Q & A

Q & A

This page as an open thread for reader questions, especially questions about personal health concerns.

I am putting this page up as a way to share knowledge — my knowledge with questioners, but also so that others with similar concerns can read the conversation, and readers with relevant knowledge can chip in with their own thoughts.

Please keep in mind that I can’t research questions in any depth, so my answers should be considered tentative, incomplete, and subject to later correction. Also, I am not a doctor, and nothing I say should be construed as a substitute for medical diagnosis and treatment. I am only sharing opinions about disease origins and general therapeutic strategies which may or may not be applicable in any given case.

To get the page started, I’ll put up a few questions from recent emails. Here is an index by disease, with clickable links:

And here are my answers.

Chronic Lymphocytic Leukemia (CLL)


Been following your work on the PHD before the publication of the book and commented on my CLL and the usefulness of Vitamin D once on your blog and you responded to keep an eye on my Vitamin K intake, which I do now.. Am fortunate in a way to have my form of CLL as it indolent which gives me the opportunity to experiment without the pressure of undergoing conventional treatment. The PHD, I think, is helpful in this regard.

Wonder if you could point anything out to me that may be useful. Anything at all. And I will be happy to share with you my results.

Surely you know of the helpfulness of green tea with CLL. You may not be familiar with research that points out that those with low levels of Vitamin D need treatment for CLL far sooner than those with elevated levels.

Feel strongly that your version of a ketogenic diet would be helpful but also feel I need some direction in this area. Do you have any suggestions?

Warmest Regards,


Hi A,

I remember your comment, thanks for writing back. I’m glad you’re enjoying our diet and wish you the best.

Thanks for the tips about green tea and vitamin D. Neither one surprises me.

Most likely CLL is caused by a viral infection. So enhancing viral immunity is probably a good idea. Good strategies may include: (1) low-protein dieting, which inhibits viral reproduction and can promote autophagy; (2) maintaining high vitamin D levels; and (3) intermittent fasting, which promotes autophagy.

Some food compounds have been reported to have antiviral effects. An example is green tea catechins, eg http://pmid.us/16137775, http://pmid.us/18313149, and http://pmid.us/18363746, and this could be why green tea is helpful against cancers, http://pmid.us/21595018, which are usually viral in origin.

I might search Pubmed for herbs and spices with antiviral effects, and use them abundantly in cooking, along with antiviral foods. Turmeric / curcumin is a good choice, this needs to be taken with black pepper to enter the body. See http://pmid.us/21299124, http://pmid.us/20434445, http://pmid.us/20026048.

Coconut oil / lauric acid also has some antiviral properties, so inducing ketosis with coconut oil could benefit you even aside from the ketosis. You could also try monolaurin supplements which may enter the body better and which some people have reported to help viral infections.

You might also try HDL-raising tactics as discussed in this series: HDL and Immunity, April 12; HDL: Higher is Good, But is Highest Best?, April 14; How to Raise HDL, April 20.

Another possible tactic is high-dose riboflavin with UV exposure on the eyes. This requires going outdoors at midday and not wearing glasses or contact lenses. Riboflavin+UV is toxic to blood-borne viruses, and the retina is a location where UV can reach circulating blood cells. Sun exposure will also help you optimize vitamin D.

That’s a few ideas, at some point I’ll do some research to come up with more and do a blog post. Do keep me posted on your results!

Best, Paul

Bloating, acid reflux, anxiety, depression, hypoglycemia, hypothyroidism, fatigue

Just came upon your website and had a question for you. I have had some health concerns for the last four years, bloating, acid reflux, anxiety, depression, hypoglycemia symptoms, female complaints (I am in my forties), thyroid antibodies at 333, weight gain around my middle and too tired to work out like I once did. I used to be fikiiled with energy and great health no depression or anxiety. My doctor thinks these symtoms are all from peri-menopause and wants to treat me with Zoloft.

Needless to say I have tried to avoid the Zoloft. I have tired every avenue out there to cure myself. Most recently the Primal type diet. When I eat no grains or dairy I get horrible hypoglycemia symptoms and don’t feel great like everyone else on a low carb diet. I feel weak and more anxious. Do you think your diet would be easier for me with the addition of rice and potatoes?


Hi G,

Yes, I do think our diet will be better for you. You should eat enough starches to avoid hypoglycemia.

The key thing for you is treating the infections which are consuming so much glucose and making you glucose-deficient if you don’t eat enough carbs. Whatever pathogen(s) this is, it seems to have infected your gut and caused the various gut problems; circulating pathogen-derived toxins and immune cytokines are probably responsible for the anxiety and depression. Hashimoto’s hypothyroidism may be either due to circulating toxins or a thyroid infection.

I would suspect some kind of protozoal or parasitic infection due to the hypoglycemia, but what I really recommend is getting your doctor to have a stool sample analyzed for pathogens. Metametrix has a good test. Once you know what pathogen to treat, and get on a better diet like ours, you should improve quickly.


I am writing on behalf of my mother … We live in Dhaka Bangladesh …

Before her illness, my mom was 105 lbs, 5 feet tall and always 10ft tall in spirit…. When she was diagnosed with Lupus at the age of 30, we were all overwhelmed and out of our depths. My beautiful, athletic mother was in a wheelchair and given 6 months to live….

The doctors has advised her to eat literally nothing, minimum protein (1 small piece of chicken/fish, limited to 20g protein per day), only 2-3 types of vegetable and 2-3 fruits and of course lots of carbs to apparently compensate for her failing KIDNEY and LUPUS. She is on tons of medication, no food except the wrong foods (carbs) and in chronic pain. She currently weighs 139 lbs.

