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What Doctors Don't Tell You

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October 2020 (Vol. 5 Issue 7)

7 steps to a good gut

About the author: 

7 steps to a good gut image

work and the following checklist, you canfinally end your IBS forever

With a little detective work and the following checklist, you can finally end your IBS forever

Russian biologist and Nobel laureate Elie Metchnikoff once remarked, "Death begins in the colon," and for good reason. There's no doubt that one of the major keys to a long and healthy life lies in your body's ability to digest properly.

It's your digestive system-your stomach and intestines-that does most of the work of turning what you eat into fuel and nourishment for your body. This is a highly complex affair, aided by a huge army of enzymes, acids, friendly bacteria and peptides. If anything is even slightly awry or the balance is off in some way, no amount of organic food or supplements will keep you healthy.

All manner of modern-day illnesses-in fact, most of the chronic problems medicine has no answers for-joint and muscle pain, skin conditions of every sort, mood problems, chronic fatigue, allergies, sleep problems, general immune dysfunction and even emotional or mental problems of all varieties, for instance-can be linked back to disturbances in your gut.

As things now stand, not many of us are digesting particularly well. One in five people (three-quarters of them women) suffers from 'irritable bowel syndrome', a catch-all term that covers an array of abdominal and gastrointestinal symptoms, ranging from pain, bloating and belching to gas and flatulence, intermittent bouts of constipation and diarrhoea, heartburn, mucus in stools and frequent urination.

These gut issues are often accompanied by anal soreness, back pain, frequent weight fluctuations, headache, fatigue, teeth-grinding and jaw-clenching, painful menstrual periods in the case of women, and even mental issues like anxiety and depression.

Doctors tend to give these collective symptoms a number of woolly labels like 'spastic colon' or 'non-inflammatory bowel disease'-a fairly obvious sign that medicine still finds the condition utterly mysterious and hasn't a clue about how to fix it.

The problem with the medical approach is that it assumes the disorder has a single cause, when it actually may involve a number of conditions: allergies, a 'leaky' gut lining, low stomach acid, foreign invaders like Candida or parasites. Only by diagnosing your particular issues will you be able to find an effective cure not only for your grumbling gut, but for other, seemingly unrelated conditions preventing you from enjoying full health.

Whether you have IBS or not, if you do a bit of detective work with the advice that follows, you may discover that one or more of your chronic complaints is actually due to one of a variety of digestive problems.

The behavioural problems of your children, for instance, could be caused by undiagnosed parasites. Shortness of breath and memory difficulties may have to do with a leaky gut-a too-permeable gut wall. The ME or chronic fatigue that has kept you virtually housebound might simply be down to low stomach acid or a lack of enzymes.

To help you sort out your problem, we've created a checklist of the seven most likely culprits of poor digestion, plus how to diagnose and rid yourself of them. And whether or not you have IBS, following our guidelines should undoubtedly help to improve your general overall health.

Allergy or food intolerance

Food intolerance is a classic cause of digestive issues that mostly have to do with the gut flora, those essential 'friendly' bugs that live in your intestines. Doctors at Addenbrooke's Hospital in Cambridge can now distinguish between true food allergy, a rare condition caused by a genuine and fairly immediate immune-system response to an offending food, and food intolerance, a far slower response (appearing hours or days later) to foods eaten regularly, like wheat and dairy products, that causes shifts in the populations of bacteria living in the bowel and so allows certain harmful bacteria to take over.

The usual suspects are wheat, cow's milk and all dairy, sugar, yeast, beef, pork, corn, coffee and oranges. If your doctor's convinced that you need more fibre and is suggesting that you pile on the wheat bran, it's more likely than not just making things worse. Also suspect yeast, anything containing modified starch, which is often used as a fat-replacing bulking agent, and artificial additives of any sort, especially food colourings and artificial sweeteners like sorbitol.

Suspect this:if you feel a good deal worse-or better-after eating common allergens.

Diagnose this:by following our suggestions for an elimination diet (see pages 44-49 in our November 2012 issue). See if you react to foods when you re-introduce them.

Solve this:by adopting the the so-called Stone Age diet-which includes fish and white meat, legumes, and fruits and vegetables of every variety. By eliminating all dairy, grains, red meat, refined sugars and processed foods, you give your gut a break from the allergens, proteins, fats, and simple and complex sugars that trigger problems and allow harmful bacteria to multiply. This dietary change by itself could sort out your gut inflammation within two years, as it has with many who have Crohn's disease.1 Also, watch your consumption of tea and coffee, both of which can dry out the protective mucous lining of the gut.

