Bowel Disease, Part III: Healing Through Nutrition

[UPDATED August 2015 with updates in italic . – Paul]

Bowel diseases are characterized by chronic infection of the gut lining (and sometimes immune cells), wounded and inflamed gut tissue, and autoimmune attacks on the gut.

Malnutrition contributes to bowel disease by impairing immunity, impairing gut motility, and slowing intestinal healing.

Conversely, bowel diseases impair nutrient absorption along with the rest of digestion, exacerbating malnutrition.  To avoid a vicious spiral, bowel disease patients should be especially attentive to their nutritional needs.

The first step toward good nutrition is to eat the Perfect Health Diet, including all of our supplemental foods. For gut health, egg yolks are especially important. Also important are extracellular matrix components from bones and joints; vegetables, herbs, and spices; and healthy fats (which trigger bile production, bile being beneficial for the gut). See our Recommended Supplements page for more on the supplemental foods.

We no longer recommend taking a multivitamin. For various reasons multivitamin formulas are incomplete:

  • Some nutrients, such as magnesium and vitamin C, are too bulky to fit in a single pill.
  • Some, such as vitamin D and iodine, have no “one size fits all” dose that manufacturers can safely include.  They therefore include a low dose that is safe for all, meaning that most receive an insufficiency.
  • Others, like melatonin, may be unnecessary for the general population but are likely to benefit bowel disease patients.

Here, then, are a few supplements that bowel disease patients may find to be helpful additions to their multivitamin.

Vitamin D3 and Partners

Vitamin D has been called the “antibiotic vitamin” [1] because it triggers the body’s production of natural antibiotic compounds.

Vitamin D is needed for the production of the antimicrobial peptides cathelicidin and beta-defensin 2, which are produced mainly in immune cells and in epithelial cells lining the gut. [2, 3] These antimicrobial peptides normally saturate the mucosal barrier, where they kill most bacteria, enveloped viruses, fungi, and protozoa.

Evidence has accumulated that deficiencies in antimicrobial peptides are causal factors in bowel diseases:

  • In Crohn’s disease, a deficiency of antimicrobial peptides allows pathogens to invade. [4, 5, 6]
  • Reduced expression of intestinal defensins predicts diarrhea two months in advance. [7]
  • When antimicrobial peptides are induced therapeutically, intestinal infections are relieved. [8]
  • Mice with no vitamin D function due to knockout of the vitamin D receptor experience bacterial overgrowth of the intestine, and even mild injury to the colon results in the death of the mouse. [9]

There is increasing awareness that vitamin D is needed for defense against infections generally. [10]

Vitamin D has other benefits besides strengthening immunity. It also suppresses autoimmunity.  For instance, there is evidence for an inverse relationship between vitamin D levels and auto-antibody levels [11]. Some autoimmune patients have experienced a disappearance of auto-antibodies upon supplementation with vitamin D. [12]

Since bowel diseases are the result of infections and autoimmunity, normalization of vitamin D levels is probably extremely helpful.

Vitamin D is also associated with reduced risk of colorectal cancer. [13] Bowel disease patients are at elevated risk for colorectal cancer.

Sunshine should be sought regularly, and supplements added to bring serum 25-hydroxyvitamin D levels to at least 40 ng/ml. In addition, vitamin D should be accompanied by supplementation of two key partners:

  • Vitamin K2 is needed for proper vitamin D function.  Most inflammatory bowel disease patients are severely deficient in vitamin K2. [14] A good daily supplement should include 100 mcg of the MK-7 form, perhaps combined with some synthetic MK-4 and plant-derived vitamin K1.
  • Magnesium is needed for proper vitamin D function and many people are deficient.  200 mg/day magnesium citrate (which is better absorbed than magnesium oxide) is appropriate.


Melatonin is a crucial hormone which is evolutionarily conserved across all nearly all animals, indicating that it is essential to health. Most know that it is produced in the pineal gland of the brain during sleep, but it is less well known that it is abundantly produced by the gut. Much of the body’s melatonin gathers in the gut, where melatonin concentrations are 100-fold greater than in blood and 400-fold greater than in the pineal gland. [15]

In the gut melatonin reduces inflammation, stimulates immune function, fosters tissue repair and helps regenerate the epithelium. [15] Melatonin also has antimicrobial effects. [16]

Clinical trials have found that melatonin can be beneficial in treating bowel conditions. [17, 18, 19] Melatonin seems to be especially effective at reducing abdominal pain. [20, 21]

To maximize night-time melatonin levels, it is best to sleep in a totally darkened room; avoid eating food at night; and avoid exercising at night. Melatonin can also be supplemented.  Supplemental melatonin should be taken immediately before bed. Time-release tablets are best, otherwise fluctuating melatonin levels may cause waking in the middle of the night. If early waking does occur, reduce the dose.

Thyroid and Immune Minerals:  Selenium and Iodine

Selenium and iodine are critical for thyroid and immune function. Adequate thyroid hormone and a well-functioning immune system, in turn, are essential for gut health.

The thyroid hormone T4 is 65% iodine by weight, and the active thyroid hormone T3 is 59% iodine by weight.  Selenium-containing deiodinase enzymes are required to convert inactive thyroid hormone to its active form. Either iodine or selenium deficiency can cause hypothyroidism, or a deficiency of thyroid hormone.

Gut problems, especially constipation, are among the primary symptoms of hypothyroidism. Thyroid hormone is important for proper wound healing – and therefore for recovery from bowel disease.