Please advise. — S

Hi S,

I believe lupus is a catch-all diagnosis for a variety of conditions which are probably caused by undiagnosed infections. In the US the infections are usually bacterial. I’ve known several people with diagnosed lupus who were cured by antibiotic treatments – in one case the problem was Lyme disease (Borrelia). I have no idea what the likely pathogens would be in Bangladesh. If she does better on low carb and coconut oil, that indicates bacteria; if she does better on high-carb, that indicates protozoa.

A healthy diet is very important. It is very bad advice to “eat literally nothing,” it is essential to be well nourished. Protein is necessary for healing and immune function, and 20 g/day is too little. Fasting is good, but it should be intermittent – not starvation! She needs healthy fats, more protein, and lots of micronutrients. Eggs, shellfish, seafood, bone broth soups, vegetable soups, and fermented vegetables may all be helpful. Coconut milk is probably good for her. You should basically follow the program in our book.

I would try to put her on a good diet, give her a little time for kidneys and other tissues to heal, and then try antimicrobial medicines. Usually, if they’re not working, then you don’t notice an effect. Any strong effect, good or bad, means they are working. Bad effects mean that pathogens are dying and releasing a lot of toxins as they disintegrate. If this occurs, detox aids (salt, water, and one of cholestyramine/charcoal/bentonite clay; also glutathione supports and vitamin C) will help.

Please stay in touch and let me know how things go.

Best, Paul


Jersie wrote:

I’ve suffered from depression for decades. A few months ago, I decided to try the Dr. Kruse protocol for jumpstarting leptin sensitivity and 2 interesting things happened.

When I went very low carb – below 50 gm -. I had half-day periods where the depression suddenly lifted (something that has rarely happened otherwise). However, I also suffered from darker than normal periods.

I stopped the Dr. Kruse protocol after 6 weeks, and went back to regular paleo (approx. 200 – 300 gm. Carb/day). I’m now generally more depressed than usual, without the good periods.

These changes seem to indicate that I can have an influence on my depression with diet, but not sure what diet to try. Thoughts?

Hi Jersie,

I think your experience on very low carb is diagnostically telling.

I would interpret it this way:

  1. Your depression is caused by an interferon-gamma mediated immune response in the brain, probably caused by a viral or bacterial infection. This leads to tryptophan being directed away from serotonin and toward the kynurenine pathway. So you have a serotonin deficiency and kynurenine excess.
  2. A ketogenic diet is both therapeutic (promotes immunity against bacterial and viral infections) and mood-improving (clears kynurenine).
  3. However, you are at risk for hypoglycemia in the brain (especially if the infection is bacterial) and hypoglycemia causes irritability/anxiety and can aggravate depression.

So the very low-carb diet had mixed effects (ketosis, hypoglycemia).

What I would do is follow our ketogenic diet advice. Eat at least 50 g/day carbs from starches to get sufficient glucose, plus sufficient protein to reach 600 calories/day protein+carb, but add in large amounts of MCT oil or coconut oil. Also, do intermittent fasting – eat all the carbs within an 8-hour window; eat at least half the MCT oil in the 16-hour fasting window.

Once on a good diet, I might experiment with antibiotics to see if they relieve symptoms.

Please let me know how things go.

Leave a comment ?


  1. Paul,
    do you have any suggestions for tweaking PHD in the presence of recurrent SIBO (methane-positive)?

    I tolerate fiber (and FODMAPS, except for lactose) very poorly, and thus can’t eat a lot of vegetable matter. Best tolerated carb is white bread and Jasmine rice (but already have some arsenic on HTMA testing so trying to eat less rice). I worry about the long-term effects of the low levels of vegetables/fruit/berries in my diet, but while antibiotics as suggested by Mark Pimentel work short-term, symptoms recur, even when using d-limonene, Mg, LDN to support motility, so it seems I’m stuck mitigating symptoms through dietary limitations.

    On a related note, do you think supplemental glycine offsets the risks involved in a high methionine intake?


    • Hi Webraven,

      Focus on beneficial acids (taurine, glycine, and vitamin C for bile; vinegar; lemon and lime juice; salt, iodine for stomach acid; extra vitamin C), intermittent fasting, and vitamins A and D.

      No, I don’t think glycine offsets methionine, but supplemental glycine is often beneficial.

      Best, Paul

      • Paul,
        thank you so much for taking the time to respond. This sounds like great advice; I’ve definitely noticed that supplemental ox bile seems to be helpful, but have gotten away from acidic substances as they seemed to irritate my stomach (probably in part because my tendency is to overdo things).
        Thanks again and happy Memorial Day to you and your family!

  2. Stuart Mather

    SIBO can be so difficult to beat. The one thing your body needs to have a healthy gut – fermentable fiber (prebiotics) is the same thing that is causing you such misery. It’s an awful Catch 22.
    I’ve read about so many people failing to get bacteria in suboptimal amounts out of their small intestine with pretty well every SIBO protocol ever suggested. but I have never heard of anyone failing with berberine. Oregon grape root is probably the best way to get it (there are lots of other beneficial alkaloids in it apart from berberine) and it will still take you a couple of months. But you can start upping you fermentable fiber intake from even a couple of days after you start bathing your G.I. tract with berberine.
    You won’t even need that high a dose. 500mg of whole oregon grape root (about 50 mg of berberine) three times a day is usually plenty. High dose berberine has its own problems.
    It also has a host of other benefits apart from eliminating SIBO. When you get to 50g/d fermentable fiber(stuff colonic bacteria can thrive on) without bloating (farting is fine, bloating – S.I. gas – isn’t) you’ve won.

  3. Stuart,
    Thank you for the comments, sympathy and the suggestion. I tested methane negative after antibiotics earlier this year, but based on symptoms the overgrowth has recurred. I’ve included Berberine in my antimicrobial regimen before, but perhaps not in the right amount and for long enough. I will give it a go – what do I have to loose other than bacteria :-)! Much appreciated!

