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. Hi John,

    Everybody has some thyroid antibodies. No, it’s not indicative of an autoimmune disorder.


    Dear Friends,

    I have hypothyroidism.

    I would like to get answer for my following questions:

    1) what are the nurtilite, supplements , i can take?
    eg. omega-3, vitamin d3, cal magnesium, multivitamin, protein, vitamin c, lechtin E?

    my emial id:

  3. Hi Mrs. Shankar,

    I would recommend our regular diet and supplement program, rather than any one supplement. See

    Minerals like magnesium, zinc, iodine, and selenium are important. Vitamin D is important for immunity and is best obtained from the sun.

    Best, Paul

  4. What is your opinion on brown rice vs white rice. What type of rice specifically do you recommend

  5. Hi John – White rice is better … fewer toxins.

  6. Hi Paul,
    You mention Ferritin should be 50 ng/ml or higher.
    What would be a good upper limit for Ferritin in your opinion.

    I did a bit of looking around and found varying recommendations for the optimal upper limit, these were; 60, 75 and 90.

  7. When Paleo Isn’t Enough, Part I | The Lazy Caveman - pingback on June 1, 2012 at 1:12 am
  8. Hi Paul,

    I had a metamatrix stool test and found h pylori, breath tests and found sibo and fructose malabsorption, I also can’t tolerate coconut oil or caffeine for some strange reason. I feel mentally my best when I eat low carb, but that has caused a uti in the past, and if I eat too low carb I can almost feel a uti coming on. I also feel good when I fast, but it seems like lately it has caused hypoglycemic like feelings, I start to get dizzy. I’m not sure where to go from here? I feel slightly depressed and tired all the time now, and I can’t seem to take and vitamins because they seem to make me feel worse. I’ve looked up fructose malabsorption lists online and try to adhere to a diet that won’t cause and symptoms for me. I also take hcl capsules. Any advice?

    • Hi Alex,

      Well, you could get a doctor to treat the SIBO with antibiotics. You could look for treatment for the UTI. If it gets worse on low carb then it might not be bacterial, perhaps it is fungal? In any case it sounds like the next step is to get medical help.

  9. I’m almost hesitant to try antibiotics because of the likeliness of reoccurrence of sibo. Or is there anything I could do to keep sibo from coming back after a course of antibiotics?

    Also, the metamatrix stool test didn’t show any yeast/fungi? It just showed that my bacteria was unbalanced, low lactobacillus, bifidobacteria, prevotella, and fusobacteria and high streptomyces, mycoplasma and E. coli. I’ve been drinking kefir and it improves my energy and constipation but I’ve read adding probiotics with sibo isn’t a good idea…

    • Eat fermented vegetables while on antibiotics, and support stomach acid and bile production.

      I think probiotics aren’t bad in SIBO, but they aren’t therapeutic for it, improving digestion and possibly oral health and immune function are major steps for SIBO.

      • Thanks Paul, my one attempt at fermented vegetables yielded moldy vegetables 🙁 I’ll have to re-read that section again. Do you think I should continue with the kefir? I haven’t noticed any negative side effects.

        As for the bile, I’ll increase my egg yolk consumption and continue with the hcl for stomach acid.

        What are your thoughts on natural antibiotics, like oregano oil, goldenseal, or something like that? Or are they too mild to clear up sibo?

        • Natural antibiotics are too mild to clear up SIBO by themselves but over time as part of a good diet antimicrobial herbs can have good effects.

          • Any thoughts about biofilms in fructose malabsorption? The Wikipedia page mentions that a mucosal biofilm is formed. Would it be smart to take something for the biofilm?

          • Good question, I don’t know. Might be worth a try. Digestive enzymes are a good start.

          • According to this recent 2014 study:
            herbal therapy can be as effective as antibiotics for SIBO.

