vit D triggers immunity

Related to public lacking nutritional information is lack of proper information on food and nutrition labels.  We put trust in nutrient supplements to help guide us in selecting foods. The real amount of nutrient absorption or bioavailability is virtually unknown.  There is good reason to suspect that most supplements, especially synthetic nutrients, may not work.  Despite all these doubts there are many practicing physicians who still prescribe nutrient supplements to heal digestive disorders. And millions more persons buying nutrient supplements on the assumption that these do heal and probably do to some degree!Nutrition has been virgin territory since the 1950's with very little research toward validating bioavailability of nutrients, identifying all the co-factors essential for supporting each nutrient, mineral ratio uncertainty [ e.g. Calcium: Magnesium = ratio is 2:1 is a guess ] and essential dosages for nutrient optimal wellbeing, as well as  revising bare-bones Recommended Daily Intakes [RDI] that were designed to avoid disease states and not elevate us toward optimal wellbeing. We have not made very much real progress in bridging nutrients to good health.

Then there is the human appestat that memorizes our taste buds for food; foods people love to eat .... that is referred to as comfort food --- like milk shakes, soft drinks, white breads, white pastas, cookies, sweets, fries and hamburgers.  The appestat center never forgets the sweet tooth that continuously rings the bell to eat more comfort foods!  These foods promote the growth of disease-causing bacteria.   Walker: Cure for Crohns Disease

Replacing bad foods with good foods requires time to stabilize the bacteria in the colon.  Bacteria may need several weeks to a month or longer to populate and become dominant.  For such stability to occur, we need to consistently eat foods that feed the good bacteria and starve out the bad ones.  This is indeed a most difficult but essential task.  James Lewis, a researcher at the University of Pennsylvania, agrees with this approach: Lewis said: "the findings suggest bacteria that live in the gut are sensitive to short term changes in diet, but it may take a long-term dietary change to significantly alter the types of bacteria that reside in the gut."

Researchers at UC Davis in 2014, discovered a biological mechanism by which harmful bacteria grow, edge out beneficial bacteria and damage the gut.  Bad bacteria get their start when antibiotics destroy the balance of bacteria in the gut.  Winter: key to bad bacteria growth 2013

Yet, in spite of these unanswered questions and food limitations, we need to do the best we can.

Remember, the top foods to remove .... that cause leaky gut are sugar, grains, conventional meat, processed foods, conventional dairy and GMO foods. The top toxic exposures to eliminate are tap water, pesticides, NSAIDS [ aspirin, painkillers ] birth control pills and antibiotics — but remember to always consult with your physician if he or she has prescribed these for you.  Axe: Getting rid of leaky gut

Good Leaky Gut Food List:    Axe: Leaky gut diet

Dr. Axe provides a list of foods on the leaky gut diet. These foods are similar to foods recommended by others. These foods support healing because these are easy to digest and can help repair the lining of the intestines:

Bone brothBone broth (made from scratch) provides important amino acids and minerals including proline, glycine and potassium that can help heal leaky gut and improve mineral deficiencies.

Raw cultured dairy Probiotic rich foods like kefir, amasai and yogurt can help heal the gut by destroying bad bacteria like candida.

Fermented vegetables – Try to add fermented foods such as coconut kefir, kvass, sauerkraut or kimchi. These fermented foods contain probiotics essential in helping repair a leaky gut that work by balancing the pH in the stomach and small intestines.

Steamed vegetables –Non-starchy vegetables that are cooked or steamed are easy to digest and are an essential part of the leaky gut diet.

Healthy fats – Consuming healthy fats in moderation like egg yolks, salmon, avocados, ghee and coconut oil are easy on the gut and promote healing.

Fruit – Consuming 1-2 servings of fruit daily is good on a leaky gut diet.  You can steam apples and pears to make homemade apple sauce or fruit sauce. Fruit is best consumed in the morning and not later on in the day and keep fruit intake in moderation.