  4. Stuart Mather

    Interesting. Can I suggest further then that if you can be bothered giving it another go, you try oregon grape root, not coptis root or goldenseal as your berberine source. I’ve personally used both, and I think whole oregon grape root is far superior ( assuming of course that you haven’t already done so.
    One of the popular mail order supplement outfits in the U.S. has it insanely cheap at the moment. There’s something a bit special about oregon grape root I think.
    Have you also specifically targeted PRO biotics, particularly L. Reuteri. It seems to really help getting the little bastards further down where they belong – past what should be that formidable barrier, the ileoceacal valve. Apparently there are specific exercises you can do to restore ileocaecal valve integrity- if that’s part of the problem of course. I’ve often wondered whether prolonged SIBO just leads to the ileocaeel valve just ‘giving up’
    Do you have a dog? Pets, (particularly the ones who lick you a lot are a great source of beneficial soil based bacteria.
    Alternatively just a daily pinch of garden soil from anywhere (vary it) in your garden (that hasn’t been sprayed with chemicals is a reliable standby. Soil tastes remarkably pleasant, in my experience. And before soap and sinks, not to mention plates and eating utensils, humans routinely consumed a regular dose of dirt without even trying, for all but the most recent blink of our evolution.
    Even modern so called ‘paleo’ food, bears little resemblance to what human anceestors called food.
    For instance, buy some of the cheapest, toughest meat (cheek is a very cheap option, cut it into very thin small strips with a pair of scissors (or just mince it), season it well, add a little garlic if desired, and then eat it raw without trying to chew it smaller. Keep it in your mouth to enjoy the taste of course. And if you already enjoy your steaks rare, you’re almost there. Delicious,very very wholesome – so much sinew and other animal ‘fiber’ your gut bacteria have been denied for millenia. Hint fir the squeamish, start with VERY small bits to begin with.
    Sorry for the rave. Try the oregon grape root if you can.

    • My understanding is that SIBO recovery results by various means varies a lot between people, partly because there may be different underlying causes of the dysbiosis. Anti-microbials do have good results with some people, but not everyone; they didn’t make any difference with me, and I’ve tried them twice, including Berberine, under supervision by some very experienced (with SIBO) functional clinicians. I don’t mean to discourage; I hope that it works for you. Our bodies are all different so hopefully it will.

  5. Hi Paul.
    What are your thoughts on using raw milk with my morning coffee in a 50:50 ration (cafe’ con leche)? This would meaning heating the raw milk, which is what I’m wondering about. Is this safe? Does it deteriorate the healthful properties of the raw milk?

  6. Stuart Mather

    @ Susan,
    I think one of the reasons people get SIBO in the first place is that they have starved their colon bacteria of fermentable fiber ever since weaning. It’s always struck me that the reason breast milk contains so much fermentable fiber is that the human digestive tract is quite literally designed to eat copious quantities of fermentable fiber every single day of our entire lives. It’s such a huge bag of bacteria after all. And every single one of the 100 trillion we all carry thrive on it alone. If your microbiome isn’t getting at least 80 g of ferrmentable fibre (not the nonfermentable fibre/cellulose) every day I’m not even sure the human animal can ever hope for lasting health.
    Well fed gut bacteria are so integral to brain health, immune system integrity etc.
    And I wonder whether the people for whom berberine too fails to beat SIBO, are those who just mask the problem of out of whack bacteria numbers in their S.I. by long term avoidance of the very thing their guts need for real recovery.
    In other words FODMAPS etc. may certainly bring bloating relief, but only at the cost of a starving microbiome, with all its attendant miseries.
    But I’m the first to admit that bloating discomfort ain’t fun.
    I do think if kids went on getting the amount of fermentable fiber post weaning (even formula is chockers with a similar amount of it as the real McCoy) there would probably be no SIBO in adulthood, not to mention a host of other chronic diseases which plague humanity.

    • According to leading SIBO authorities like Drs. Pimentel and Siebecker, food poisoning is the most common cause…something along the lines of the toxins secreted from the bad bacteria can cause damage to the migrating motor complex, thus impacting the downward sweeping motion. When the MMC becomes impaired, bacteria that belongs in the large can migrate up intoto the small intestine. I have definitely suffered from food poisoning a few times in my life.
      I believe that factors like changes in hormones, aging, stress and other environmental factors definitely play roles too because they can lead to or aggrevate things like constipation, low stomach acid, lack of adequate chewing, and poor lifestyle quality such as lack of sleep and worry.
      Your suggested cause was certainly not the case for me. I was born naturally and breast fed for as long as possible. My parents were nutritionally and medically very ahead of their time, tons of veggies and fruits growing up (no sugar, soda, etc), followed Dr. Spock’s guidelines, etc.
      My understanding is that while FODMAP restriction has the potential to reduce or manage symptoms, it does not to fix the underlying cause. I’ve tried low FODMAPs before and during antimicrobials, and they made no apparent difference for me clinically or in retest.

  7. @Stuart,Susan,
    thanks for your comments. I agree with both of you about the underlying reasons for SIBO. I think another underlying cause, certainly for me at least, is chronic stress. Always feel well after being on vacation for a while, too. Stress will decrease your production of stomach acid, and affect digestion in general. That’s why I liked Paul’s suggestion to increase acidity and support bile production. Stuart, I have three dogs (don’t ask, long story :^), and the suggestion to expose oneself to soil in general is a good one, I think. I largely avoid probiotics because they exacerbate symptoms, but I seem to tolerate certain ones (e.g. lactobacillus plantarum) okay. The Oregon grape is on order, until then I’ll continue with my old Berberine prouct.
    Thanks again for the input and suggestions!