            I’ve been researching SIBO as I’ve been advised that it is highly likely I have it due to my elevated stool sIgA and Klebsiella p. infection (Dr Jill Carnahan wrote on her blog she often sees klebsiella infections together with SIBO).
            I was previously trying to include all your recommended supplements but started feeling worse, and felt better once I stopped all supplements. Haven’t figured out why or specifically which ones were causing me problems. I’m now back on the Vit C and K2 and fine with those. Getting there slowly with incorporating all your advise.

  10. Paul,

    I’ve been trying to figure out what would be the best diet for me right now to heal my gut, I haven’t eliminated nightshades, dairy, egg whites, nuts, sugar and alcohol. Is that something that should be completely eliminated until I’m rid of the sibo, or should I eliminate for a week or two and introduce back in to see if its affecting me? Also, carb sources for sibo and fructose malabsorption? I believe I can tolerate white rice well? I also eat potatoes and some berries but wonder if those should be taken out of my diet too.

    • Hi Alex,

      It’s hard to generalize about gut disorders so you have to experiment and personalize your diet.

      It’s always good to do controlled experiments, change one thing for at least a week, then change it back, maybe duplicate the experiment several times if you think there is an effect.

      In general minimizing fructose in SIBO is a good idea, similarly minimizing fiber/starch in colitis is a good idea. You can experiment whether something like rice or potatoes, or a pre-digested sugar like dextrose works better for you. If you tolerate rice well that is a good sign. If you tolerate potatoes and berries then eat them, both promote healthy probiotic flora and are excellent foods.

      • I’m excited to say I think I finally found a magnesium supplement I can tolerate: magnesium sulfate. I had bought some for baths, then decided to try 1/4 tsp in water, and in 15-30 minutes the sun all of a sudden seemed to shine brighter! It was odd, I assumed maybe the placebo effect. When I tried it again later on, I again became more relaxed and happier 🙂 I’m so excited.

        Anyway, I stumbled upon this site for making mineral water:
        What are your thoughts on this? I’m curious to try it since the magnesium sulfate alone had such wonderful effects on me. Maybe I should be balancing it with other minerals?

        • Good work Alex.

          I formulated a similar recipe for homemade mineral water, but later decided that it was better to get most minerals from foods (eg bone broth for calcium, salt for sodium, tomatoes etc for potassium) so only magnesium and maybe sulfate are problems. That suggests an epsom salt drink, but oral intake of sulfate is not without risk, it can promote sulfur-utilizing bacteria in the digestive tract which may cause problems. So keep an eye out for possible digestive issues, and don’t overdo the oral magnesium sulfate to the point of creating bacterial overgrowth.

          • Thanks for the warning. Is there anything specific I should be looking out for? How much is too much? 1/4 tsp a day ok or is that too much? According to the mineral page that should be about 120mg of magnesium.

          • Just be on the lookout for digestive issues, esp gas or smelly stool. Bacterial sulfur metabolism produces hydrogen sulfide which is the rotten egg smell.

          • Well the magnesium sulfate started giving me negative side effects right away 😥 I guess I’m sticking with baths. My digestive sibo symptoms seem ok as long as I follow a low fodmop diet, but the fatigue I can’t seem to shake. I can barely function some days if I don’t rest a lot. I also have to eat regularly or I start to get dizzy 🙁
            I’ve decided to attempt the elemental diet for 2 weeks and if that doesn’t help I’m giving in and trying antibiotics.
            With the elemental diet I found one called Absorb Plus that looks ok, you add your own fat and I figured I’d add mct oil and also sip bone broth. Supposedly it has a high cure rate for sibo. Another idea was to do the elemental diet either every other day, or for breakfast and lunch and just consume meat and fat. Any thoughts on this?
            Also, you said probiotics aren’t therapeutic for sibo, do you believe they hinder progress? A cup of kefir has been the best thing I’ve found for my fatigue.

          • Hi Alex,

            Kefir has yeast which compete with the bacteria, that may be why it helps. Kombucha might help too.

            Other aids like DGL, digestive enzymes, undecylenic acid, and various essential oils and herbs have been reported to potentially help. I don’t have a strong opinion on any of them. DGL increases mucus which might help.