Bad Foods that Cause Leaky Gut:  Axe: Leaky gut diet

Foods that create intestinal inflammation and candida, thereby causing a leaky gut are:

Gluten – A gluten free diet can help improve the symptoms of leaky gut. Gluten is the sticky protein found in most grain products including wheat and is difficult to digest unless it’s been brought through a sourdough or sprouting process. On the leaky gut diet you will want to avoid all foods that contain gluten and wheat products.

Cows Dairy – The protein in cows dairy, called A1 casein, can trigger a similar reaction as gluten and therefore should be avoided. In fact, A1 casein may be 26x more inflammatory than gluten!

Sugar – Feeds yeast and bad bacteria that can damage the intestinal wall creating a leaky gut. If you are going to use a sweetener, raw local honey is your best option but even that should be consumed in moderation at 1 tbsp daily.

Unsprouted Grains – Grains and soy when unsprouted and unfermented contain phytic acid which can irritate the intestines causing leaky gut.

GMO – Genetically modified organisms contain herbicides and pesticides that damage the gut lining. Studies out of the Journal of Environmental Sciences have found that GMO foods destroy the probiotics in your gut and cause organ inflammation.

Remember, the top foods to remove .... that cause leaky gut are sugar, grains, conventional meat, processed foods, conventional dairy and GMO foods. The top toxic exposures to eliminate are tap water, pesticides, NSAIDS [ aspirin, painkillers], birth control pills and antibiotics — but remember to always consult with your physician if he or she has prescribed these for you.  Axe: Getting rid of leaky gut

Dr. Josh Axe suggests ingesting Bentonite clay to help the digestive system and digestive health. You can take about one teaspoon of clay a day mixed with water to get this bentonite clay benefit. He recommend doing that right before you go to bed or first thing in the morning. You want to do it between meals, about an hour apart from a meal. So, if you struggle with an issue — especially like diarrhea, loose stools, leaky gut, etc. — you can benefit from taking a teaspoon of clay a day and again, especially useful as a step to cure diarrhea. Just one teaspoon a day will really go through your system. If you have pathogenic bacteria, or different types of metals or toxins within the body, the clay will absorb and help your body eliminate any of this junk. Axe: Clay benefits 2016

Sample list of Good & Bad Bacteria & food:

Research healers may specify bacteria but almost never mention the foods that the bacteria need to feed on. Such missing information prompted this researcher to do an in depth search for this information. The surprise finding was that there is little good information available. If this is true, one wonders how effective therapists are in helping their patients with Leaky Gut, Intestinal Bowel Syndrome and so on. An example summary is presented in the tables below with reluctance. You should be aware that there are an estimated 500 bacteria in the colon. Although most research deals with somewhere between 30 to 50 of the 500 bacteria residing in the colon, the number reviewed in both tables is much smaller and may not be a representative sample of your gut bacteria. Two major species of good bacteria are Lactobacillia & Bifidobacteria. Thus, the bacteria in the tables is a random sample that serves to illustrate what may be possible as each human body is different. Each person probably has a different species of bacteria.

Good bacteria

Symptoms & Health Conditions

Food sources

Lactobacilli acidophilis

Makes vit K

Yogurt; sauerkraut, Kefir, miso, chlorella, spirulina,  pickles, Kombucha tea

L brevis

Sauerkraut, pickles, chocolates

L bulgarius

Prevents bad guys: keep the pH in the small intestine too low for harmful bacteria growth to occur.

Swiss cheese and yogurt

Improves arthritis; increases Ca absorption; protect against bad bacteria forming in the intestine.

Swiss-type cheeses and long-ripened Italian cheeses such as Emmental, Gruyere, Grana Padano and Parmigiano Reggiano.

