The Leaky Gut Syndrome


Author: Susan R. Johnson MD, F.A.A.P.

Published: Feb 28th, 2009

Updated: Aug 26th, 2017

I have learned a great deal from the Naturopathic and Osteopathic students who have visited my clinic. They have taught me most of what I know about the Leaky Gut Syndrome. In this syndrome, the lining of the colon and small intestine becomes inflamed and allows partially digested proteins and undigested proteins to be absorbed into the lymphatics and blood stream. The immune system reacts to these foreign proteins, triggering general inflammation and causing allergy symptoms, autoimmune diseases, speech delays, and behavioral abnormalities. There are several good books on the topic of the Leaky Gut Syndrome such as Gut and Psychology Syndrome (GAPS) by Natasha Campbell-McBride, MD, The Plant Paradox by Steven Gundry, MD, Children With Starving Brains by Jaquelyn McCandless, MD, and Renew your Life: Improved Digestion and Detoxification by Brenda Watson, ND.

There are many things about the American diet and Western medical practices which weaken the immune system and result in the Leaky Gut Syndrome. To begin with, exposure to antibiotics, especially in the first two years of life, destroys good intestinal bacteria and thereby promotes the overgrowth of yeast in both the large and small intestines. Yeast in the intestinal tract acts as a parasite and in essence steals many vitamins and minerals before they can be absorbed through the intestinal wall.

In addition, the American diet with its overabundance of and reliance on simple carbohydrates such as candy, breads, and pastas, depletes the body of zinc, magnesium, chromium, and several B vitamins. These simple carbohydrates rapidly convert to sugar and trigger the pancreas to secrete too much insulin. Because insulin requires trace minerals and B vitamins as co-factors in sugar metabolism, the more the body consumes sugar, the more the body's B vitamins and trace minerals are depleted. The immune system as well as the metabolic system and brain can not function well when certain trace metals and B vitamins are deficient.

This typical American diet, often consisting of fast foods such as hamburgers, french fries, sodas, and milkshakes, also lacks fiber and enzymes. Plant enzymes, which naturally occur in raw fruits and vegetables, help break down fats, proteins, and carbohydrates in the food we eat and allow this food to be more readily absorbed in the small intestine. Without a daily diet of raw vegetables and fruit, the body is stressed and overburdened by having to produce these enzymes in the pancreas. The pancreas now is overworked. In addition to secreting insulin for glucose metabolism, it must also secrete digestive enzymes to break down fats, proteins, and carbohydrates in the small intestine. As a result, metabolism becomes sluggish. Now, undigested and partially digested proteins, fats, and carbohydrates end up in the large intestine, where they ferment and create abdominal discomfort and odorous gas.

Because of inflammation of the intestinal lining, a lack of fiber in the diet, and the failure to drink enough water between meals, constipation occurs. Sometimes the intestinal inflammation causes foods to irritate the lining of the intestines so motility or peristalsis is too quick, leading to loose or mushy stools. Other times the intestinal lining is so inflamed and ulcerated that this interferes with bowel motility, creating severe constipation. Sometimes children show both constipation and diarrhea as more watery stool flows past the blockages of harder stool in their intestines.

Also, the increased pressure it takes to push stool out of the colon often causes fecal material to travel backwards up into the small intestine by forcing the valve between the small and large intestine to open. Now yeast, parasites, and unhealthy bacteria set up residence in the small intestine as well and directly block the absorption of minerals, vitamins, amino acids (proteins), and fats. In addition, we often do not eat foods that would provide a consistent source of good intestinal bacteria, such as fermented vegetables, quality unsweetened yogurts, kefir, and/or soil bacteria by eating fresh organic vegetables from the garden or drinking freshly juiced (non-pasteurized) organic vegetables.

With the good bacteria gone, yeast overgrows and burrows into the intestinal wall, causing inflammation. Now, instead of partially digested and undigested proteins being excreted in the stool, these proteins get reabsorbed back into the lymphatic and blood streams through this leaky intestinal wall. Partially and digested proteins, including pollens that are swallowed, act like foreign proteins and trigger the body's immune response (IgG antibodies) resulting in chronic inflammation, asthma, eczema, or autoimmune diseases. Once children or adults have developed a leaky intestinal lining, their bodies will react to numerous proteins in food and the environment.