          • The elemental diet pretty much sucked, I quit after 2 days…on the plus side I made my first bone broth a week ago. I could kick myself for not trying this sooner. My energy and mood have improved so much! 😀

          • I just realized I have a hard time digesting fat or fat soluble vitamins. When I drink bone broth I have to have a teaspoon of bitters afterwards or else I get dizzy and nauseas. sometimes i get dizzy and nauseas anyway….Is there anything else I could do? I would really like to supplement with vitamin d as I am very deficient.

  11. Hi Paul,

    Do you have a recommendation for a multi-vitamin?

    Also, I’ve been trying to make beef bone broth but the marrow won’t dissolve 🙁 Is it because I did it in a slow cooker? Or did I not use enough ACV? (only about 2 tablespoons)


  12. Paul, I can’t seem to get melatonin to work for me – no matter the dose – 300 mcg of time release versus a dose of 1 mg taken with a 5 mg time-released tablet. I always wake after 4.5-6 hours into the night.

    I haven’t tried the exact 1 mg sublingual melatonin you recommend on your supplements page, but I did order it, in case there is a difference between sublingual and the nature’s made melatonin I had purchased, which does not say sublingual.

    Do you have any other advice on melatonin supplementation (or other advice) to avoid early waking?

    I’ve always been a nervous kid – for example, not being able to fall asleep before the first day of school – more of the skimp on sleep during the week and then catch-up on the weekend type, but as I became an adult, I was no longer able to do this. My body started wanting to wake at the same time, no matter when I went to sleep.

    I found that I was able to sleep through the night for a while after supplemeting GABA, phosphatidyl serine, and L-Theanine. I was taking about 100 mg of each, two or three times a day and I think they lower cortisol levels, but I stopped because you wrote that you generally don’t think amino acid supplementation is good (except for Lysine for cold sores, which works! but generally following your diet also does that), and like the mice fed trypophan who began tearing their hair out, I wondered about causing some other bad effects.

    Some other things I found that helped (calms forte – a homeopathic product, but it has oat seed, which alas, contains gluten, possibly 30 ppm, because it’s a homeopathic remedy), blue light blocking glasses, and trying to avoid eating a big meal before bed, which is sometimes difficult because I get home late from work.

    The intermittent fasting I can do, but I feel stressed by it since I’m not sleeping. So sometimes I do ten hours, sometimes I do 8 or 9 hours of eating throughout the day, and I try to always maintain eating schedule during light hours. I take Vitamin D and receive a lot during the summer, but I must admit that with my job I get a very small amount during the day (and I wear contacts, so no sun in my eyes). I also lift weights in the mornings before work, because this has also sometimes helped to tire me out enough to sleep well. On the other hand, with poor sleep, recovery is also poor and my muscles will ache for longer than when I have slept well.

    I wonder if this inability to sleep well could point to a brain infection of some sort, because my melatonin production, despite sleeping in a completely darkened room, is clearly mis-timed and varies significantly from day to day.

    However, the other thing I should mention is that when I go on vacation I sleep much, much better – and I end up in a somewhat biphasic schedule – getting about 6 or 7 hours at night and 2-3 hours in the afternoon. Sometimes I feel that I sleep better in the afternoon than at night, that it’s a much more rested and deep sleep. In the book, “Mutiny on the Bounty” – the island natives also slept this way – about 5-6 hours at night but the book says you could find people gathered at the fire, and then the island natives (the cook islands I believe) took naps in the afternoon, when the sun was extremely hot. The sailors visiting the island also fell into this schedule, similar to the sleep historian Roger ekirch’s research, and I wonder if any of the other readers have been able to switch from biphasic to monophasic sleep?

    I wonder if there would also be an evolutionary reason for breaking sleep into 2 phases? my ancestors would be somewhat tropical/islander in origin.

    I’m only 27 and when you wrote in your book, “Shou-Ching and I had regained our health – we felt like we were in our 20’s again!” and my only thought was, “Gosh, I hope I don’t feel like I do now in my 40’s!”