L plantatarum

Reduce cold infections

sauerkraut, pickles, brined olives, kimchi sourdough cheeses fermented sausages, and stockfish

L paracasei

Reduce cold infections

fermented vegetables, milk, and meat

L.reuteri [Lassesen] 55% of the Lactobacillus species colonize gut; L reuten produces reuterin and cobalamin (B12); L Reuteri and Glutathione should be taken together; Need to find probiotic with L reuten. Glutathione; Rye Bread (100% Rye)

L rhamnosus

Bolsters immune sys

yogurt, fermented milk, pasteurized milk, and semi-hard cheese

L salvarius

Extend longevity

Yogurt and mozzarella cheese

L casei [References: Hon;Sarver]

Activates cell immunity & lowers influenza virus (IFV); anti-obesity effects

Possibly dairy products

L thermphilus




Stabilizes human intestinal microflora and hastens the removal of pathogenic microorganisms.

Bifidobacteria bifidum [Andrew]

Prevent tumors; low count clinked to Crohn'

Kefir; Beans, peas, and lentils

B laterosporus

Enhances immune system

Onions, garlic, milk, bananas, wheat, oats, leeks, asparagus, artichokes, chicory

B longum

[Wiki longum

Enhances immune sys; prevent tumors; make vit B-complex & vit C; improves lactose tolerance and preventing diarrhea, food allergies, and colonization by pathogens; scavenge free radicals, lowering a person’s chance of atherosclerosis, stroke; lowers cholesterol; significantly suppress tumor volume and incidence; represents up to 90% of the bacteria of an infant’s gastrointestinal tract, lowered to 2-3% in childhood; treat cold, flu', lyme disease, eczema. yeast infections

B subtilis

Produce vitamins, antibacterial chemicals and antibiotic substances; prevent or slow growth of harmful bacteria; prevents IBS or irritable Bowel Syndrome

B lactis; [Bruso

Prevent and treat diarrhea; improve your immune function


B infantis References: Panyko Probiotic Organization

Helps prevent leaky gut; helps immune system to suppress inflammatory chemicals that damage the intestines; prevents or slows growth of harmful bacteria; may be beneficial to those that suffer from symptoms of irritable bowel syndrome (IBS) including bloating, gas, diarrhea, constipation, urgency and abdominal discomfort

Streptococcus thermophilus



E. Coli [Lassesen] E.coli population may be low in chronic fatigue syndrome. E.coli’s production of NADH; 66% of ME/CFS/Fibromyalgia patients taking it improved. Artichoke, cheese spread, chicory root, chocolate, garlic, onion, pasta, rye bread [100%]

The bad bacteria are usually found in very small numbers in the colon in healthy persons. The bad bacteria population is kept under control by the friendly or good bacteria in your gut; provided that the ratio of good to bad bacteria is maintained at about 80%:20% ratio. However, when your immune system is down, then the bad guys like Candida start to multiply and can quickly overrun the good bacteria. Eating bad foods like sugar sweets and processed foods feed the bad bacteria, but many bad bacteria can also get their start from contaminated foods [ food poisoning ].

Bad bacteria become a problem when they increase in numbers in the colon, giving off toxins that cause digestive disorders and illness symptoms. The column 'Food Sources' in the Bad bacteria table has fewer foods than the same column for Good bacteria Table.

The worst bacteria [the ugly] either directly destroy tissue by feeding upon it or produce a toxin that destroys tissue. Other bad bacteria react negatively to food, or are poor fomenters of food, creating IBS symptoms like gas and diarrhea. And some species of yeast and bacteria are bad simply because they take up space, thereby crowding out the good bacteria and depriving your body of all the health-giving benefits that friendly bacteria provide; resulting in the poor digestion of food and the poor absorption of nutrients.

If bad bacteria manage to increase its population and gain territory in your intestinal tract, you may experience gas, bloating, abdominal pain, or loose stools. You’re probably not dying, but you are very uncomfortable.