Some of the most difficult proteins to digest include casein from milk products and gluten from wheat, rye, barley, and oats. There are also other types of gluten-like proteins, called lectins, that are also hard to digest and occur in corn, millet, and other grains, as well as certain seeds (See the book, The Plant Paradox, for more details). Breakdown products from gluten, lectins, casein, or unfermented soy, that are able to enter the bloodstream, can trigger an inflammatory response. This inflammatory response somehow involves the speech and receptive language centers of the brain, causing "brain fog", language delay, or the type of speech patterns noted in children with Autistic Spectrum Disorder. The milk protein, casein, if reabsorbed back into the body is thought to trigger eczema and create allergy-related conditions of sinusitis and serous otitis.

What can be done to heal the body and strengthen the immune system? Here is what I have learned so far:

1) To restore normal intestinal bacteria:

a) Take a good probiotic (usually the best have 10 to 14 different strains of bacteria, often are refrigerated, come in powder form, and are encapsulated). A good probiotic contains resident strains of intestinal bacteria such as Lactobacillus acidophilus, Bifidobacerium bifidum, and Bifidobacterium longum (infants need Bifodobacterium infantis). Probiotics should be taken for 4 to 6 months after any antibiotic use. In my practice, I recommend Bio-Kult capsules ( for older children and adults. For younger children and toddlers, the capsules can be opened and the probiotic can be mixed into a little applesauce. For infants, I recommend Life Start by Natrens.

b) Consume fermented foods and drinks containing good intestinal bacteria (e.g. fermented cabbage and lactic acid-fermented beverages). Look in the book Nourishing Traditions written by Sally Fallon, for recipes. When looking for fermented vegetables at health food stores, check to see that vinegar is not listed among the ingredients.

c) Make your own yogurt and kefir. I make yogurt or kefir by adding 1/2 cup of yogurt starter (one can use 1/2 cup of Strauss organic whole milk yogurt) or 1/2 cup of a live kefir culture (check the web site for sources of Doms kefir) to 16 oz raw organic whole milk from a certified dairy. Now pour the mixture into pint-sized jars and cover with a paper towel or cheese cloth. I place the jars with the kefir mixture on my counter for 24 hours and then refrigerate. You now have kefir. I heat the yogurt mixture gently to room temperature and then place jar(s) of the yogurt mixture into a cooler that contains another jar full of boiling hot water, which serves as the heat source. Close the cooler and recheck after 6 to 8 hours. You now have yogurt, which you can place in the refrigerator.

d) Eat plenty of organic raw nuts, seeds, fruits, and vegetables. They serve as a source of fiber for the good intestinal bacteria which cannot survive without them. Fiber also bulks up the stool and stimulates the bowel to contract which ensures regularity. Flax seeds are a great source of fiber, both soluble and insoluble. It is recommended that 14 grams of fiber (an apple contains about 4 grams of fiber) be consumed for every 1000 calories of food eaten each day.

Another great source of vitamins, enzymes, minerals, and fiber is to juice 9 organic large carrots, 6 stalks of organic dino kale, 1 organic cucumber, 1 organic red beet plus beet greens (i.e. leaves), 1 organic red apple, 1 peeled lemon and 1 peeled orange in a juicer. Drink at least 8 to 12 ounces of this juice every morning. The left over pulp (fiber) from the juicer can be frozen overnight and then combined in a blender with fresh orange juice and a banana. This smoothie can be eaten with a spoon and is loaded with fiber. The fiber smoothie will increase contractility of the small and large intestine and could cause a stomachache if the intestinal lining is still inflamed.

e) Drastically reduce sugar in your diet and avoid concentrated fruit juices, white bread, candy, and sodas. Sodas, besides containing lots of sugar, contain phosphoric acid which leaches calcium from the bones and contributes to the development of osteoporosis and loss of cartilage. Also avoid all artificial sweeteners, they are toxic, except for Stevia, although Stevia will fool your body to release insulin in response to the perceived sweetness, despite the lack of calories.