  8. Stiart Msther

    I’m certainly not disparaging your parents’ nutritional nouse. It wouldn’t matter how many modern fruits and vegetables are eaten though. It’s almost impossible to even get close to the amount of fermentable fiber in breast milk or formula (not questioning the nutritional superiority of breast milk of course, but in fermentable fiber they aren’t that different – by design).
    What’s important, in terms of fermentable fiber in adult food, is the amount of resistant starch, gums, and fructans that you consume. Modern fruits and vegetables, with a couple of notable exceptions(like green bananas and leeks) are woefully lacking in fermentable fiber. Even if you ate vast quantities of modern fruits and vegetables, it’s very difficult to even get within cooee of the amount of fermentable fiber in formula or breast milk.
    Also, I think that the lack of hygiene whuch was a hallmark of ancestral human lifestyles makes your food poisoning theory about SIBO unlikely. Food poisonuing was a daily workout for healthy ancestral guts don’t you think? And everyone was happier for the constant bacterial (not to mention viral) challenges keeping their immune systems ‘on song’ .
    Also, although I do concede that various ‘experts’ in the field of SIBO treatment do exist, I wonder whether the intetgral role of microbiome health is being completely overlooked. I do find your deferencce to the ‘experts’ a bit daft, I have to admit.
    One thing seems certain though, a healthy digestive tract actually makes the lower reaches of the S.I. inhospitable to overgrowths of bacteria, while just beyond the ileocaecal valve, not cenimetres further on the bacterial party is in full and appropriate swing. pH? Tcells Mast cells? There’s probably a whole raft of variables the body tightly controls to effect bacterial frenzy in the colon, and not so much only millimetres back up the pipeline. And they’re all signaling the brain using communication channels we have as yet only a glimmer of understanding of.
    For me, the amount of fermentable fiber in breast milk (and formula- by design) makes the appalling lack of it in post weaning modern (even the high fruit and vegetable, no junk food diet of which you speak so proudly) diet a chorua oF alarm bells. Is it really any surprise modern humans are so unwell when they starve such an important part of their anatomy as soon as they start eating solid food, not to mention becoming clean freaks and starving their immune systems of the light constant exercise they crave?

    On a lighter note, Spock has been thoroughly debunked hasn’t he? Although in his day many people probably considered him an ‘expert’ in his field too no doubt. The damage that well meaning fool did is breathtaking I would have thought.

    Now in my first comment on this topic I stressed that the intestinal discomfort a SIBOtic small intestine suffers from fermentable fiber makes it such an awful Catch 22. In fact, I think all those methane and hydrogen tests are even a bit unnecessary. If you eat a small amount of fermentable fiber and you get gas in your S.I. (bloating) you’ve got SIBO. If you only get gas in your colon (which exits normally through your sphincter (farting) , you haven’t got SIBO. It really is that simple to diagnose don’t you think?
    And the reason so many people complain that fermentablle fibre ‘doesn’t agree with them’ is because most modern humans have SIBO.

    So how do you ‘reteach’ your body to make your lower intestines appropriately inhospitable to bacterial overgrowth above the optimum (far far less than in the colon). No Idea. But I don’t think any of the SIBO ‘exoerts’ do either. Berberine seems to work pretty well (and I seriously doubt whether it has much do do with whatever antimicrobial prowess it has either) and Oregon Grape Root seems to have something special going for it.

    • 1) The point was simply that despite proper nutrition in early childhood, one can still develop SIBO later.
      2) Food poisoning is not “my theory”; it is the leading cause according to the top doctors and researchers in this area, such as Pimentel, widely considered a, if not the, leading authority on SIBO, and revered both in the functional and conventional communities as such. He is the one who both discovered and proved the link between SIBO and IBS. It is certainly your choice if you wish to view him as “daft”.
      3) I don’t believe that everything that Spock recommended has been thrown out the window.

  9. David Andrews

    Where do you purchase your “oregon grape roots”?

  10. Stuart Mather

    @ Susan
    Pointing out Spocks comphrensve failings is probably a bit beside the point of this forum I’d say.

    You said that ‘good” nutrition in childhood is no guarantee of not developing SIBO later in life.
    Actually that’s my point. It is. I would say that coninuing the amount of fermentable fiber infants consume pre- weaning in either breast milk or formula throughout later life is unheard of in non ancestral humans. One of the few remaining extant ancestral human groups, the Hadza in Tanzania, routinely consume about 200 g of fermentable fiber -mostly from baobab . The kids a bit less proportional to their bodyweight of course. And SIBO is unheard of. Ever. It simply doesn’t exist.
    Now curing non ancestral humans of SIBO is obviously mot as simple as throwing fermentable fiber at a dybiotic, post weaning life deprived of fermentable fiber. I’ve never suggested that it was.
    And life is pretty resilient after all. Plenty of people who’ve starved their colonic bacteria of fermentable fiber never get SIBO either.
    But if you’ve provided the fermentable fiber your microbiome is designed for. as ancestral humans did and do. SIBO didn’t and doesn’t happen.
    Also, I thought your point about IBS and SIBO was really important. I think they’re both on the same spectrum of long term fermentable fiber deprived gut dysbiosis. In fact I think All , and I really do mean all gut dysbiosis, can be traced back to fermentable fiber deprivation in earlier life.
    How you cure gut dysbiosis, SIBO or anything else, once you’ve starved your microbiome of the fermentablle fiber it is deigned for and are unlucky enough to be suffering the consequences of so doing IS far more challenging of course.
    Look, I’m sure every ‘expert’ in the field is well intention ed and sincere. Daft certainly wasn’t meant to denigrate their earnest attempts to make sense of the challenges gut dysbiosis presents.
    But I do detect a certain reverence for so called ‘experts’ Susan. I think it’s misguided. The history of human scientific endeavor surely reminds us all constantly that current ‘expertise’ in any area of peeling back the curtains on the unknown all too often turn out to be misguided fools.
    Spock, I think, is a particularly good example. Just my opinion.

    @ David.
    There are two main supplement mail order outfits in the U.S. It’s one of them.