    I’m not sure I’ve ever had good health in my 20’s, sadly, because of my sleeping issue, which I admit is entirely because of several things – 1) poor sleeping habits for several years, and 2) the mental blockade that even with natural supplementation I can’t attain a good night of sleep. I suppose a tendency to overthink sleeping could be the 3rd cause of the situation that I am in.

    Thanks for you blog and book – I bought copies for family and appreciate everything you and Shou-Ching do and have done.


    • i forgot to mention – I did my first 36 hour “fast” (I ate some vegetables cooked in beef fat/broth but no protein) with coconut oil, and it was the first time I was successful fasting! I have been following PHD for about 3 months now and I am happy with this development because previously, taking coconut oil made me completely nauseous. Now I am able to withstand a whole tablespoon+ per hour! Two+ tablespoons will still make me feel a little nauseous, but I feel certain that I had some type of gut dysbiosis which is resolving because of this change in my tolerance to coconut oil. One of the Q&A on your site (jersie) says, “There were times I felt worse on VLC and times where I felt better.” – I think this could be true for me too. Any news back from her on her situation? Thank you again.

      Small steps, every day.

      • Hi Lyon,

        A whole tablespoon per hour adds up to a lot of coconut oil. Is there a reason you are taking so much? I think it’s about 120 calories per tablespoon so 16 tablespoons per day is already 2000 calories.

        • One of the reasons I had not tried fasting earlier was because coconut oil had made me so nauseous. Now I take 1 tbsp every 2 hours or so. It’s the first time I’ve tried intermittent fasting without calorie restriction but also I’m so glad that I can actually do it! as you said, when your health was not so good, it was much more difficult for you to fast. I think that this time last year, on VLC, improper paleo, I could not have stood to fast – because of my poor health, and because I couldn’t stand coconut oil. So thank you for the idea that one can fast, and still maintain calories.
          Thank you as well for your response.
          God Bless.

    • Hi Lyon,

      I am not opposed to amino acid supplements for therapeutic reasons, just for general use. It sounds like they were benefiting you and if so I think you should consider them.

      Phosphatidylserine is a powerful phospholipid and it can be beneficial but also harmful and it is hard to control the dose. I think if you benefit from it it suggests you are probably deficient in a number of other phospholipids to, eg phosphatidylcholine, phosphatidylinositol, phosphatidylethanolamine, and would benefit by eating phospholipid rich foods like liver, brain, marrow, and egg yolks.

      I’m not sure about the merits of afternoon naps. Sleep patterns are an interesting question but I’m not expert enough to comment on whether that pattern is chosen for health, or just as a way to kill time in the hot part of the day.

      I do think going out in the sunshine is very important. Just 10 minute walks or jogs outdoors every 3-4 hours will do you good, even if you have contact lenses in.

      • Thanks for the suggestions Paul. Another reason I stopped supplementing with those supplements was that they seemed to help on improper paleo – i.e. before PHD they were a huge help, and not as much now, so perhaps eating liver, marrow, and egg yolks for the past 3 months have increased the phosphatidyl serine significantly in my diet.

  13. Hi Lyon,

    I remember reading that if taking melatonin does not help (& possibly make things worse) then melatonin is likely not the issue.

    In otherwords, the causes for your sleep issues lie elsewhere.

    You can get a saliva test done to confirm melatonin levels. You take a sample at midnight & another in the morning.

    & it is recommended to test for saliva cortisol levels as well. you need to take 4 samples during a day so you get the ‘full picture’…of what’s going on with cortisol levels thu-out the day.

    • Thanks Darrin for the advice! I have a saliva cortisol test in my home, but haven’t taken it because I read here:

      that there are certain medications which can affect the results of the test. I’ve been following the PHD minerals supplementation – 1 tablet of zinc per week (~25 mg) and occasionally melatonin, and I believe that site says one should avoid those medications if you do not wish to alter the results of the salivary test.