Don't forget to keep active. Research shows that patients who exercise regularly, even mildly, can improve constipation, and reduce abdominal gas and bloating.2

Finally, avoid hair dye, as it's now been shown to increase your likelihood of developing gut allergies.3 And cut the junk food, now proven to quadruple your chances of inflammatory gut disease, even if you indulge only twice a week.4

Bad-guy gut bacteria

More than two-thirds of IBS patients, who regularly suffer from diarrhoea, have bacterial overgrowth in the gut, as do nearly a third of IBS patients overall, say researchers from the Cedars-Sinai Medical Center in Los Angeles. With this condition, officially known as 'bacterial dysbiosis', the bacteria alter the metabolic and immune responses of the body, causing the immune system to turn against the normal gut flora.5 According to research, this situation is an early complication of a 'leaky gut' (see page 38).6

In addition to food intolerance, this phenomenon can also be caused by non-steroidal anti-inflammatory drugs (NSAIDs). It's well known that even a single dose of either aspirin or indomethacin can increase permeability in the gut wall by stopping the synthesis of the protective fatty-acid prostaglandin;7 long-term use of such drugs can leave the gut very inflamed and highly permeable. Also, people with rheumatoid arthritis taking NSAIDs have been found to have increased levels of antibodies to Clostridium perfringens bacteria, so revealing that bacterial toxins are involved in this vicious cycle.8

Suspect this:if you have taken multiple courses of NSAIDs and antibiotics, and eat genetically modified (GM) foods and saturated milk fats, all of which may be responsible for many gut problems.

Those fats-found in processed foods and confectionery-upset bacteria in the gut within six months of eating a diet high in them, say researchers from the University of Chicago; they also encourage proliferation of Bilophila wadsworthia bacteria in the gut, a microbe associated with inflammatory gut disorders.9

Diagnose this:by taking the Breath Hydrogen & Methane Test, which involves swallowing a carbohydrate and measuring bacterial fermentation of the carb through breath samples of hydrogen and methane. Biolab in London offers the test (see address bellow)

Solve this:by taking the following supplements:

ovitamin D, as people suffering from gut problems are usually deficient in this vitamin

o25-50 mg of zinc, 2-4 mg of copper, 800 mcg of folic acid and 800 mcg of vitamin B12, all of which can help repair the gut, and check your iron status too

osupplements of homoeostatic soil organisms (HSOs), good-guy organisms found naturally in soil that were part of the human diet before 1930, which have been shown to calm an inflamed gut

obentonite, or hydrated aluminium silicate, which has the remarkable ability to get bacteria and viruses to stick to it and, as bentonite is not absorbed, it passes through the colon, taking toxins with it.

Too much fruit sugar

About a third of IBS patients have 'fructose malabsorption', or difficulty processing fructose-the type of sugar found in fruits, some vegetables, honey and high-fructose corn syrup-as it passes through the small intestine.10

Suspect this:if your gut gets worse after eating fruit.

Diagnose this:by taking a fructose intolerance test, another breath test measuring your capacity to absorb any sort of fructose .

Solve this:by limiting the amount of fruit sugar you eat. One Mayo Health System study in America found that 38 per cent of patients improved their symptoms just by lowering their consumption of fruit sugars; in particular, children do well on a low-fructose diet.11

Also watch out for other fermentable, poorly absorbed carbohydrates like lactose (found in milk), fructans (found in wheat and onions) and sorbitol (a common sweetener),12 and avoid amines (cheese, chocolate, citrus fruits, coffee and red wine) and food additives (benzoates, sulphites, nitrates and nitrites, and tartrazine and other artificial colours).

Low stomach acid

In many cases, people with IBS produce too little or no stomach acid or digestive enzymes.

Suspect this:if you feel especially uncomfortable after eating.

Diagnose this:by getting a stomach acid analysis done to discover how much gastric acid your tum produces and also whether you've got enough pancreatic enzymes. Biolab does these tests (see box, page 39).

Solve this:Supplement your diet (according to directions on the label) with the stomach acid betaine hydrochloride (HCl plus pepsin) and pancreatic enzymes for at least 12 weeks.

Avoidhistamine blockers-or 'histamine H2-receptor antagonists' in medicospeak-sold over-the-counter to ease heartburn and acid reflux, as they do this by reducing levels of stomach acid.19

Taking 500 mg of l-histadine can also improve gastric-acid production.

A leaky gut wall

When working at peak condition, the lining of your small intestine acts like a smart sieve that only allows small particles of food-amino acids, carbs and essential fatty acids-to pass through it to reach your bloodstream and be transported to other cells in the body, while blocking other, larger food molecules and toxins or bacteria that might cause harm.

But if this tiny sieve is damaged in some way, a large number of these toxic substances are then able to breach the gut wall, triggering the production of antibodies that can lead to allergies, altering the bacterial composition of the gut and even allowing the overgrowth of fungal yeasts like Candida. A range of conditions-from ulcerative colitis, poor food absorption, Crohn's disease and IBS to malnutrition, joint diseases, and skin complaints like acne, psoriasis and dermatitis-often hark back to having a sieve with holes that are just too big.