Selenium and iodine are also essential for immune function.  Iodine along with the enzyme myeloperoxidase is needed to produce respiratory bursts – the burst of reactive oxygen species (ROS) that white blood cells use to kill pathogens.  Selenium is necessary both to strip iodine from thyroid hormone in the white blood cells, and to maintain (via the enzyme glutathione peroxidase) the function of the antioxidant glutathione which protects both white blood cells and gut cells from ROS.  Deficiency of either selenium or iodine leads to an immediate reduction in the killing activity of white blood cells.

Iodine was widely prescribed for infectious diseases in the 19th century. The Nobel laureate Dr. Albert Szent Györgyi, the discoverer of vitamin C, recounted this anecdote:

When I was a medical student, iodine in the form of KI was the universal medicine. Nobody knew what it did, but it did something and did something good. We students used to sum up the situation in this little rhyme:

If ye don’t know where, what, and why

Prescribe ye then K and I. [22]

Doses as large as 1 gram potassium iodide, containing 770 mg of iodine, were given. In practice, however, it’s highly desirable to start with a low dose of iodine, around 1 mg/day, and allow the thyroid to adapt before gradually increasing the dose.

The great danger of high doses of iodine is that it will make autoimmune attacks, as well as attacks on pathogens, more powerful. Therefore large supplemental doses of iodine should be taken only after grains and legumes have been eliminated from the diet for at least 3 months. Bowel disease patients should also be tested for the presence of thyroid auto-antibodies before beginning high-dose iodine.

Related minerals: 

  • Myeloperoxidase requires iron (heme), and unfortunately anemia due to iron deficiency is common in bowel disease patients, especially among menstruating women. [23] A good way to judge the need for iron is to measure blood ferritin levels, which should be 50 ng/ml or higher.

Thyroid hormone

If auto-antibodies are present, then hypothyroidism cannot be repaired by iodine supplementation. Yet thyroid hormone is necessary for gut healing.  In such cases, prescription thyroid hormone should be taken.

Hypothyroidism is widely undiagnosed, because the “normal” range of thyroid stimulating hormone (TSH) is far too wide. TSH levels over 1.5 mIU/L may indicate a subclinical hypothyroidism that is sufficient to measurably raise mortality. [24] Anyone with a TSH over 1.5 mIU/L and a basal body temperature below 98 F should consider obtaining prescription thyroid hormone to test whether it helps relieves hypothyroidism-associated symptoms such as constipation and improves general health. Generally, a good dose of thyroid hormone will eliminate symptoms of hypothyroidism and reduce TSH to 2.0 or so – still elevated, to stimulate thyroid healing.

Antioxidants and Bile Supports: Vitamin C, Glutathione, N-Acetylcysteine, Taurine, Glycine

Since the main immune defense (and autoimmune) mechanisms in the gut involve around ROS-producing respiratory bursts, the gut of any bowel disease patient is a ROS-rich environment.

It is therefore desirable to maximize the ability of both gut and immune cells to protect themselves against ROS with native antioxidants.

Foremost among the native antioxidants is glutathione, the primary immune and gut antioxidant. Glutathione may be supplemented directly, or its levels may be raised by supplementing with vitamin C and N-acetylcysteine.

Vitamin C has other important functions:  it is needed for wound healing and to maintain the collagen-based extracellular matrix which backs the gut and gives it integrity. One of the symptoms of scurvy (extreme vitamin C deficiency) is bleeding from the mucus membranes, including the gut lining.

A Japanese study found that vitamin C was highly protective against ulcerative colitis, reducing incidence by 55%. [25]

In rats, glutathione deficiency leads to elevated infection-induced bowel inflammation. [26] Glycine (the most abundant amino acid in extracellular matrix) and taurine both support glutathione synthesis.

Related minerals: 

  • Zinc and copper are both required for the function of another antioxidant, zinc-copper superoxide dismutase.  We recommend supplementing dietary intake with another 15 mg zinc and 2 mg copper. This can be achieved by taking a daily multivitamin plus eating occasional beef or lamb liver.
  • Magnesium is needed for glutathione synthesis. As noted before, 200 mg/day magnesium citrate is a highly desirable supplement for bowel disease patients.

Magnesium and copper deficiencies contribute to necrotizing enterocolitis [27], and probably worsen all bowel diseases.

Bile is an important aid to gut health, in part because it helps to clear the small intestine of bacteria. Bile needs vitamin C for its manufacture and needs to be conjugated with glycine or taurine. Glycine can be obtained from food as extracellular matrix material, or as a powder which you can sprinkle on food. Taurine is an excellent supplement for patients with gut disorders.


Although not a complete list of the vitamins and minerals which may be helpful to bowel disease patients, these are among the most important – and most often overlooked:

  • Vitamin D3 sufficient to raise serum 25-hydroxyvitamin D above 40 ng/ml.
  • Vitamin K2, at least 100 mcg/day.
  • Magnesium citrate or bis-glycinate, 200 mg/day.
  • Melatonin, if needed for deep restful sleep.
  • Selenium, 200 mcg/week.
  • Iodine, 225 mcg/day.
  • Thyroid hormone sufficient to bring TSH below 2.0.
  • Vitamin C, 1 g/day.
  • Glutathione, 500 mg/day, preferably in the reduced form, taken between meals on an empty stomach with a full glass of water (since it is destroyed by stomach acid).
  • N-acetylcysteine, 500 mg/day.
  • Iron, zinc, and copper sufficient to relieve deficiencies.
  • Taurine, 1 g/day.
  • Glycine (if insufficient extracellular matrix is eaten), up to 5 g/day.