Bad bacteria

Symptoms & Health conditions

Food sources

Campylobacter Jejuni  [Reference: Canada Govt]

Diarrhea, bloating, dehydration, food poisoning = diarrhea, cramps, fever, vomiting; diarrhea may be bloody

raw or undercooked meat like poultry, beef, pork and lamb; raw milk and other raw dairy products; raw vegetables; shellfish; untreated drinking water

Fusobacteria;[Blanchard Public Health Agency Canada]

Cause cancer;

Dog bites


IBS; found in animals fertilized soil & water as secondary contamination; Citrobacter produces hydrogen sulfide which can cause fatigue, mental disorders, etc.

meats, spices, and freshwater fish, vegetables

imported semi-soft cheeses like Brie, Camembert


IBS; causes obesity




May pick up from infected meats


IBS; can cause urinary tract infections [bladder]; stuffy nose and post-nasal drip; arthritis and ankylosing spondylitis. Endotoxin can lead to general malaise, fatigue and other common symptoms.


Serratia [ Wikipedia Serratia ]


Grows in food in damp places; Found in bathroom soap areas

E coli

Causes most of urinary tract infections


Enterococcus faecalis

contaminants’ if found in processed dairy foods; used as fermenting agents<

cheeses and fermented sausages

Clostridium difficile

Bladder infections; can cause diarrhea


Candida albicans Wilder

Headaches, abdominal pain, fatigue, depression

Sugar sweet foods; sugar, refined carbohydrates, and gluten.


Cooking destroys most fungi; can cause cancer; mucus infections, eczema, depression, general malaise and bloating and gas.

Sugar foods; sausage, bacon, salami, and ham; corn; peanuts; stored potatoes, hydrogenated oils

Pseudamonas University of Sunderland

Superbug infects patients with cystic fibrosis, and systemic immune defects, such as those suffering with burns, patients with AIDS and cance; IBS

Found in fish [suchi]; fresh meat; cheese

References: for this section:

Andrews Salette, "Feeding Your Probiotic Microbes," Human Living, December 3, 2012.   Andrews: Feeding microbes 2012

Bruso Jessica, "Bifidobacterium lactis benefits,"Healthy Eating. SFGate.  Bruso: Biofidia benefits

NUTRITION REVIEW ARCHIV, April 22, 2013.  Nutrition Review: 2013

Flynn Dan, "Study: some klebsiella pneumonia illnesses are foodborne," Food Safety News, July 24, 2015.   Flynn: Foodborne illnesses 2015

Goldman Leslie, "The Flat Belly Food You Don't Know About: Kefir," The Huffngton Post, Nov 17, 2011. Goldman: Kefir fat belly food 2011

Government of Canada, "Campylobacter jejuni," January 12, 2012. Govt Canada: Campylobacter 2012

Hon, Tetsuji, "Augmentation of Cellular Immunity and Reduction of Influenza Virus Titer in Aged Mice Fed Lactobacillus casei Strain Shirota," Clin Diagn Lab Immunol," January 09, 2002, (1): 105–108. Hon: 2002

Lassesen Ken, "Changing Your Gut Flora Pt I: Food to Feed the Good Bacteria in Chronic Fatigue Syndrome," Health Rising, September 5, 2013.   Lassesen: Feeding good bacteria 2013

Leach Jeff, "Are you carrying the obesity pathogen?" Human Food Project, December 29, 2012.  Leach: Obesity pathogen 2012

Panyko Jo, "Biofidobacterium infantis: Can it help IBS?"  Panyko: Biofido helps IBS

University Sunderland, "Breakthrough In Fight Against Deadly Superbug: Early Detection Method Greatly Increases Chances Of Survival," ScienceDaily, 21 July 2008.   U Sutherland: Detect superbug 2008

Wikipedia, "Serrastia marcescens."  Wiki: Serrastia marcescens

Awareness check:  What are the two dominant foods that good bacteria like most [refer to first table]?

There are several guides to fixing a digestive disorder like leaky gut. You should do so under the guidance of an informed therapist. 