Suspect this:if you've been diagnosed with Candida infection but the treatment hasn't worked, or if you've had radiotherapy, severe burns, periodic hives or dermatitis, or you suddenly seem to be reacting to an ever-increasing number of foods, particularly those from a range of different food groups.13 Other causes are alcohol abuse, NSAIDs and recreational drugs, and chemotherapy.14

A too permeable gut is also often the result of a mouth full of amalgam fillings, after microscopic amounts of the mercury migrate.

Diagnose this:by taking a 'lactulose/mannitol challenge test'. Neither of these sugars is metabolized in the healthy gut and so should mostly be excreted in the urine after six hours.

You can have this and other gut permeability tests done by Biolab and Genova Diagnostics in Europe or the US (see box, page 39). If the tests show more sugar than normal is taken up, you've got a gut that leaks.

Solve this:by chewing your food thoroughly as that releases epidermal growth factor (EGF), a polypeptide that stimulates the growth and repair of the small intestinal walls.15

And stop eating too much insoluble dietary fibre, which may also increase gut permeability.16

Finally, take supplements to heal your gut wall (see below).

Healing your 'leaky' gut

Take supplements of any or all of the following and experiment to see which ones work best for you, or work with a qualified naturopath.

Probioticshave long been shown to improve gut permeability.1 Choose strains containing lactobacilli, bifidobacteria, Saccharomyces boulardii and non-disease-causing strains of Escherichia coli and streptococci.

Vitamin Ais necessary for the growth and repair of cells that line both the small and large intestines. Suggested dosage: 10,000 IU.

Colostrum-derived supplements(available online at sites like and can improve the state of your gut lining and also encourage the growth of natural gut flora.

Glutamine, an amino acid essential for a sound gut wall, can repair the gut mucosal lining damage caused by chemotherapy and radiation.2

Glutathione (GSH)is an antioxidant, levels of which are often low in people with leaky gut syndromes. If you've got parasites too, don't supplement until you've cleared them first (see page 39).

Flavonoidslike those found in milk thistle (Silybum marianum) and dandelion root (Taraxacum officinale), when taken before eating, can block allergic reactions that increase gut permeability.

Fish oilscan protect the body against toxins produced in the gut and prevent injury to the gut wall caused by the drug methotrexate,3 while rice bran oil (gamma oryzanol) can heal gut ulcers.4

Saccharomyces boulardii, a gut-friendly yeast originally isolated from the skins of lychee fruits and used in 'yeast against yeast' treatment in France, can by itself reduce bouts of diarrhoea and colitis.5

The B vitaminsand vitamins A, C and E, zinc, selenium, molybdenum, manganese and magnesium can be taken as additional supplements.


1. Ann Med, 1990; 22: 57-9

2. Arch Surg, 1990; 125: 1040-5

3. Am J Clin Nutr, 1991; 54: 346-50

4. Rep Hokkaido Inst Publ Hlth, 1966; 16: 111-4

5. Am J Gastroenterol, 1989; 84: 1285-7; Gastroenterology, 1989; 96: 981-8


About one in six of us is walking around with Giardia lamblia, a minuscule flagellated protozoan that causes severe fatigue and bowel disturbances, and one in 10 is infested with cryptosporidia, another group of diarrhoea-causing protozoans.

These and other gut parasites like Blastocystis hominis can cause vague gut symptoms that come and go or that mimic those of IBS.

Suspect this:if you have a mouth full of amalgam fillings (mercury has been shown to alter the gut's ecology) or if elimination diets don't help.

Diagnose this:by getting your stools tested for parasites. Contact Genova Diagnostics (see box, below right).

Solve this:If the test comes back positive, here's our Medical Detective Harald Gaier's favourite formula for most parasites.

On weeks 1 and 3, take:

o Berberis vulgaris (barberry) tincture (15 mL three times a day)

o Oregano oil (1 capsule a day), shown to inhibit parasites like Giardia

o Artemisia absinthium (wormwood) tincture (15 mL three times a day)

o Clove powder (one capsule a day).

On weeks 2 and 4, take:

o Hydrastis canadensis (goldenseal) tincture (15 mL three times/day)

oOlive leaf extract (one capsule a day)

o l-Glutamine (5 g/day).

Berberisand Artemisia can attack all manner of gut bacteria, protozoans and yeasts,17 and add supplements of propolis, which work well against Giardia.18 According to Essex-based medical herbalist Susan Koten, also consider seeing a herbalist about a gallbladder flush made up of fringetree (Chionanthus virginicus), Leptandra virginica (Culver's root) and Berberis vulgaris, as the gallbladder is also often affected.