Related Posts

Other posts in this series:

  1. Bowel Disorders, Part I: About Gut Disease July 14, 2010
  2. Bowel Disease, Part II: Healing the Gut By Eliminating Food Toxins m July 19, 2010
  3. Bowel Disease, Part IV: Restoring Healthful Gut Flora July 27, 2010


[1] “The antibiotic vitamin: deficiency in vitamin D may predispose people to infection,” Science News, Nov 11, 2006,

[2] Liu PT et al. Cutting edge: vitamin D-mediated human antimicrobial activity against Mycobacterium tuberculosis is dependent on the induction of cathelicidin. J Immunol. 2007 Aug 15;179(4):2060-3.

[3] Lehrer RI, Ganz T. Defensins of vertebrate animals. Curr Opin Immunol. 2002 Feb;14(1):96-102.

[4] Rivas-Santiago B et al. Susceptibility to infectious diseases based on antimicrobial peptide production. Infect Immun. 2009 Nov;77(11):4690-5.

[5] Wehkamp J et al. Inducible and constitutive beta-defensins are differentially expressed in Crohn’s disease and ulcerative colitis. Inflamm Bowel Dis. 2003 Jul;9(4):215-23.

[6] Barrier dysfunction due to distinct defensin deficiencies in small intestinal and colonic Crohn’s disease. Mucosal Immunol. 2008 Nov;1 Suppl 1:S67-74.

[7] Kelly P et al. Reduced gene expression of intestinal alpha-defensins predicts diarrhea in a cohort of African adults. J Infect Dis. 2006 May 15;193(10):1464-70.

[8] Wehkamp J et al. Defensins and cathelicidins in gastrointestinal infections. Curr Opin Gastroenterol. 2007 Jan;23(1):32-8.

[9] Froicu M, Cantorna MT. Vitamin D and the vitamin D receptor are critical for control of the innate immune response to colonic injury. BMC Immunol. 2007 Mar 30;8:5.

[10] Yamshchikov AV et al. Vitamin D for treatment and prevention of infectious diseases: a systematic review of randomized controlled trials. Endocr Pract. 2009 Jul-Aug;15(5):438-49.

[11] Goswami R et al. Prevalence of vitamin D deficiency and its relationship with thyroid autoimmunity in Asian Indians: a community-based survey. Br J Nutr. 2009 Aug;102(3):382-6.

[12] Dr. John Cannell, The Vitamin D Newsletter, March 9, 2009.

[13] Woolcott CG et al. Plasma 25-hydroxyvitamin D levels and the risk of colorectal cancer: the multiethnic cohort study. Cancer Epidemiol Biomarkers Prev. 2010 Jan;19(1):130-4.

[14] Kuwabara A et al. High prevalence of vitamin K and D deficiency and decreased BMD in inflammatory bowel disease. Osteoporos Int. 2009 Jun;20(6):935-42.

[15] Bubenik GA. Gastrointestinal melatonin: localization, function, and clinical relevance. Dig Dis Sci. 2002 Oct;47(10):2336-48.

[16] Tekbas OF et al. Melatonin as an antibiotic: new insights into the actions of this ubiquitous molecule. J Pineal Res. 2008 Mar;44(2):222-6.

[17] Sánchez-Barceló EJ et al. Clinical uses of melatonin: evaluation of human trials. Curr Med Chem. 2010;17(19):2070-95.

[18] Terry PD et al. Melatonin and ulcerative colitis: evidence, biological mechanisms, and future research. Inflamm Bowel Dis. 2009 Jan;15(1):134-40.

[19] Chang FY, Lu CL.Treatment of irritable bowel syndrome using complementary and alternative medicine. J Chin Med Assoc. 2009 Jun;72(6):294-300.

[20] Lu WZ et al. Melatonin improves bowel symptoms in female patients with irritable bowel syndrome: a double-blind placebo-controlled study. Aliment Pharmacol Ther. 2005 Nov 15;22(10):927-34.

[21] Song GH et al. Melatonin improves abdominal pain in irritable bowel syndrome patients who have sleep disturbances: a randomised, double blind, placebo controlled study.  Gut. 2005 Oct;54(10):1402-7.

[22] Szent-Györgyi, A. (1957) Bioenergetics. New York: Academic Press, p. 112.

[23] Gomollón F, Gisbert JP. Anemia and inflammatory bowel diseases. World J Gastroenterol. 2009 Oct 7;15(37):4659-65.

[24] Asvold BO et al. Thyrotropin levels and risk of fatal coronary heart disease: the HUNT study. Arch Intern Med. 2008 Apr 28;168(8):855-60.

[25] Sakamoto N et al. Dietary risk factors for inflammatory bowel disease: a multicenter case-control study in Japan. Inflamm Bowel Dis. 2005 Feb;11(2):154-63.

[26] van Ampting MT et al. Intestinal barrier function in response to abundant or depleted mucosal glutathione in Salmonella-infected rats. BMC Physiol. 2009 Apr 17;9:6.

[27] Caddell JL. A review of evidence for a role of magnesium and possibly copper deficiency in necrotizing enterocolitis. Magnes Res.1996 Mar;9(1):55-66.

Leave a comment ?