f) Increase alkaline-forming foods such as organic fruits, vegetables, herbs, and almonds. Make these foods 80% of your daily diet. Alkaline forming foods provide lots of minerals that neutralize acids in our body. Keep the pH of your saliva between 7.0 and 7.4 for good health. Test your saliva upon awakening and 2 hours after eating a meal to determine baseline values. I use Vivid pH paper with a pH range of 6.0 to 8.0 that I order from Micro Essential Laboratory in New York. Their phone number is 718-338-3618 (

g) Drink an herbal tea which is highly alkaline or tea made from fresh lemon juice. These teas help to discourage yeast growth . In my practice I also recommend drinking Liver Tea from Uriel Pharmacy and/or taking Amara Drops from Weleda Pharmacy which both contain bitter herbs like dandelion and yarrow. Both support digestion and liver function. Chinese medicine also recommends teas made from bitter tasting herbs. Bitter herbs, in general, also stimulate bile secretion which helps with fat absorption in the small intestine and serves as a way for the liver to excrete toxins from the body.

h) Consume plenty of fresh or cooked garlic (See my chicken-vegetable, detox, mineral bone soup recipe on my website), since garlic discourages the growth of yeast. Another approach is to drink raw, juiced vegetables between meals, rather than with a meal, since the plant enzymes in the raw juice will help the body break down the cell wall of the yeast and destroy parasites living in the intestines. Raw, juiced vegetables also provide beneficial soil bacteria for the small intestine and the colon.

i) Make organic chicken, mineral bone broth by putting a whole organic chicken in a large crock pot filled with good quality water (I use several cartons of organic vegetable broth from Trader Joes, instead of water) and 1 Tbsp of apple cider vinegar. Set the crock pot to low. Remove the chicken meat after 8 hours and consume the meat or refrigerate it for later. Continue simmering (on low) the bones with the broth for an additional 12 to 16 hours (I usually need to add another carton or two of organic vegetable broth to the crock pot, when I remove the chicken meat). Now strain the broth of bones and refrigerate the broth. Now the broth is ready to heat and serve, pour on rice, or add to the chicken-vegetable, detox soup recipe. This broth can also be frozen in ice-cube trays and then used when cooking. This bone broth helps to heal the intestinal lining.

2) To reduce casein and gluten protein sensitivities:

a) First, stop all milk products for at least three weeks, then add back milk products on day 22 and see if congestion increases, eczema worsens, or snoring increases. Naturopathic physicians have taught me that it takes at least two months to clear the casein protein from the bloodstream and the lymphatics, but symptoms will worsen when milk products are reintroduced on day 22. Repeat this same process with all grain products that contain gluten or Lectins (e.g. wheat, rye, barley, and also corn, oats, and other grains that our highlighted in Dr. Steven Gundry's book, The Plant Paradox). Children and adults may need to avoid casein and gluten/lectin grain products for the next 4 to 6 months, while the intestinal wall heals and the beneficial intestinal bacteria are restored.

A great website to help with the casein/grain free diet is Also read about the GAPS diet in the book, Gut and Psychology Syndrome, by Dr. Natasha Campbell-McBride, as well the book, The GAPS Guide-Simple Steps to Heal Bowels, Body, and Brain, by Baden Lashkov at Check the GAPS cookbooks listed online and in the Publication section, under Resources, on my website. Be careful of store-bought, gluten-free products that may contain other ingredients that are harmful to the intestinal lining. When reintroducing milk products, yogurt and kefir made from raw organic milk are the easiest to digest. Also, milk products from cows that produce A2-casein milk, rather than A1-casein milk, are much easier to digest. Just contact the dairy to find out which type of milk their cows produce.

b) Take supplemental plant-based enzymes for a few months, preferably from organically grown plants, at the beginning of each meal to help with digestion (especially when not eating any raw vegetables during the meal) or better yet get fresh plant enzymes by drinking at least 8 to 12 ounces/day of the juiced raw vegetable and fruit drink, I mentioned earlier.