Below is a video by Myers: Heal leaky gut naturally 2013:

Dr. Amy Myers video on how to heal a leaky gut, length = 7:03mns:

Source: Myers: Heal leaky gut naturally 2013

This author suggests the following general approach [ based on review of research ]:

Step 1: Work with an informed therapist: Losing body weight can cause major changes in your metabolism and how your body responds to weight lose. Your therapist needs to monitor your weight lose. If your doctor is not informed about digestive disorders such as leaky gut, then you need to find one who is informed.

Step 2: Stop creating excess toxins in your body: This is a very important step! Stop creating more toxins to a body that is already overburdened with toxins. For example, ingesting aspirin, non-steroidal anti-inflammatory drugs (NSAIDs), laxatives, birth control pills, cough medicines, antibiotics and using skin creams. You may also need to stop other prescription medications but consult with your medical doctor before doing so. Change the toxic environment that you may be living with, such as radiation, Electro Magnetic Forces, lead and mercury, chlorinated and fluoridated water and auto pollution. These are environments that create toxins that destroy good and bad bacteria in the gut. When toxins destroy good bacteria, a vacuum is created; allowing the bad bacteria usually to rush in and suppress the good bacteria. You need to minimize the toxins in your body and give your liver a chance to get rid of them. Drink lots of water to help the liver and kidney flush out these toxins out of your body. The body needs time to all of this. Detoxifying your body begins to destabilize the bacteria in the colon.

Step 3: Destabilize the existing bacteria in the colon: If you do not cause a little bit of chaos and instability in the colon, then the bad bacteria will continue to suppress the good bacteria and make it difficult to bring about change. You can safely destabilize the colon in two basic ways. One way is to begin eating fermented food like sauerkraut or dill pickles along with your regular diet over several days. To help the fermented sauerkraut, you can eat foods that have good live bacteria like cottage cheese or yogurt. Do so over several days. Avoid eating sweets like puddings, pies and ice-cream, soft drinks and processed foods that are full of white sugar or corn syrup. This is a step to prepare your colon for a big change.

Step 4. Inoculate good bacteria: You can do this with probiotic bacteria for three to five consecutive days or longer. You can do this with probiotic bacteria for three to five consecutive days or longer. Check your body for a change in previous symptoms like change in bowel movement, bloating and flatulence [gas]. Keep in mind that many probiotics on sale do not work because the bacteria are dead, the bacteria are too few in number or the bacteria are of the wrong kind. You should take probiotics in between meals so these are not partially or totally destroyed by digestive enzymes. Look for a probiotic that has Firmicutes, and Mollicutes as well as other bacteria. For more information about probiotics

Step 5. Cultivate the new probiotic bacteria:  You need to feed your baby probiotics with good food so the young bacteria may grow and repopulate the colon.  Avoid eating the bad foods for these feed the bad bacteria and will retard the growth of good bacteria.  Eat the good foods continuously for three to five or more days. Good food allows the good bacteria to multiply and suppress the bad bacteria. This takes time and patience.

You will know if the good bacteria are winning the colon war. How? By monitoring how you feel, has bloating and pain subsided?  Has there been a change in your bowel movement as well as change from constipation or diarrhea? Has the pain in joints subsided?  Your natural body sensors are more accurate than any blood or urine test.

Step 6. Stabilize the probiotic bacteria:  This is a must.  You do this by eating a constant and consistent diet to feed the good bacteria and starve the bad guys.  Good bacteria need time to increase in population and become dominant in the colon.  Also, you should consider ingesting some herbs that help this healing process.  How long a time? Well, everyone is different but the answer is in the next step.

Step 7.  Maintenance of healthy gut:  This is the missing key for most persons trying to fix a digestive disorder.  Once you have established a normal functioning gut with good bacteria and good diet, then you have to evolve two other essential supporting habits: First, you need to continue to eat good foods and avoid the bad foods.  Even having a sugar desert once a week can jump start starving bad bacteria to become aggressive and explode in number.  Avoid bad foods, even an ice cream cone with a passion.