  1. Do you recommend a multi-cap?

  2. Yes I do. Just with a few things on the side, like vitamins D, K, C, magnesium, iodine.

  3. Paul,

    I know this iodine vs hashimoto and thyroid antibodies is a really polemic subject, but I want to let you know some facts.

    Iodine, at least in rats, only flare a thyroid attack in a person that has selenium deficiency, as has been show in the study below. Note that there was no difference in autoimmunity markers between the group without iodine suplementation (group I) and the group with excessive iodine plus selenium (group IV).

    Some other articles of interest about iodine and selenium:

    Some doctors (Dr. Kharrazian for example) cite some studies carried on various countries that showed a increased Hashimoto incidence after salt iodinization ( The countries often cited are Brazil (São Paulo), Sri Lanka, Turkey, China and Greece. Are these countries deficient in selenium? Let’s see some evidence:

    Brazil: the study was done in São Paulo, city where most of the brazilian japanese live. Japanese living in Sao Paulo-Brazil have significant lower levels of Se than japanese living in Japan (

    Greece: selenium status is one of the lowest of the Europe (

    China: Minerals as calcium, zinc, selenium, kalium and vitamins as vitamin A, B1, B2 were insufficient (

    Turkey: Selenium status of Turkish children is found to be lower than that found in the literature (

    Turkey: Turkey is one of those countries where iodine deficiency (ID) is widespread, Se levels are marginal (

    Sri Lanka: This study has shown for the first time that significant proportions of the Sri Lankan female population may be Se deficient (

    So, what we are seeing in salt iodinization could be in reality a selenium deificiency.

    • Mario, thank you very much for commenting, these are fascinating studies.

      I am grateful that you have compiled this evidence. It will take me some time to work through those papers to decide whether I need to revise any of my assertions. For the moment I’ll just reiterate that selenium and iodine are both crucial for healthy thyroid and immune function, should never be allowed to be deficient, but that high-dose iodine supplementation can produce negative effects in those with anti-thyroid autoantibodies. If these autoimmune conditions are caused in part by selenium deficiency, and can sometimes be cured by selenium supplementation, that by itself would be great news. However, if selenium can do even more and prevent iodine-induced autoimmune attacks in people with pre-existing autoimmune hypothyroiditis, that would be amazing.

      For the moment, I’m going to stick with the standard position that people with autoimmune thyroiditis should reverse that condition before beginning high-dose iodine.

  4. Paul,

    Just to reinforce this iodine-selenium sinergy and the importance that we shouldn’t be deficient in neither of them, is the dangerous of selenium supplementation in a iodine deficient person:

  5. That’s a great point. Yes, iodine and selenium are very intimately related, that’s why we always treat them together in this blog and in our book. You need them both together.

    A few years after the paper you cite the same group wrote a paper in AJCN for which the full text is freely available: Figure 3 is fascinating: selenium supplementation reduces levels of T4 hormone in all subjects, hypothyroid or normal.

    This happens in part because selenium deiodinase enzymes convert T4 to the active T3, but also inactivate T3 by further stripping iodine, and reduce the supply of T4 and T3 by stripping iodine within immune cells to support immune function. So, under iodine deficiency where there is too little T4 to begin with, selenium helps redirect iodine from T4 to immune function and aggravates the hypothyroidism.

    In their discussion they point out that the central nervous system can convert T4 to T3 without selenium; thus in selenium deficiency the CNS, but not the peripheral body, is able to maintain thyroid hormone status. This is a neat way to redirect thyroid hormone in cases of deficiency to where it is most needed.

    These are neat results. There are other nutrients that need to be kept in a proper ratio — e.g. vitamins A/D/K, omega-6 and omega-3 fats — and it appears that selenium and iodine also belong in this group.

  6. Thank you for your extremely insightful and fascinating articles. Just a thought- I have given up taking most supplements myself, as it seems that I do not absorb them. Do you have any recommendations for what kind of supplements are best absorbed by those with damaged intestines? One can take these vitamins in pills, but they are not necessarily absorbed by the body.

  7. Hi jamie,

    That is a difficult question. I really don’t know much about absorption. Most supplements will be absorbed more readily if you take them with food. Also, for supplements that are not destroyed by stomach acid, you may wish to grind the pills up and distribute them in your food. Some specific forms are better absorbed, e.g. magnesium citrate is better than magnesium oxide. But I haven’t researched the matter in any detail.

    I know this is a big problem for bowel disease patients – It’s a vicious circle where bowel disease prevents absorption of nutrients and malnutrition prevents healing. But I don’t know what techniques have been developed to get around the problem. I haven’t heard of intravenous injections of micronutrients for bowel disease patients.

    Best, Paul

  8. Paul,

    You say that magnesium citrate is absorbed better than magnesium oxide. I’ve read that chelated magnesium (such as magnesium glycinate) is absorbed best of all. Besides, magnesium citrate is very good at creating loose bowel movements! Also, what is your opinion about dark chocolate as a magnesium “supplement”?

  9. Hi Art,

    Yes, magnesium glycinate and in general any chelated mineral supplements are good. Chelation with amino acids is generally how minerals are found in food.

    I’ve never had a loose bowel from 200 mg magnesium tablets, but I suppose it could happen.

    Dark chocolate is great and we eat a lot of it — just bought a 1 lb block of 70% chocolate yesterday, and I’ve had 3 chunks so far. It is nutritious. I take the pills anyway, just to be careful. But if you prefer chocolate, go for it!

  10. Paul, I was eating a couple of dark choc. covered almonds every day, but stopped when you said to cut out all sugar. Can I go back to them. They were my reward in the evening for staying on target all day.