  11. Stuart Mather

    Just a thought, have you ever tried supplementing with butyrate? I mean if fermentable fiber itself causes SIBOtic discomfort, why not circumvent the gas part of ‘in situ’ butyrate production from gut bacteria fermenting polysaccharides the upper digestive tract can’t metabolize (fermentable fiber). Butyrate seems so important to maintaining tight intestinal junctions and preventing gut dysbiosis in general.
    So why not just provide the butyrate, and avoid the gas that goes with it and can so often cause problems -as with SIBO.
    Butyrate is such a wonderful super-saturated fat after all. Even if it doesn’t help with the SIBO, you’ll get the other benefits it provides. And if it does help, you can start eating moore fermentable fiber and get that cascade of benefits a butyrate producing bacterial frenzy in your colon provides.
    Not least of which. of course. is a considerably improved ability to cope with stress.
    You’re a walking fermentable fiber/butyrate Catch 22 man.
    No idea how expensive supplementary butyrate is though.
    And it may not even show immediate results. With the SIBO, I mean.

    • Stuart,
      that’s a potentially excellent suggestion, so thank you. OI have used Butyric acid in the past, and whileI seems to tolerate it well, it also made no noticeable effect. Since I had read some claims that supplemental Butyrate didn’t make it to the distal colon I drifted away from using it. Do you have any idea if these claims are correct?

      • Stuart Mather

        Why are you worried about whether supplemental butyrate makes it to the distal colon? That’s the lower end of the colon right? We’re talking about the same place? I’m not entirely sure whether any fatty acid, butyrate included that you consume as a fat rather than as a polysaccharide (fermentable fiber) that is metabolized by gut bacteria to produce butyrate and various gases -which depending upon your populations of gas eating bacteria may be eaten before it makes it out as a fart.
        I do know that the butyrate that colon bacteria produce can be used in the colon to produce energy like any other fatty acid metabolized in the mormal way in the small intestine by enzymatic degradation (rather than bacterial),
        I also think that even if dietary butyrate doesn’t get to the colon, it’s probably doing you a lot of good in many other ways, some of which may contribute to making the S.I less hospitable to bacterial overgrowth.
        Joseph Cohen at SELF HACKED is a full book on the purported benefits of dietary butyrate. He also says that it’s far better to produce your butyrate in situ (in the colon , from fermentable fiber) rather than just eating it straight.
        On that note, I also wanted to ask you whether you’d ever tried LONG CHAIN inulin as a source of fementable fiber? It used to be available online under the brand name ‘Syontix’. Long chain inulin seems to be one of the best tollerated fermentable fibers in SIBOtic guts. If you can no longer obtain Syontix, another way of getting long chain inulin is GLOBE artichokes. Not the Jerusalem variety of artichoke. It must be Globe artichokes, which have pretty much all long chain inulin, and lots of it.
        Long chain inulin is purportedly the bees’ knees when it comes to flooding the distal end of the colon in butyrate.
        I bought a couple of big bags of the long chain inulin produced by the Belgian inulin specialist ‘Beneo’ years ago which I’ve been slowly working my way through ever since.
        ]t really is quite magical stuff. But then I don’t have SIBO. And if I’m right about the importance of lifelong (particularly throughout childhood) copious consumption of fermentable fiber, just like babies get pre weaning, I don’t think I ever will.
        Babies throughout human history without exception -both formula and breastfed, still living ancestral humans like the Hadza, and the incontrovertible overwhelming weight of coprolite evidence of how much fermentable fiber prehistoric ancestral humans routinely consumed. I personally think it’s a no brainer. But that’s just me.
        Now what you probably need, along with other SIBO sufferers, is some way of encapsulating dietary butyrate so it is only released at the lower in of the S.I. – where the SIBO overgrowths occur.

        So… try the oregon grape root, see if you can get hold of some Syontix, or just get some Globe artichokes, and also just try the dietary butyrate. None of it will do you anything but good, and although Syontix is/was pretty pricey, most grocery stores sell canned globe artichkes very cheaply. And it just might help with the SIBO.
        A word of warning though. If you do decide to try the long Chain inulin, start with an infinitesimally small dose (seriously, only a pinch). If all’s Well, increase it every couple of days by degrees. If you’re ramping it up too fast, you’ll know.

  12. Hi Paul:

    Question: On page 290 in your book, you state:

    Seaweed concentrates many toxins including bromine compounds, arsenic and mercury, and radioactive iodine.

    Why then, do you recommend various types of seaweed in your “Food” recommendations section within your site. Why not, seafood consumption instead?

    BTW: I mention your work frequently in my blog: http://www.organizeandrealize.wordpress.com. Check out some of my latest article on breast cancer — something I’m sure your wife studies in her field.

    • Hi Eddie,

      Most commercial seaweeds are safe, they are collected from places largely unpolluted by metals, and do not concentrate much. Kelp is the most likely to concentrate harmful metals, but kelp is not commonly eaten in the US. Most common is laver/nori which is pretty safe.

      Best, Paul

      • Stuart Mather

        What do you make of the hormetic benefit of very low dose heavy metals? For example arsenic, which there seems to be good data that anything up to 50 ppb of inorganic arsenic seems to have a potent anticarcinogenic effect.
        As soon as I saw that mentioned often, I started to worry less about the arsenic in white rice.
        So do you think hormetic doses of heavy metals conferring hormetic benefits is codswallop or credible?
        Also, I’ve read that infusing dry rice grains with a little coconut oil (about 1 tsp /cup of dry rice), cooking it normally, and then refrigerating it for at least 12 hrs makes its G.I. (even after reheating) about half what it would be otherwise.
        My own experiments with a blood glucometer seem to bear this out. In fact freezing the coconut oil cooked rice seems to reduce its G.I. even further.
        I know that eating carbs with fat reduces the G.I. anyway, but do you think there’s anything in this coconut oil/ cooling cooking approach? It’s often mentioned that parboiled rice has a much lower G.I. than any other rice (including brown – not that I eat brown rice) . So maybe parboiled rice cooked in coconut oil and then frozen/ reheated would be off the scale (in the right direction).
        I worry a bit that having a very short eating window puts a bit of a G.I. stress on your system.