Secondly, there are many scientists who advocate taking a probiotic pill every day as a maintenance precaution.  You should expect to occasionally eat a bad food that disrupts the normal balance of bacteria in the colon. Taking a probiotic pill every day ensures that the good bacteria will help regulate the colon in spite of you letting your guard down.  Preventing a digestive disorder like leaky gut is something you have to work on every day.

Yet, in spite of these mysteries and food limitations, we need to do the best we can.

Recall the phrase "once an alcoholic, always an alcoholic!" And likewise once you have been obese, you can always become one again! Consult with your informed therapist before trying to lose body weight.

Conclusion:  "Forgive them, Father ... for they know not what they do!" This phrase best describes the medical practice dealing with digestive disorders. Vasquez points out that healers are slow in implementing the new leaky gut information into their practice.

Hughes sums it best: "Despite several decades of promising evidence implicating the immune system in IBS, the extent to which it is involved in clinical symptoms remains controversial and many questions remain. Foremost is causation; what is driving the immune activation? Hughes: IBS symptoms 2013

"You are what you eat!" But it is more than just what you gulp down.  Are the vitamins, minerals, complex carbohydrates, fats and amino acids absorbed or assimilated into the blood stream?  Assimilation makes the difference whether you are healthy or sick.  This aspect of eating, bioavailability, is ignored and short-changed!  You really don't know how much of a vitamin or mineral in a food or supplement, or as specified in the label, is really absorbed into your blood stream and more importantly, transported to the somatic cells!  So, not only do we need more immediate research about food and nutrients but also to educate the public about same.

The field of digestive disorders [ dysbiosis ] is a very complex issue.  It is only since 1990 that science has been exploring the microflora in the digestive system.  It is a relatively new field of medicine. The bacteria in the colon have been linked causatively to many of our human diseases and disorders.

"Dysbiosis or changes in the microbiota in the colon could be a predisposing factor to SIBO and SIBO recurrence.  Dysbiosis is an imbalance between beneficial and harmful species of bacteria in your gut. For many, this imbalance can begin at birth because of a C-section or because the mother didn’t have a healthy gut herself. The overuse of prescription antibiotic drugs, tap water with chlorine and fluoride, and the lack of probiotic-rich foods can also contribute to this imbalance of good and bad bacteria."  Axe: Getting rid of leaky gut

The relationship between the host and the microbiome is only just beginning to be investigated in detail. Patient selection for leaky gut research can clearly confound studies and more attention needs to be placed on the reporting of patient symptoms and similarities or differences between IBS cohorts, and also the adequate selection of control subjects.  Hughes: IBS symptoms 2013

From a review of the medical literature, it is apparent that researchers have difficulty finding patients on whom to do research. They are selecting sick persons in their clinics and such choices limit the outcome of such biased research designs as well as validity of research findings. Hence, the treatment modalities more often than not short-change sick patients with digestive disorders as well as those with auto-immune disorders.  It makes no sense to generalize digestive disorder functions and findings from a sick population to a general healthy population. It is no wonder that millions still suffer from disorders that the medical community does not fully understand.

Perhaps an equally important reason why we cannot seem to get a handle on leaky gut is that having good research does not translate into practicing good leaky gut medicine. Most doctors do not have the time in their busy practice schedule to update themselves. Hence, being uninformed is not transfer-implementing information into good practice.  There is an information-implementation time-lag and those with leaky gut syndrome are the ones who continue to suffer!  

Most therapists, trying to help their sick leaky gut patients, are practicing experimental medicine with good intentions.