    Please say yes. :-}

    • Yes.

      Do I look like Captain Bligh? 🙂

      (We eat chocolate covered almonds often. I prefer blocks of 70% to 80% chocolate myself, but a small amount of sugar is OK if you’re low-carb generally.)

  11. Thank you kind sir!

  12. Can you say what multivitamin you use? Or give a guide to what you look for in a multivitamin? There are so many different combinations sold that I find it difficult to pick one, and I don’t want to get one of those “super” multis. Just something that meets the RDAs, I think.

  13. Hi Gary,

    We also get an RDA level multivitamin. We buy Centrum Silver – no reason in particular, it’s cheap and available.

    We will put up a supplement guide, probably next week. But we don’t have any particular brands to recommend.

  14. Im really sorry for sticking this in here…but I really didnt know where to go with this concern. Just wondering if you have any clues on this one and if you do , could you do a series on this one.
    I would like to know if there are any dietary cures for dysfunctional menstrual bleeding, especially associated with perimenopause. I have come across all kinds of things about this across the web, but it really is all very conflicting, and it does affect a huge section of women. I am looking for causes, prevention and ways to control it
    I would appreciate any help that you could give.

  15. Hi java,

    In my own experience, it was vital to try to find out what was wrong first. For me, that meant checking thyroid function, a full GI panel to look for infections, parasites, dysbiosis, a CBC plus serum iron & ferritin, testing for stealth infections (arthritis) and a female hormone panel by saliva. Many weak areas were revealed!

    Don’t get me wrong, I think the food/diet is crucial. I feel that in my case, approaching 50 years, many of those years spent eating SAD, interventions beyond diet were needed to help my body function better.

    My cycles are much improved after I’ve fixed gut infections, gotten rid of gluten, helped thyroid, antibiotics for the arthritis, normalized CBC, and taking a low dose of progesterone…..and eating nutrient dense foods of course!

    Good luck,


  16. Hi java,

    Michelle’s reply is excellent. When the cause is uncertain, it’s good to just start fixing things.

    Because some of the possible causes of perimenopausal bleeding are very serious, it’s important to have doctors look into the cause.

    According to this paper on peri- and post-menopausal bleeding,, it can be caused by cervical or endometrial cancer.

    Another cause of perimenopausal bleeding is chronic infection of the cervix, for instance by Mycobacterium tuberculosis: 6 months of antibiotics cured it.

    Abnormal bleeding is the most common overt symptom of uterine fibroids:
    We think elimination of food toxins, esp grains, legumes, and vegetable oils, is important for fibroids.

    Vascular malformations can cause perimenopausal bleeding: We argued in an earlier post ( that gluten autoimmunity and vitamin D and K2 deficiency could cause vascular malformations.

    Certain nutritional deficiencies can cause bleeding, notably vitamin C and vitamin K.

    This is not a complete list of possible causes. With so many possible reasons for the bleeding, a doctor’s investigation is necessary.

    However, in general I would say that following our diet and nutritional recommendations would be an important step forward. That might cure it directly, e.g. if it is due to food toxins or missing nutrients, and will make both diagnosis and cure easier if it is infectious or has some other cause.

    Best, Paul

  17. Thanx for your reply Paul , and your concern. I would like to point out that I am under a doctors care. But medicine is only treating the symptoms , not the cause. I have a normal thyroid panel, no fibroids, no cancer { pap smears and ultrasounds are all normal]. My doctors all say that this sometimes happens around menopause, but i am sure there should be a reason.
    Incidentally I am grain,sugar and PUFA oils free.I may have rice about once a month,but thats it. Is there any specific testing that crosses your mind ??

    Michelle, thanks for your reply. Interestingly I was on progesterone loaded IUD[Mirena] for 5years and had virtually no bleeding. But once off it,Im back to square one because the cause has not been addressed.Are there any specific tests that you have had done to find the underlying causes ? I am 50 as well.

  18. Hi java,

    Can you give us a little more information? Where is the blood coming from — cervix, endometrial lining? How much and how often? What do hormone levels look like?

    It sounds like you had bleeding in the middle of your period before you started the IUD? That could suggest a long-term issue like a chronic infection. So you might consider a TB test.

    Wikipedia on the page for van Willebrand’s disease, an inherited bleeding disorder, has a good table of diagnostic possibilities for bleeding: This lists 14 conditions that cause bleeding and 4 tests that help distinguish them.

    Bleeding is such a common symptom of so many conditions that it’s hard to enumerate all the possible causes. If you push on your doctors or a specialist they may be able to help.

  19. I think it’s very important to note that the “progesterone” in Mirena is not bio-identical progesterone. A very important distinction!

  20. Below is some info from the Yahoo list, Hormones and Health Naturally:

    “Birth control pills are generally a Lot of estrogen combined with an anti-progesterone drug called a progestin.

    The progestin has a lot of side effects AND blocks any real progesterone your body may be producing.

    Mirena is a progestin without the estrogen that is frequently in birth control pills.”


    Java, a properly administered saliva test by a competent health care professional will likely reveal a sex hormone imbalance. I had my female sex hormone saliva testing done by an experienced practitioner who uses Diagnos-Techs lab.