      I hope it’s not too soon to report some improvement – I don’t need melatonin to fall asleep, but taking 500 mg of the sublingual melatonin recommended here for two nights in a row, when I woke at 2 AM in the morning, has helped me sleep more soundly through the rest of the night. I believe your melatonin is supposed to be highest then (I can’t quite find where I read this). But as well, in case I had some sort of virus causing an issue, I made sure to get sun directly on my eyes. who knows, it could be a placebo effect, but if my journey can provide some kind of help for someone else I hope it does.

      God bless this site and the people who help run it, by providing reasoning, logic, and information.

      • i also have no trouble falling asleep.
        but will wake in the early hours (usually between 2 am & 4 am), this will happen every night (bar once in a blue noon).

        some people may say this is normal biphasic sleep, but not me. I feel better when i sleep thru.

        i have experimented with all sorts of changes, too many to list, but nothing really works.

        however, i have not tried the sublingual melatonin taken when woken in the night.
        So i will order the 1 mg source naturals sublingual & give that a go as well.

  14. I developed in 2009 secondary TMAU, could this be related to gut dysfunction. I have chronic constipation since I was a child. I’m now in my 60’s. I need to reverse this horrible condition of 2nd TMAU, can you help with advice?
    Thank you.

  15. I have to ask in hope that this question is answered.
    What is your opinion on the relationship between AMPs and rosacea, specifically ll-37 cathelicidin. I am male with bad rosacea and was previously doing VLC but am now trying PHD. Thank you for your work.

    • Hi Miles,

      I think it’s interesting from a mechanisms perspective but it doesn’t tell us much about treatment. It shows that something is generating serine proteases that cleave cathelicidin. But it doesn’t say what or how to arrest it.

      To me the main aspect of rosacea is that immunity is somewhat suppressed leading to various skin infections/problems. It seems to clear up pretty effectively with PHD including vitamin A, vitamin D, zinc, iodine, intermittent fasting, circadian rhythm entrainment, and the other basic PHD diet+lifestyle interventions.

  16. Hi there,
    Thank you for your amazing work and information. I suffer from Issues such as bloating, constipation, no appetite, burping, gas. I also have rosacea. I am of Chinese/Vietnamese descent and never see someone of my ethnicity suffer from rosacea.
    Apparently there is strong evidence that rosacea is a symptom of SIBO. I really believe i may have SIBO.
    From reading your articles i believe you would recommend i eat a high starch diet. Thank you for clearing this up as i believed for a long time starches are bad for SIBO and that i must consume lots of fats to cure myself through nutrition.
    I also notice excess mucus when wiping after bowel movements, should i supplement Bifidobacterium bifidum to help this issue?
    I truly hope you can reply to this. Thank you very much.

    • Hi Samara,

      We do not advocate a high starch diet so much as a moderate starch diet. We recommend getting 30% of calories as carbs and about 20-25% of calories from starch. This is less than most people get, but it is the right amount for good nourishment.

      Some keys are circadian rhythm entrainment, intermittent fasting, and good nutrition including vitamin A (liver, spinach, sweet potatoes, carrots), vitamin D, vitamin C, zinc, iodine, and collagen from bone and joint soups and stews. Fermented foods and a diversity of vegetables and fiber can help build a better gut flora. Zinc-copper balance is important.

      • Hi Paul,
        Thank you for replying. I asked about high starch because i really believe i have an issue with my small intestine. I find fermented foods cause me to have stomach discomfort and flare my rosacea.
        Ive recently followed all your supplement recommendations, looking forward to healing with PHD. Is there any probiotic you would recommend?
        Can you please tell me why i have excess mucus in stools, and phlegm in my throat, im very sorry to bother you but no doctor or even chinese doctor can figure out why i have these symptoms or cure them.
        Im willing to pay you an amount of money for an email consultation with you if that is ok?

        • Hi Samara,

          Here’s a list of some conditions that can generate mucus in stool:

          I’m afraid I don’t do consultations. If you want to know the specific cause, a doctor is the best resource.

          But, speaking generally, it is likely due to some sort of intestinal and sinus infection that triggers mucus production as part of the immune response.