Axe Josh, "4 Steps to Heal Leaky Gut and Autoimmune Disease," Axe: Getting rid of leaky gut

Ace Josh, "The 4 Main Benefits of Bentonite Clay," Dr. Ace Food is medicine, 2016.  Axe: Clay benefits 2016

Axe Josh, "The Leaky Gut Diet and Treatment Plan," Food and medicine. Axe: Leaky gut diet

Blaser Martin J. and James M. Musser, "Bacterial polymorphisms and disease in humans," J Clin Invest, February 15, 2001, 107(4): 391–392.   Blaser: Polymorphisms & disease 2001

Carnahan Jill, "6 Signs That SIBO Might be the Root Cause of Your IBS," Flatiron Functional Medicine, May 16, 2014.   Carnahan: signs IBS 2014

Chey William D., "Current Insights into the Pathophysiology of Irritable Bowel Syndrome," CLINICAL ROUNDTABLE MONOGRAPH 2, Gastroenterology & Hepatology, April 2015, Volume 11, Issue 4, Supplement 2.   Chey: Update IBS 2015

Galland Leo, "Leaky gut syndromes: Breaking the vicious cycle, 2007.   Article by Galland: Breaking leacky gut cycle is no longer active.

Galland Leo, "Do You Have Leaky Gut Syndrome?" HuffPost Healthy Living, Nov 17, 2011.   Galland: Leaky gut syndrome 2011

"Leaky Gut Syndrome is associated with: inflammatory and infectious bowel diseases,several types of arthritis, acne, psoriasis, AIDS, chronic liver disease, pancreatic disease as well as numerous conditions triggered by food allergy, including eczema, hives, and irritable bowel syndrome."

Hamilton, I., et al., "Small intestinal permeability in dermatological disease." Q J Med, 1985. 56(221): p. 559-67;

Hyman Mark, "How to Cure Irritable Bowel Syndrome in a Few Days," The Blog, January 23, 2014.  Hyman: fixing IBS 2013

Kresser Chris, "Is Fibromyalgia Caused By SIBO and Leaky Gut?" LET'S TAKE BACK YOUR HEALTH, JUNE 6, 2014.  Kresser: Leaky gut & Fibromyalgia 2014

INRA-France, "Revolutionary approach to studying intestinal microbiota," Nature Biotechnology, July 6, 2014.   INRA-France: studying microbiota 2014

LifeScript Health with Heart, "Gut bacteria picky about what we eat: study," September 02, 2011.   Article by Longstreth: Functional bowel disorders is no longer active.

Longstreth Geotge and others, "Functional Bowel Disorders," GASTROENTEROLOGY, 2006 ;130:1480 –1491,   Longstreth: Functional bowel disorders 2006

Maes M,  and Leunis JC, "Normalization of leaky gut in chronic fatigue syndrome (CFS) is accompanied by a clinical improvement: effects of age, duration of illness and the translocation of LPS from gram-negative bacteria." Neuro Endocrinol Lett, December 29, 2008,(6):902-10. Maes: Leaky gut can be treated 2008

Myers Amy, "How To Heal Your Gut Naturally," U-Tube, February 28, 2013.  Myers: video Heal leaky gut naturally 2013

Myers Amy, "8 Supplements to Heal a Leaky Gut," May 3, 2013.  Myers: Supplements to heal leaky gut 2013

Pimentel Mark, "Cedars-Sinai Physician Definitively Links Irritable Bowel Syndrome (IBS) and Bacteria in Gut," Cedars Sinai, May 25, 2012.   Article by Pimentel: :IBS linked to gut bacteria is no longer active

Pimentel Mark ahd Lezcano S., "Irritable Bowel Syndrome: Bacterial Overgrowth--What's Known and What to Do," Curr Treat Options Gastroenterol, August 10, 2007, 10(4):328-37.   Article by Pimentel: IBS & treatment is no longer active

Pimentel Mark et al., "Methane production during lactulose breath test is associated with gastrointestinal disease presentation," Dig Dis Sci, 2003, 48, 86–92.   Pimentel:Methane in lactulose breath test & gastrointestinal disease 2003

"Intestinal CH 4 production is a complex mechanism from specific colonic bacteria, involving the metabolism of other gases, particularly H 2 . In about one third of adult healthy individuals, it is pos-sible to detect intestinal CH 4 production with no specific clinical relevance. However, an unbalance of gas metabolism and abnormal CH 4 production have been considered in the pathogenesis of several intestinal disorders, including colon cancer, IBD, IBS, and diverticulosis."