      • Paul:

        Please, if you could, provide us with references that support your conclusions that, “Most commercial seaweeds are safe, they are collected from places largely unpolluted by metals, and do not concentrate much.”

        Look forward to your additional response.

  13. Stuart Mather

    Also wanted to hear your take on whether the ‘parboiling’ process just forces many of the ‘antinutrients’ in the whole rice grain that you are trying to avoid by eating white rice, back into the parboiled endosperm.

  14. What about someone with high cholesterol eating all of the eggs recomended?

  15. Any thoughts about Pyroluria and their own personal protocols? I’m not sure if Paul has published anything related to this.. B6/Zinc etc?


  16. Hello Paul!

    First of all, thank you really much for your work and effort.

    I want to completely adapt the diet, but at the moment I have some limitations to deal with.

    Background information: In the past I had food intolerances that have been healed, e.g. fructose, lactose and protein. I had also heavier food intolerance concerning fats. I still have problems with wheat.

    Following food I cannot digest correctly:

    – fats (stomach ache and bloating 4-5 hours after consuming; animal fat, oil)
    – potatoes (stomach ache and bloating 4-5 hours after consuming)
    – carrots (stomach ache and bloating)
    – some types of fruits (e.g. watermelon; stomach ache); also I think I have a very very very little allergic reaction when some types of fruit are entering my mouth (irritated tongue and mouth; orange, apple, banana).
    – Seasonings (stomach ache right after consuming)
    – too much of these types of vegetables: pepper, cucumber, onion, tomatoes (stomach ache, but not due to fructose intolerance)

    My current meal plan for a day is:

    – 3 meals consisting of white rice & vegetables (broccoli, cauliflower, zucchini, mushrooms, spinach etc.) & acid (lemon or lime)
    – 1 meal: fruit of choice
    – Intermittent fasting (16 hours)
    – I only drink filtered water.

    Do you have suggestions in what I can do to complete the diet?

    And can you recommend supplements that would/can help me in my current situation?

    If you need more information, please let me know! 🙂

    Thanks in advance!

    Best regards


  17. Stuart Mather

    What is the ideal amount of acid (vinegar or lemon juice) to consume daily? Is there some amount above which it beccomes unhealthy.
    Assuming of course that you are prepared to go to the trouble of ensuring it doesn’t contact with your dental enamel.
    In other words, is more better. I take about 200 ml of lemon juice/d now. I don’t notice anything, either good or bad.
    Is that amount too much?

    • There is always an amount that becomes too much. I don’t think you need 200 ml of lemon juice but I doubt that is harmful.

      • Stuart Mather

        Thanks Paul. perhaps 100ml is a better amount then. The digestive tract tightly controls the pH of the various stages anyway doesn’t it? But it is important to get enough potassium so skeletal calcium is not robbed to provide alkalizing buffering isn’t it?. Is that one of the reasons the daily potassium requirement is so high? 4g is a lot of potassium. every single day.

        What would be your suggestion for an ideal amount of vinegar or lemon juice to consume daily?

        • Stuart and Paul, I’m in Paul’s recs too.
          I’ve recently cut WAY back (over the past 1-2 years I was using lemon and lime in mineral water, salad dressings, and lavishly applied it to food — probably juice from 1 -2 fruits per day). I have noticed a few things over the past year and have cut back: 1) causes some gum/root irritation (I have some mild recessions from early years with braces and also chronic grinding for which I wear a night guard) and 2) more acutely, reflux!!! I didn’t realize that it was reflux until I started having more apparent symptoms after a string of days away from home when I drank more and stronger coffee than I’m used to. That led me to research the symptoms of reflux and also Norm Robillard’s writings. I have always done a lot of throat clearing and having a bit of a sour taste in my mouth after laying down, after consuming anything with citric juice in it, and I didn’t realize that that was a mild form of reflux; I’d attributed it to post nasal drip which I had quite a bit of before eliminating gluten.
          I don’t go hog wild with vinegar either, but for some reason ACV and rice vinegar don’t seem as problematic to me.
          So I would love to know what Paul thinks is an appropriate amount to consume in 1 day, including amounts in dressings etc.

          • Stuart Mather

            If you haven’t got any specific health issues to deal with why do you need any additional acid at all for perfect health. Normal stomach pH is pretty low anyway isn’t it? Even 200 ml of lemon juice wouldn’t lower it even further anyway.
            So what’s the point of adding acids apart from flavour?
            Our tastebuds seem to respond favourably to mild acidity. So there must be some evolutionary reason for developing a liking for it you would think. Although junk food tastes wonderful too.
            So what is the beneficial effect of consuming acids, and how much is a good amount for perfect health, assuming that you are aiming to avoid future health problems rather than address current issues?

            @ Susan
            Did the reflux resolve itself with far lower acid intake?

  18. Paul, what is your view on using oral antifungal medication, in conjunction with your nutritional program, for severe toenail fungus and athletes foot? Do you think it can help people enough to outweigh the side effects? I am about to read your book and embark on diet and supplement recommendations. In the meantime, I am considering starting 3-6+ months of turbinafine. I have resisted the medication due to my ultra sensitive nature (fear of sideeffects), but my condition keeps getting worse. I also realize it will take time to educate myself & implement dietary changes. I have been searching for an opinion on this on your website but not seeing it directly addressed. Also, any readers’ experiences are welcome. Thank you so much. M

    • Michele, not sure what Paul thinks, but IMO, oral antifungals are a huge mistake. My whole life, nothing has made me more sick to my stomach. I don’t know anything about that specific drug that you mention, but in my experience they are horrible for the liver and can do damage. My recommendation would be NOT to take the drug.
      Toenail fungus is an extremely hard problem to overcome, and I still haven’t, but IMO I would focus on holistic/lifestyle approaches to overcome it. In my experience it is also at least partially hereditary (both of my parents had it badly).
      I haven’t tried a candida curing diet, but wonder if that would help. Dr. Axe’s website has a lot of info on dietary and topical solutions, but as he emphasizes, you’ve got to treat it 2-3 times per day, which is really hard to do in my experience. Based on everything that I’ve read and researched, this is one of those problems that is REALLY hard to overcome (similar to rosacea, though presumably unrelated).