          The most helpful things will be vitamin A (liver, spinach, sweet potatoes, carrots; if you don’t eat liver weekly then supplement preformed A from cod liver oil), vitamin D (sun or supplements), and vitamin C to near bowel tolerance. Make sure you optimize zinc and supplement a low dose of iodine daily. Entrain circadian rhythms.

  17. Hello, I’ve had some strange health problems the past few months and was wondering if anyone had any thoughts on what exactly is going on:

    A few months ago I tried supplementing with iodine to hopefully heal some toenail fungus and maybe give me some more energy. At first it went fine, but at a certain point it was like I developed a sensitivity to it, and even one drop would cause my throat to get tight and make me feel like achy like I had the flu, but with no fever, so I stopped the iodine.

    A bit later I tested as Vitamin D deficient (about 20) and so started taking some D3. What was weird was that the D3 made me feel tired and achy, almost like the iodine. I could handle it for a few days, but as time went on, it became intolerable and I quit the D3.

    Then I tried adding some vitamin k2, first in mk7 form, then in mk4. Both forms had a similar effect, though the mk7 seemed more potent, so I quickly switched to mk4. K2 made me feel absolutely great–full of energy, better sleep, increased libido, etc., but I noticed after about a week that I was getting heart palpitations and chest pains. Around the same time I developed a bunch of eye floaters, and it turned out I had a hole in my retina, which had to be lasered. Eye doctors don’t think the cause was a vitamin, but the timing seems pretty suspicious to me.

    Anyway, I’m scared to take K2 anymore, if not for the eye, then certainly for the heart, but I still have this problem where vitamin D makes me feel extremely achy, almost like an immune reaction. Also, this didn’t happen prior to the iodine thing. Prior to that, I had been able to take vitamin D without much problem, except maybe a little sleepiness. The sun seems to have a similar effect to the pills, but milder.

    Even weirder, I’ve noticed that my reaction to magnesium has totally changed since taking the K2. I knew magnesium was also a “co-factor” for D and so I had been trying to take that along with it, and it mostly created a mild, pleasant relaxation. Now, I can no longer take magnesium because it fills me with so much energy I want to climb up the walls and can’t sleep all night. It makes every muscle in my body feel like it wants to tense up at the same time.

    I feel like my thyroid and/or vitamin d/calcium/magnesium system is all screwed up, but I don’t know exactly how, or how to fix it.

    Tests I’ve done show low-ish blood calcium, lowish vitamin d, a low-ish but not extremely low tsh (it dropped after I took the iodine but then came back up, albeit not to its original level–it’s ranged from 1.9 before the iodine, to .9 after, and 1.5 more recently).

    I have not had 1,25 D or parathyroid tests, but I’m looking into that next.

    Any thoughts or suggestions? Thank you.

  18. Dr. Jaminet, what do you think of the use of topical magnesium supplements, such as magnesium oil spray, lotion, gel etc? Do you think that internally taken supplements (such as pills or Natural Calm) are absorbed more efficiently? I’m just starting on this PHD path and am a little wary of taking all the recommended supplements – I don’t do well with pills. Thanks.

  19. Paul, will supplemented glutathione (in liposomal form) down regulate the body’s own glutathione production? If so, could glutathione supplementation be pulsed in order to avoid this effect. I feel great when on a high does of glutathione (and don’t t operate NAC well, hard on the stomach) but am worried about the long-term effect


  20. I know this page was written in 2010 so this comment might go unseen for quite some time.
    You recommend a multivitamin as a starting point for IBD patients, & the other supplements listed here in addition to the multivitamin. What brand multivitamin do you recommend? I was looking at the Garden of Life Vitamin Code for women because it seems to have modest amounts of most nutrients, provided you only take 1 capsule a day. What do you think?
    Anyone else who sees this comment is free to chime in!

  21. Hi Paul,

    Your recommend Thyroid hormone sufficient to bring TSH below 2.0. My TSH levels are 3,43. How much thyroid hormone (levothyroxine) would I need to take daily to bring TSH below 2.0? Would 50 mcg be enough or maybe less? P.S. I know you can’t give medical advise but I would like to know what you would recommend.


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