Roccarina Davide and others, "The Role of Methane in Intestinal Diseases," The American Journal of Gastroenterology, March, 2010, 105(6):1250-6.   Roccarina: Methane & diseases 2010

Seo A Young, Nayoung Kim1 and Dong Hyun Oh, "Abdominal Bloating: Pathophysiology and Treatment," J Neurogastroenterol Motil, 2013; 19(4): 433-453.   Seo: bloating therapy 2013   [ Bloating is defined as subjective discomfort by patient's sensation of intestinal gas; otherwise, abdominal distension is a visible increase in abdominal girth. ]

Shaw George Bernard, ""A good set of bowels is worth more than any amount of brains." The Riit of Health, 2011.

Smith M. and K. Kasteleinet, "Your Colon and Psoriasis," Dermaharmony, June, 07,2011.  Article by Smith: Psoriasis & colon is no longer active.

Vasquez Alex, "Translating microbiome [Microbiota] and dysbiosis research into clinical practice: The 20 year development of a structured approach that gives actionable form to intellectual concepts," [ Alex Vasquez [DC ND] explains how SIBO leads to FM], International Journal of Human Nutrition and Functional Medicine, 2015. Article by Vasquez: SIBO leads to FM Update is no longer active.

Vasquez  Article by Vasquez: SIBO leads to FM Update is no longer active. explains how SIBO leads to FM. The bacteria overgrowing in the small intestine make toxic chemicals which they pour into the bloodstream. These include a toxin known as LPS (actually fragments of the outer 'covering' of the bacteria); the toxic gas hydrogen sulphide; D-lactic acid, which causes a chronic acidosis; and an enzyme (tryptophanase) that depletes two important brain chemicals (serotonin and melatonin). These toxic chemicals circulate in the blood, and cause mitochondrial dysfunction, oxidative stress and other damage. This results in muscle pain, depression, food cravings, and inflammation. Article by Agius: Bacterial overgrowth is no longer active.

The body's main detox defence is the liver, which can filter the blood flowing through it, and remove any toxins it might contain. These toxins are then processed chemically, and then gotten rid of by being passed out in the bile (ultimately leaving the body in the stools) or in the urine. When there are too many toxins, however, the liver will be unable to cope, and not all toxins will be removed from the blood. This occurs especially if the liver is functioning poorly. In theory the above toxins should all be detoxified ... but in practice some of these can spill over into the systemic circulation with a simple poisoning effect and resultant production of free radicals and inhibition of mitochondria.

A vicious circle occurs in the gut: Once SIBO becomes established, the main factor that perpetuates it is carbohydrate malabsorption. This means that a significant amount of the carbohydrate a person eats escapes digestion and absorption. It is then available to feed the bad bacteria in the small intestine. These ferment mainly simple sugars, and produce a lot of gas, which causes many of the symptoms of IBS. So, bacterial toxins and waste products cause the gut wall to become inflamed; the inflamed gut wall is less able to digest and absorb carbohydrates; unabsorbed carbohydrates feed the bacteria, which become more active and multiply; bacteria make more toxins. A vicious circle is thus set up.  Article by Vasquez: SIBO leads to FM Update is no onger active.

Wikipedia, Gut Flora."  Wiki: gut flora

Wikipedia, "Irritable bowel syndrome."  Wiki: IBS

Winter Sebastian E, and others, "Scientists find key to growth of "bad" bacteria in inflammatory bowel disease, " Science, [NEWS UC Davis],  February 8, 2013.  Article by Winter: key to bad bacteria growth is no longer active   [ Research is the first to shed light on how harmful gut bacteria thrive in the intestine. ]