    • Stuart Mather

      I inherited scary toenails from my Dad. I think he and I (and to a far more moderate extent my two brothers) suffered from the neurological/behavioral downside of basically being ridden with yeast/fungal overgrowths – of which candida was but one, for most of our lives. I’ve taken systemic antifungals over the years. They all worked for a while, until they stopped working. Amphotericin, Grisavin, Ketocazoles , Turbinafine… etc the whole hepatoxic kit and caboodle. I learnt recently that when candida transitions to the dark side from its beneficial role in human metabolism, it can actually hide INSIDE macrophages. Seriously I doubt that oral anti fungal/ anti yeast medications will ever work long term. They’re without exception expensive hepatoxic bandaids.
      The only thing that worked initially with me was resurrecting my gut with daily dirt and fermentable fiber. I managed to punch through the initial bloating symptoms without exploding. Others just aren’t so lucky.
      And even then it had taken two years of very slow but consistent improvement in my toenails and the other symptoms of fungal overgrowth (seriously, they were yellow scary ruins- and that was just the toenails! There was also the brain fog/ impulsive behavioral stuff too). Seborrheaic dermatitis, jock itch – I had it all) Years of low carbing had made it a whole lot worse.
      Reintroducing safe starches and particularly the autophagic effects of gradually more prolonged intermittent fasting have added to the beneficial of having very well fed gut microbes.
      Watching my toenails gradually recover over the last few years has been nothing short of astonishing. It’s been far and away the most exciting experience of my life so far.
      Anyone who has suffered from scary toenails will appreciate that simply isn’t an exaggeration, or that I must just have a boring life.
      My Dad took his yellow toenails to his grave. It’s pretty sad really.

  19. Stuart Mather

    That should have been ‘KetoCONazole’ Oops.

  20. thank you Susan. Your response is so helpful. (I’m not sure how to post a reply on the site so this may show in the wrong string.) Paul, if you have time, I would welcome insight. My toenails are almost gone. I am just beginning the diet/lifestyle changes, and going on seversl years now trying to avoid antifungal meds. I’m afraid though about the impact of chronic fungal infection. could it be more dangerous than the side effects of oral meds? …. which may not even work. I am suffering from multiple gut brain imbalance symptoms and need to prevent worsening problems so I am embarking on holistic changes regardless. Also wondering if my nails could ever grow back without antifungal meds (in 2-3 yrs perhaps) if I sort out my diet etc per your regime. So grateful for your work & compassion. Thank you.

  21. I have crohn’s disease, BPPV due to Meniere’s Disease and a host of other autoimmune diseases. I have read your book even though i dislike all meat, i have eaten eggs, fish, and dairy and even started with limited beef products for the first time in my life. I started to try the 16 hour fasts with coconut oil. Did it for several days and then i stumbled into a podcast you did (Wendy Myers -Live to 110 on July 24, 2014 #68 Perfect Health Diet for Weight Loss) where you said you do not recommend coconut oil during a 16 hour fast. I am so confused now. Can you please let me know which one you recommend since now i don’t know whether you have updated your thoughts from the book and this website. Thank you.

    • Cindy,
      Paul has stated elsewhere on this site that he changed his opinion about taking coconut oil during the fasting portion of the day. He used to recommend it, but he does not recommend it now.

  22. Hi Paul,

    I am sure you read the article/study “High Serum Immunoglobulin G and M Levels Predict Freedom From Adverse Cardiovascular Events in Hypertension”.

    Do you think that Immunoglobulin G is a good risk measure no matter what blood pressure?

    I checked my lab values for the past 10 years and it always shows the same pattern: low and below normal IgG levels and on the other side elevated albumin.

    I do have some mineral deficiencies like zinc and copper and as I am intolerant to supplements I have a hard time to fix those by diet alone. Do you have any tips regarding diet and lifestyle to increase IgG?

  23. Hello,

    Does anyone has experienced hormone balance improvements(well this question is targeted for women over 40) following this diet? Do you know somebody who has? Any feedback?
    I am a 46 years old woman experiencing hormonal changes like weight gain/dofficulty losing it, loss of motivation, loss of libido, hair falling, etc.

    • Hi Sandra,

      As a first step, yes, you should adopt PHD, but also go to your doctor and ask to be evaluated for hypothyroidism. Look up the symptoms online, and if you have symptoms then ask for levothyroxine if TSH is over 2.5.

      Best, Paul

      • Paul thanks for your answer! I am actually being treated for hypothyrodism, since I am 15 years old. And I check my TSH, T3, T4 every 6 months. The symtomps I have right now are new, except hair falling which i have suffered for a long time now. I will start on your diet, and hopefully will see improvements. I wanted to know any feedback from a woman with similar symptoms like mine and the PHD diet. Thanks again. 🙂

  24. Hi Paul,

    I have a question about copper and zinc and how they affect the thyroid. When I eat oysters or beef liver, I feel very stimulated, have great difficulty getting to sleep on time and then crash pretty hard the next day. This has become a consistent pattern when consuming either one alone or both together.

    This made me think of something you mentioned a long time ago about your wife experiencing hyperthyroid symptoms from copper when she was copper-deficient.

    I’ve incorporated all the PHD recommendations, but I’ve never been able to supplement zinc or copper for long without getting symptoms of intolerance like insomnia, anxiety, and mood instability. And my TSH is consistently a little high (2-4) despite the fact that I take both T4 and T3.