    Good luck, and I encourage you to read up on bioidentical hormones. Ray Peat, John Lee, Virginia Hopkins…

  21. Paul… Michelle…..THanks so much for your help and time. I will look at the above issues. It is endometrial bleeding, and according to my gynae due to Estrogen Dominance. But I think that is such a vague term, as there must be something causing the ED. I am overweight. I have more or less beenfollowing your nutrition guidelines for a while now. I exercise daily. Yet I am unable to shed any weight,even at 1200 calories of clean food. My gynae feels that is the vicious cycle ED causes.
    I really appreciate your help, and will revert once I have talked with my doctor about the above recommendations. If you have any dietary guidelines to reduce ED ,do let me know. Otherwise I will let you know of my follow up. Thanks again…

  22. An MD who thinks Mirena is safe is unlikely to differentiate between an unnatural anti-progesterone like progestin, and real bio-identical progesterone.

    This type of conventional MD is also likely to rely on inaccurate serum testing to measure sex hormone levels. Serum will only give you what is bound up and floating around in the blood. Saliva will give you what you need to know: how much is at the tissue level.

    To my thinking, it’s very much like going to a conventional MD and being told to avoid saturated fat, and take this statin. It’s the standard of care right now, and things are slow to change.

    Progesterone levels decline ahead of estrogen levels as we age, hence the term “estrogen dominance”. There’s too much estrogen relative to too little progesterone.

    Perhaps if we were all healthy, and weren’t swimming in a sea of xenoestrogens, and weren’t exposed to anti-progesterones like progestin in birth control pills & products like Mirena, we wouldn’t suffer from estrogen dominance as we age. But we do.

  23. Hi java,

    Obesity raises estrogen levels, so I think the best approach might be to solve the weight problem. Probably the two health issues are connected.

    Have you tried intermittent fasting? What about nutritional supplements? Choline is important in animals, probably humans too, plus all our supplement list.

  24. No I havnt tried intermittent fasting…but perhaps I will. I am also planning on starting a ketogenic diet later this week. Normally I try to keep my carbs below 50.No, i havnt tried nutritional supplements because i really dont know what to take and what not to take. Where and in what form would I find choline ? I have tried it all to lose weight and thats how I came across your site, but nothing really seems to be working. I am 5’4” and weigh 70kgs.
    Michelle, you are right . I think we encounter xenoestrogens at every level, and I guess some of us are just more sensitive to them than others. I try my very best to live as natural as possible, but something just catches up.Wish I knew what it was.

  25. Hi java,

    It’s very important for weight loss to be well nourished. We recommend a multivitamin plus D, K2, C, magnesium, iodine, selenium, copper, chromium. I would add choline to that if I were you.

    I’ll put up a supplement page later this week.

  26. I really really appreciate your help…

  27. At the risk of stating the obvious, sex hormones are involved in fat regulation. Think of the body changes in puberty, and in menopause.

    In other words, don’t be too hard on yourself, java, re: your diet and weight. Keep looking for those weak areas and fix them. It’ll all fall into place.

  28. Thanx michelle…

    I just feel so much better with help like yours and Pauls. Just a question… in what form do you take low dose progesterone ? I shall get all the other tests done soon.

  29. ProgonB, taken vaginally.

    IME, it’s very easy for women to seriously overdose on progesterone creams.

    Another benefit to using ProgonB is the dose can be fine tuned up and down because each pellet taken vaginally is a low dose. Also, it’s possible to run a proper saliva test while taking it.

    It’s NOT easy to find a good practitioner though. The lab I use, Diagnos-Techs, has a Provider Directory, but even that is no guarantee the MD took the time to learn how to use the test kits.

    I have also consulted with Dr. Mark Rhodes,, and he helped fill in the what was missing from my MDs.

    I have learned a lot from the Yahoo Group I mentioned too.

    Good luck!

  30. Im back with a little bit of diagnoses… have not had all the tests , but I had an ultrasound scan, and my doctor feels that I might have had an unresolved case of PCOS in the past, which may be partly responsible for anovulation and estrogen dominance. Now that seems to make sense to me. Suddenly it adds up.Do you have any ideas on being able to treat this one. I have been told that a hysterectomy is the best way out and I would like to avoid a hysterectomy at any cost.I would love to know if you have any ideas on how to deal with this one . Thanx

    • Hi java, It’s great that you have a diagnosis!

      I don’t know much about PCOS other than that insulin is important. I would definitely recommend intermittent fasting and the ketogenic variant of our diet — lots of coconut oil, about 200 calories of carbs per day from our safe starches, not too many extra calories.

      Best, Paul

  31. Paul,

    Loved this article on healing through nutrition..also wondering your thoughts on the popular colon cleanses, parastite cleanses, etc.. My acupuncturist has suggested trying these cleanses yet Im hesitant as my condition is as of yet undiagnosed (reflux, IBS, etc..) and I do not want to overburden my body. Ive been following your dietary recommendations so working on the food angle..wondering if taking it a step further with herb cleanses is a wise move.


  32. Hi Kayla,

    I’m not sure either. Definitely some people report being helped by them. I do think temporarily starving the gut pathogens can give your immune system a chance to get a leg up, and help give subsequent probiotics a better chance of gaining a foothold. But using herbs makes me nervous, since we don’t really know what’s in them, they can be toxic as well as beneficial.

    In general I think experimentation is in order and that calls for changing only one thing at a time, and waiting for stability before changing the next. Otherwise, it’s hard to know what’s helping and what’s hurting.