c) Make homemade almond milk by soaking almonds overnight in water containing unrefined Celtic sea salt (I use 1 tsp of salt per cup of almonds). The next morning briefly blanch the almonds in hot water or put the pre-soaked almonds in fresh water and refrigerate for 3 to 4 hours, so the skins can be more easily removed. Using a blender, mix the peeled almonds with water or organic rice milk. Crispy nuts can be made by slowly roasting the almonds in an oven on the lowest setting (warm, on my oven) for 36 to 48 hours, or a little longer, after soaking them overnight in salty water. Almonds are a great source of protein and fat as well as calcium, magnesium, and other trace minerals. Good fats, like almonds, avocados, and eggs, slow the emptying time of the stomach and thereby lower the concentration of sugar that triggers insulin release. Proteins and fats, by themselves, do not stimulate insulin release, and eating complex carbohydrates, which are high in fiber, also reduce the amount of insulin that the pancreas needs to secrete.

d) Avoid soy milk or any other unfermented soy product. Miso soup is okay because it is fermented. Unfermented soy products block thyroid hormone function, protein and calcium absorption, and have strong estrogen effects. Organic rice milk is okay but it mostly consists of carbohydrates. Homemade almond milk is healthier. With regard to cows milk, I learned during my training at the Lukas Clinic in Arlesheim, Switzerland that the healthiest milk to drink is raw organic whole milk. Ultra-pasteurized, homogenized non-organic milk is seen as the least healthy milk to drink because all the natural enzymes and vitamins are destroyed by processing, and the fat is disrupted by homogenization. The book Nourishing Traditions also discusses the advantages of raw milk as does the journal, Wise Traditions, published by the Weston A. Price Foundation.

3) To strengthen immune system so it is not so reactive:

a) Keep hands, feet, and kidneys as warm as the skin over the heart.

b) I also recommend that children and adults take pharmaceutical-grade, molecularly-distilled, cod liver oil or fish oil, to provide lots of DHA and EPA, omega-3-fatty acids, for brain myelination as well as their anti-inflammatory effects. If the oil has been carefully processed, it will not smell fishy.

In my practice, I use Nordic Naturals Arctic D Cod Liver Oil, but there also are other good brands. Be sure and look at the ratio of vitamin A to vitamin D in the cod liver oil products. The ratio needs to be around 1:1 and not 1000:1 (many cod liver oil products have too much vitamin A relative to vitamin D). I recommend taking 1 tsp/day, for children 6 years and older and adults, and 1/2 tsp/day, for children 3 to 5 years of age. For toddlers, I recommend Barleans flax seed oil mixed with butter and used as a spread on toast. Look at the skin and hair for signs of omega 3 fatty acid deficiency. Hair will be coarse and dull while skin may develop sandpaper-like bumps all over the upper arms, back of thighs, back, and sometimes abdomen. Sometimes the child (or adult) needs to consume a fat, like butter or ghee, with the cod liver oil, to stimulate more bile release from the gall bladder, and therefore increase the absorption of the cod liver oil or fish oil.

c) AVOID partially hydrogenated oils and trans-fats. Do not cook in corn oil, canola oil, or olive oil since these oils are heat sensitive and quickly convert to trans-fatty acids. Cook only in coconut oil (high temp), and butter (low-med temp). Use ghee if one is sensitive to milk products. Ghee does not contain casein.

d) Eat at least a handful of soaked and slow-roasted almonds every day. Almonds are a great source of calcium and magnesium. Hemp organic protein powder by Nutiva is reportedly a good source of magnesium, protein, and fiber and is recommended in Ayurvedic medicine.

e) Prepare Vegetable or Chicken Vegetable Detox Mineral Bone Soups for extra minerals.

f) Increase magnesium in your diet by eating pre-soaked/slow-roasted almonds, green colored pumpkin seeks, kale, seaweed, spirulina, and mineral bone broth (See my recipes for chicken vegetable mineral bone soup and detox vegetable bone soup and Nourishing Traditions Cookbook). Magnesium along with Vitamin D3 is required for calcium absorption in the bones and teeth. One of the main causes of dental decay is magnesium deficiency. Magnesium also calms the nervous system. The production of serotonin, dopamine and other neurotransmitters are dependent on magnesium as well as other minerals and vitamins. Magnesium also supports adrenal gland function. Magnesium deficiency can cause increased anxiety, fears, panic attacks, insomnia, headaches, heart palpitations, coronary artery spasms, and even seizures.