Candida albicans overgrowth

"When all you've got is a hammer, everything starts looking like a nail." So said British nutritional pioneer Dr Stephen Davies about Candida albicans infection and the tendency of many doctors and alternative practitioners to diagnose anyone suffering from a collection of unexplained symptoms as victims of 'yeast syndrome'.

Some 25 years after Dr Orian Truss of Birmingham, Alabama, first theorized that overgrowth of the normally harmless Candida fungal yeast can wreak untold havoc in the gut, nutritional doctors like our medical detective,
Dr Harald Gaier, now believe the situation is rather more complex. Candida may be only one of several culprits, and so-called candidiasis sufferers may have several, quite distinct problems, including those listed in this article.

Suspect this:if you don't improve on a Stone Age diet.

Diagnose this:by having a gut fermentation test. This measures whether you ferment ethyl alcohol in your gut after consuming glucose sugars, as often happens with yeast overgrowth, and so distinguish yeast from bacterial overgrowth. The test can be done by Biolab (see box, right) In North America, Genova Labs offers a Candida antibody test, a simple saliva test that can confirm whether it's Candida or not.

Solve this:Kill Candida with a natural antifungal like barberry (Berberis) tincture (15 mL twice a day). Besides this, caprylic acid, goldenseal and a number of other traditional treatments have shown promise, including tea tree oil (Melaleuca alternifolia), oregano oil, proven to have potent anti-Candida effects, olive oil and oil of cloves.20

Follow a low-carb diet and be sure to avoid sugars, yeast, alcohol and the usual allergy-related foods and, for a week or two, fruit. Check your nutritional status and take supplements if necessary.

Doctors on our panel find their patients are usually deficient in magnesium, zinc, vitamins A, B1 and B6, and omega-6 fatty acids. Take pancreatic enzymes (called 'proteases'), which keep the small intestine free of parasites and aid digestion.21 A lack of protease greatly increases the risk of intestinal infections, including chronic Candida infections.

Add supplements of choline, betaine and methionine to clean up the workings of your liver, as mild liver damage is often behind chronic Candida overgrowth. These liver enzymes boost your levels of two important antioxidants: S-adenosylmethionine and glutathione.22

Extract of milk thistle (Silybum marianum) at dosages of 70-210 mg three times a day can stimulate the formation of new liver cells, and increase the production of glutathione and bile. It can also reduce liver injury.23

Where to get tested


Biolab Medical Unit

The Stone House

9 Weymouth St

London, W1N 3FF

0171 636 5959

Genova Diagnostics Europe

Parkgate House
356 West Barnes Lane
New Malden
Surrey, KT3 6NB

020 8336 7750


Genova Diagnostics

63 Zillicoa Street

Suite A

Asheville, NC 28801-1074

800 522 4762


1. Gottschall E. Breaking the Vicious Cycle. Ontario, Canada: Kirkton Press, 1994

2. Int J Sports Med, 2008; 29: 778-82; Am J Gastroenterol, 2006; 101: 2552-7

3. Gut, 2010; 59: 508-12

4. Epidemiology, 1992; 3: 47-52

5. J Adv Med, 1993; 6: 67-82; Br J Exp Pathol, 1980; 61: 92-6

6. Baillieres Clin Rheumatol, 1989; 3: 271-84

7. Br J Rheumatol, 1987; 26: 103-7

8. Br J Rheumatol, 1992; 31: 443-7

9. Nature, 2012; 487: 104-8

10. J Am Diet Assoc, 2006; 106: 1631-9

11. J Clin Gastroenterol, 2008; 42: 233-8; J Pediatr Gastroenterol Nutr, 2008; 47: 303-8

12. J Am Diet Assoc, 2009; 109: 1204-14; Curr Gastroenterol Rep, 2009; 11: 368-74

13. Surgery, 1990; 107: 411-6; Allergy, 1989; 44 Suppl 9: 47-51; Ann Allergy, 1987; 59: 127-30; 1991; 66: 181-4

14. Lancet, 1984; 1: 179-82; Gut, 1991; 32: 66-9; Eur J Pediatr, 1988; 147: 123-7

15. Lancet, 1993; 341: 843-8

16. J Nutr, 1983; 113: 2300-7

17. Tokai J Exp Clin Med, 1990; 15: 417-23; J Infect Dis, 1987; 155: 979-84; Nature; 1967; 215: 527-8

18. Acta Gastroenterol Latinoam, 1988; 18: 195-201

19. PLoS One, 2013; 8: e56498

20. Clin Microbiol Rev, 2006; 19: 50-62; Phytomedicine, 2009; 16: 972-5; J Appl Bacteriol, 1989; 66: 69-75

21. Gut, 1992; 33: 987-93

22. Alcohol Clin Exp Res, 1993; 17: 552-5; FASEB J, 1991; 5: 2093-8

23. Phytother Res, 2010; 24: 1423-32; J Hepatol, 1989; 9: 105-13

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