  33. I have had autoimmune hypothyroidism (Hashimoto’s, with confirmed elevated antibodies) for years. After researching all sides of the debate about the use of high-dose iodine with Hashimoto’s, I decided it was a good idea to try it. The docs with the most experience doing this (Abraham, Brownstein, Flechas) have all reported good results, and (except in rare cases of autonomous nodules), exacerbating the thyroid disease does not seem to be a real danger.

    My results? On 12.5mg Iodoral per day (the very low end of the dose range used by these docs), my required dose of supplemental T4 thyroid hormone has decreased from 164ug/day to under 100ug/day. None of my docs has ever seen anyone with Hashimoto’s improve like this. My primary care doc (not involved with this experiment, said it was “impossible.”) The progress is continuing, though based on the reports of others I expect it to plateau at some point due to the long-term damage done to my thyroid. I cannot reconcile these results with the notion that iodine is like “fuel on the fire” of autoimmune hypothyroidism.

    My endocrinologist is so impressed with my results that he has started recommending Iodoral routinely to his patients (all of whom are hypothyroid). I asked him about following my antibodies, but he thought it was pointless since he believes no one really understand what those levels mean and how they fluctuate over time anyway.

    I did make sure to follow the entire “iodine protocol” as recommended by Dr. Abraham and the other iodine docs, including selenium, magnesium, vitamin C, and lots of unrefined salt. That may have contributed to my good results.

    The only drawback to my experiment is that I’ve been chronically overdosed on T4 since my required dose is now a moving target and we’ve always seemed to be giving too much even as we continually lower it. My TSH has stayed near zero despite the massive reduction of T4 dose.

    I am waiting on results of a 24-hour iodine loading urine test for iodine and bromine, and based on that I plan to increase my Iodoral dose as needed to achieve sufficiency as measured by that test.

    From what I understand, not all Hashimoto’s sufferers get the good results I have with iodine. I don’t know why. But aside from the few with autonomous nodules, has anyone actually experienced a true flare of their Hashimoto’s? You can’t go by TSH levels alone, since apparently they often rise dramatically for a while (mine didn’t), but with no clinical signs of worsened hypothyroidism and normal free T4 levels. I suspect that TSH spike has sometimes been confused with a worsening of the autoimmune disease.

  34. Hi Bill,

    Thanks for sharing your experience.

    I do believe high-dose iodine is beneficial, and that most problems can be avoided if the dose is increased slowly.

    It also amuses me that doctors think these diseases are impossible to improve. The body is always trying to heal itself. Drugs don’t work, but the medical toolkit needs to expand to include diet, nutrition, and lifestyle.

    I’ve just put up a new post on fasting as a therapy for hypothyroidism, you might want to read that if you haven’t already:

    Best, Paul

  35. I’ve been taking Iodoral since…2008? I’m currently taking 1/2 tablet, or 6.25 mg per day.

    I don’t have a lot of thyroid tests over that time frame, but I’ve been positive for TPO antibodies, then negative. Positive for TgAb antibodies, then negative. TSH has been suppressed (less than 0.1), then not (0.45). FT3 has been normal, then high out of range.

    This is on zero thyroid meds, and gluten free since 2007.

    IME, high dose iodine such as Iodoral is volatile. It clearly affects thyroid. I wish I had kept better notes of the variables relative to my test results!

    My MD strongly recommends testing thyroid AND progesterone by saliva before taking Iodoral and at every increase thereafter. Iodoral will raise progesterone. Eventually, there will be a dose of Iodoral that will produce good thyroid and progesterone scores, sometimes with thyroid meds and/or supplemental progesterone, sometimes without.

    I don’t read many online conversations about Iodoral’s affect on progesterone levels.
    It could be that most focus on thyroid. Another factor could be that so many rely on inaccurate serum tests for sex hormone levels, or, don’t bother testing at all.

  36. Perfect Health Diet » Bowel Disorders, Part I: About Gut Disease - pingback on January 18, 2011 at 7:19 pm
  37. Hi Paul, I have a health concern that I was wondering if you had some insights on. I used to eat a really high carb diet (300g or more) till about Oct last year. I switched to a moderate carb (approx 150g) and have seen some good changes. Lost a bit of weight, have had my menstrual cycles return to normal (once a month instead of once in 2 or 3 months). There has been one -ve change in this period. I have developed a large polyp in my right nostril that bleeds intermittently. I am wondering if this was caused by the hormonal changes. Apparently pregnant women are prone to this type of thing in their nose, but I am not pregnant. But maybe my body normalizing its hormone levels has made this thing grow? I don’t really know.
    I live in Canada and my doc appt is still several weeks away (despite a referral in November). I expect diagnosis and treatment to be drawn over several months…and was wondering if there was something I could do meanwhile. Any specific nutritional recommendations that you might have?

  38. Hmmm … I’m afraid I don’t have specific knowledge about polyps and hormonal influences on them. I think most often these things are caused by local infections, and our normal diet and list of supplements is pretty good at maximizing immunity. See for the supplements.

    Hopefully your doctor will be able to give a specific diagnosis.

  39. Hello,

    Thanks for all of your help with my digestive concerns over the past few months. I am not usually one to post lab results, however, just came from the doctor and was dismayed to note that my thyroid is elevated again (TSH–3.4, free T3 is low at 50 (70 is starting range), as is my cholesterol (total is 416, LDL 281 and HDL at 114 (I think). My thyroid has been up and down since my stomach issues started (bloating, food intolerance, reflux, chemical sensitivity) going from .6 – 4.0 since late 2009. I also was doing extreme low-carb dieting for a while and thought that the thyroid issue resolved with my recent weight gain and eating starches now. Is it possible that the thyroid is being impacted by gut pathogens, and the cholesterol reflecting my body fighting something? I also have a family history of Hashimotos so I feel like Im chasing many things at once, and hesitant to start thyroid meds now. Perhaps iodine would be helpful? Very interested in your feedback and thoughts if this could all be related to the gut.