Magnesium deficiency also causes constipation because it slows down peristalsis. It contributes to attention problems and mood swings, and magnesium is crucial for detoxification of heavy metals like mercury, lead, and aluminum. Leg and foot cramps, growing pains, and the restless leg syndrome also result from magnesium deficiency. Magnesium supports sugar metabolism and insulin secretion. Magnesium deficiency causes insulin and glucose to build up in the blood contributing to diabetes types I and II. Fatigue is one of the earliest symptoms because magnesium is a co-factor in many enzymatic reactions throughout the body and in the immune system. Therefore, magnesium deficiency can predispose us to infections and even cancer.

g) Besides increasing magnesium-containing foods, consider taking a magnesium supplement like CALM (containing ionized magnesium only), by Natural Vitality. Children can take 1 tsp/day and adults 2 tsp/day, usually mixed into 8 to 12 ounces of cool or warm water, and taken orally in the late afternoon or early evening. Magnesium also helps to make Melatonin, which helps us to feel sleepy at bedtime. Children (and adults) that take baths, instead of showers, can add 1 to 2 cups of Epsom Salts (magnesium sulfate crystals) to their bath water. Magnesium-containing water can also be sprayed or rubbed into the skin (See General Clinic Recommendations article, #18 for more details about magnesium).

h) Do Therapeutic Eurythmy movement therapy (especially the allergy sequence) with a trained Therapeutic Eurythmist. Trained Eurythmy Therapists are affiliated with Waldorf Schools, and a physicians evaluation is helpful. Any other harmonious, noncompetitive, rhythmic movement, including walking and hiking, stimulate lymphatic flow and are very beneficial (See General Clinic Recommendations article, #2 for more details).

i) See an Osteopathic physician for Biodynamic Cranial Osteopathy ( or a very experienced practitioner in Upledger Cranial-Sacral Therapy. These treatments can help drain fluid from the middle ear by relieving cranial compressions that compress the Eustachian tubes or alter the angle of the tubes causing fluid to accumulate behind the ear drums. Biodynamic Cranial Osteopathy treatments can also help to relax the autonomic nervous system and resolve cranial compressions (from the birth process) which also strengthens immune function (See General Clinic Recommendations article, #1 for more details).

j) Consider visiting a N.A.E.T practitioner. N.A.E.T. is an energetic technique that reportedly decreases the immune system's reactivity to specific proteins like dairy, wheat, and soy. In my experience, a child's allergy symptoms to a particular protein can be immediately reduced, but the child still needs to follow the guidelines for healing the leaky gut. Otherwise children will just develop sensitivities to other proteins they eat or breathe in from their environment.

k) Be aware of the immune-suppressive effects of electromagnetic fields (EMF). Avoid using electric blankets and be aware of other EMF sources from household appliances, computers, and cell phones. Avoid charging cell phones, iPads, and computers in the room, when you are asleep. If you use WIFI in your home, then turn it off while you are asleep or better yet switch back to a cable system. Always keep your cell phone at least 6 feet away from your brain, while sleeping, if cell phone is kept on. Try to use a landline as much as possible, especially with long calls or use a speaker phone and texting, instead. If you do place a cell phone next to your ear, then hold it at least 1 to 2 inches away to minimize your exposure to EMFs, and any increased risk of brain tumors. Bluetooth does not reduce the exposure to EMFs, though you can purchase a Blue Tube Headset from that does reduce your EMF exposure for approximately $30.

Make sure your home and office are up to code with respect to electrical wiring. Electric companies will screen your home and office with an EMF meter at no charge. If you have a "SMART" meter, then contact PGE to replace it with a meter that is manually read (like it used to be done). There are shields that can be placed over a SMART meter, though I do not know how effective they are. Especially replace the SMART meter if it is attached on the other side of a bedroom wall. Microwave radiation from cell phone towers may also affect the immune system and overall health. Read Katie Singer's new book, "An Electronic Silent Spring", that reviews all the new research in this area. Her website and newsletters can be found at

4) Symptomatic relief for allergies, sinusitis, and congestion:

a) Try Homeopathic, Anthroposophic, and herbal remedies.

b) Take a good sublingual (under the tongue) supplement containing B12 (methyl not cyano form), B6, and methylated Folic acid, as well as a whole food complex type of vitamin C (antioxidant). I usually recommend Oxylent ( powdered vitamin and mineral supplement, which contains methylated B12 and methylated Folic acid as well as Vitamin D3 and many other vitamins and minerals. I recommend the adult form, mixing 1/2 of the adult packet in 12 to 16 ounces (or more) of water, for children. Teenagers and adults can take a whole packet mixed into 16 or more ounces of water. The child form has iron which can upset the stomach. The flavor I like the best is Blackberry Pomegranate. If adults or children do not like the taste of oxylent then I recommend B Complex Plus, B Vitamin capsules, by Pure Encapsulations. This vitamin capsule also contains methylated B12 and methylated Folic acid.

There is a relatively common genetic defect known as MTHFR, which blocks one's ability to attach a carbon and 3 hydrogens (i.e. methyl group) on Vitamin B12 and Folic acid, which makes these vitamins active. Methylated B12 and methylated Folic acid are co-factors (along with magnesium, zinc, and several other vitamins and minerals) in 100's of biochemical reactions, and therefore any deficiencies are thought to lead to immune dysfunction (i.e. autoimmune conditions. Autism, Alzheimer's, allergies, asthma, frequent illnesses etc.), and an inability to produce adequate neuro-hormones , leading to depression, bipolar, and severe behavior problems.

There is a website, where you can purchase a kit that allows you to send in a saliva sample and have your chromosomes assessed for numerous genetic disorders, if you so choose. When you receive your results, you can put them through a free application at and specifically find out if you are missing the methylation gene on one or both chromosomes. If you have a methylation problem, then you should always take methylated B12 and methylated Folic acid, on a daily basis, to maximize your health. The website, sells all the above products at sometimes less than retail cost.

c) Keep well hydrated by drinking plenty of good quality, non-chlorinated water and decaffeinated herbal teas. As a guideline, it is recommended to drink half of ones weight in ounces of water that is sipped throughout the day. Do not drink too much water during meals, since water dilutes the acid concentration in the stomach and makes it harder for the stomach to break down proteins.

5) May need a dental consult:

a) When children develop chronic allergies as a result of the leaky gut syndrome, the adenoids and tonsils enlarge, obstructing the nasal passages. This causes a child to breathe more through the mouth rather than through the nose. Mouth breathing causes the upper palatal arch to increase (high arch) which causes crowding of the upper teeth. Dentists are now trained to use small wire retainers (ALF) which gently re-expand the upper jaw, reducing overcrowding, tooth extraction, and the need to remove the tonsils and adenoids. For information and names of practitioners (i.e. dentists, orthodontists, and osteopathic physicians) that know how to apply the ALF appliance, see the website,

6) Ways to maximize health:

a) Be sure to get plenty of sleep and avoid getting into a second wind at night, remember that sleep before midnight counts as double, walk an hour every day, meditate, sing, plant a garden, breathe deeply, laugh, practice yoga, tai chi, or eurythmy, do things you love like art, music, handwork, etc., put your life into rhythm with regular meals and a regular sleep schedule, reduce stress, slow down (remember less is best), practice being in the present moment, turn off the television, VCR, and computer games, spend more time in nature, work on yourself and work on your relationships so they are win/win instead of lose/lose, forgive yourself, forgive others, find work that you love and do it.

1Also read the updated General Clinic Recommendations

Please Note: I decided to give a few names of products I am using in my clinic but I have no financial interest or connection with any of the products or companies. They are just the best have found so far.