    The blog/book has been so helpful!


  40. Hi Devi,

    Do you have symptoms of hypothyroidism? Weight gain is one symptom, are there others? If you have symptoms then I would definitely look to get thyroid hormones while fixing it. I would start iodine and selenium supplementation regardless of whether you have hypothyroid symptoms, but be sure to start small with iodine and work up slowly.

    Thyroid problems often do follow gut problems. Have you still eliminated wheat?

    I assume you’ve discussed possible causes of the high LDL with your doctor? No kidney disease, no diabetes?

    If I recall you had Candida overgrowth in the small intestine or something resembling it — is that right? No change since December?

    Our supplement regimen is very good for Candida, including iodine and selenium, so it would be good to be on that.

    Best, Paul

  41. Do you recommend iodine supplementation for people with Hashimoto’s (i.e. are you in the Brownstein or Kharrazzian camp)? Both put up good arguments.

  42. Hi Poisonguy,

    I still have a somewhat open mind as it’s clear some people with Hashimoto’s have experienced benefits from high-dose iodine and some have run into trouble.

    Since even non-Hashimoto’s people with healthy thyroids and immune systems will run into trouble with iodine if they increase the dose too fast, it’s possible that a significant fraction of the people who had trouble might have been OK if they had increased iodine intake more slowly.

    If iodine is raised slowly, then I think any damage is likely to be mild and healable. So my recommendation is that people try iodine. Starting low and increasing very slowly, and monitoring thyroid status with their doctor. If negative effects appear, then back off.

    That way, the people who benefit can obtain the benefits … and maybe nearly everyone can do it successfully.

  43. Hi Devi,

    did your gut/thyroid problems began when you started a low/zero carb diet?

    I ran into similar problems (low FT3, bloating, food intolerance, acid reflux, high LDL cholesterol) and adding some safe starches made me feel better!
    I’ll test my thyroid soon.

  44. Hello,

    In terms of hypothyroid symptoms, I havent gained any extra weight, I was trying to gain weight as it was initially hard to put on weight when my stomach issues began. My TSH was 4.0 when I was underweight a year ago. I am more tired and constipated than usual, although that is resolving with the strong probiotic I am on. I am having an open mind to start thyroid hormone.

    No problems with my kidneys and no diabetes. I have been gluten free for a over a year and follow the PHD health suggestions. The working hypothesis right now is candida overgrowth in the small intestine. I am having trouble integrating supplements as most of them bother my stomach, its very easily irritated. Do you have any suggestions for gentle ways of taking in iodine/selenium, and what iodine dosage do you suggest starting at for the very supplement sensitive person? Lastly, what is your thoughts on family history in terms of illness if most is based on pathogens? My mother suffers from a similar stomach condition as did her mother, etc..

    Interestingly my symptoms became more intense when I added in safe starches after five years of low-carb, although I believe that way of eating led to the damage. Glad you are feeling better!


  45. Hi Devi,

    With iodine you could try a 500 mcg kelp tablet for a month, then if that goes well 2 a day of those for 1 mg from kelp for the next month. If that goes well, 4 a day for the next month. Then if that goes well, a quarter Iodoral tablet (cut with a razor blade) for 3 mg/day.

    Candida does sound like a plausible explanation for your symptoms. I’m not aware that it can affect the thyroid directly, but it does lead to greater iodine usage by the immune system and thus can create iodine deficiency hypothyroidism; also it increases gut permeability and food toxins might contribute to thyroid problems.

    For selenium you could try Brazil nuts or foods like liver. For iodine I prefer the supplements as that allows you better control over dose, but you can take them with food.

    Many infections are passed on maternally, for instance Candida infections are often picked up by the infant as it passes through the vaginal canal during birth. But it would be a surprise if the symptoms were very similar. I’m not sure how to account for 3 generations of a similar stomach condition.

    You might try rice syrup as a source of carbs, the glucose sugars are quicker to digest than rice itself and that may keep more of them away from the pathogens.

    Also, lately I’ve been finding that lemon juice can be quite helpful, so I recommend putting lemon slices in water or tea and drinking it regularly.

  46. Thanks for the feedback, Paul. That’s my take on it as well given my limited foray into this stuff as we speak. I’ve recently started iodine myself (1 mg/day), but wondered for my wife. I think I’ll have her start with 1 mg every other day and see how that works out for her.

  47. Thanks, Mario.

    It looks like (1) hypothyroidism usually leads to Candida infection, and (2) people with genetic deficiencies in anti-Candidal immunity ( or immunosuppression of fungal resistance due to cancer will get extensive fungal infections including fungal thyroiditis.

    Possibly an inherited immunodeficiency could explain Devi’s mother and grandmother; possibly the hypothyroidism could be contributing to her gut problems.

    It seems she should normalize thyroid hormones to help her gut.

  48. What constitutes the presence of thyroid antibodies. I have had antibody tests (all the different kinds) dozens of times and they tend to fall any where from 3-10 on a scale of 0-30 or 40. IS the presence of anything above 0 indicative of an autoimmune disorder?? Everything with my thyroid is fine except slightly low normal free t3.

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