    My best guess is that I’m deficient in copper, and maybe zinc as well, and eating oysters and liver (or supplementing Cu and Zn in large doses right off the bat) causes a temporary hyperthyroidism. This dissuades me from eating more of these foods or from supplementing zinc or copper, so the deficiency gets worse and the intolerance is even worse the next time around.

    I’m wondering if you agree, or if I’m missing something. Thanks for your time. 🙂

  25. Hi Paul,

    What is the ideal TSH level?


  26. Hi paul,

    how do you weight food, raw or cooked? e.g. you recommend 1lb of safe starches per day but potatoes lose weight when cooked while the weigh of rice increases after cooking it. same for meat and other food. might be stupid question but i m just starting out cooking… thanks

    • Hi rocky,

      For rice, the “1 lb” would refer to cooked weight.

      More precisely, you want enough rice to provide 400 glucose calories. That’s 0.7 cup of raw rice = 2.3 cups cooked rice = 0.3 lb raw rice = 0.8 lb cooked rice.

      For meat and potatoes, the cooked weight and raw weight are very close if you use gentle cooking methods like steaming and boiling. So measuring either cooked or raw is fine.


      • thank you eric, makes sense… seems to me that is more convenient to aim for a specific amount of calories than weight

        • Hi Paul: Rocky suggests, “the cooked weight and raw weight are very close” however, on page 309 in your book, you state to “BE CAREFUL to eat no more than a 1/4 pound [of liver].”

          What’s your take: measure raw or cooked?

          • Eddie,
            Paul has written elsewhere on this site that he wants people to weigh foods that are purchased dehydrated (and which need to be rehydrated before they are eaten, like rice) AFTER they are cooked,
            and to weigh most other foods before they are cooked. (You can also weigh that second category of foods after cooking, if they are cooked via moist methods that do not result in much water loss or shrinkage, such as boiling or steaming.)
            If you need to be careful about not going over a maximum weight of liver, you could always weigh an amount of liver before and after cooking it (in your preferred cooking style) and see which weight is heavier — the weight before or after your preferred liver cooking method. Then, you would want to use the heavier weight and its measurement timing (whether that is before or after cooking) as your guideline for your future maximum liver intake.

  27. Hi Paul,

    My 2yo daughter is reacting to histamine and phenols/salicylates and red meat.

    Can you recommend anything for her? Anything that would improve her methylation and sulfation pathways?

    Thank you,


    • Hi Fleur,

      She should eat liver or supplement copper 1 mg/day and vitamin A 2000 IU/day; eat egg yolks (2-3/day, mixed with food and cooked, no whites, she probably will develop food sensitivities or allergies easily) and carotenoid rich plants; B6 (100 mg/wk) and B12 (5 mg/wk); zinc up to 50 mg/week; taurine 1 g/week; glycine 2 g/day sprinkled on food; vitamin C up to 1 g/day sprinkled on food. You can crush tablets or open capsules to sprinkled them on food or mix with milk or yogurt; don’t give her pills for choking risk. A little iodine would not be out of place either if she doesn’t eat seaweed.

      Best, Paul

  28. Hi Paul:

    I re-read Chapter’s 28 – 36 in your book (which I have referenced for 4 years now). Request:

    If you formulated a multivitamin based on your recommended doses, I would SO buy your multivitamin for me and so many people!

    What are the chances you would do something like this?

  29. Hi Paul,

    I am enjoying your book.

    My 18-year-old son has such high reactivity to everything, his diet is severely limited and he can take few supplements. He is severely fatigued, even though he does not do a lot. When he does something normal for his age, the recovery period is extensive.

    Doctors can offer some external modes of detoxing that help (hot foot baths), but my son cannot eat the foods or take the nutrients they prescribe. We’ve been to many medical professionals (conventional and alternative), and we have not gotten much more than maybe one little tip from each that helps. Overall, he is as weak as ever.

    I am concerned about antibiotic use, because he tends to be genetically like me, and ABs dig large holes for me to dig out of when I have had to take them. But, he’s going to take a SIBO test, and if that is positive, we’ll have to consider it.

    Thank you for any wisdom you can share.


    • Hi Jill,

      I’d be interested in Paul’s reply.
      I’m no expert but the things I would consider looking into if you haven’t already are MTHFR genetic defect, leaky gut and Cyrex labs tests, stool test eg Doctor’s data or Biohealth….

      Wish you well

      • Thanks, Claire. The 23 & Me showed MTHFR issues- plenty of detox problems. Would be shocked if he did not have leaky gut. We’re waiting on his appointment to get stool testing and breath tests. There was a test kit my alternative DO suggested, but was $500 out of pocket, so just going with what the GI doc will do under insurance. The biggest problem we have is how to get out of this downward spiral where malnutrition makes it all horribly worse, but he cannot tolerate much in the way of nutrition. The only thing we have ever seen consistently help is external things that detox (foot baths- home or ionic at a spa, accupuncture, and homeopathic detox drops applied externally only). These things help, but can easily be overdone and cause fatigue. Just have never been able to get ahead of this curve with him. Many thanks for your good wishes.

    • Hi Jill,

      I would stick with some core supplements to help improve gut integrity and digestion. These would be: taurine, glycine, vitamin C, vitamin A, vitamin D, iodine. Vitamin K2, calcium and magnesium are also important, as is adequate salt and potassium. After that, zinc and copper, molybdenum once a week, and 3 egg yolks per day or choline supplements. Cook foods with lots of extracellular matrix – stocks and stews and soups like chicken soup.

      Circadian rhythm entrainment is also crucial. Try to get as close to a balanced die as you can. Don’t let him eat at night, but eat as much as possible in the daytime of natural whole foods. Lots of sunlight and moderate activity in the daytime.

      Best, Paul

  30. Hi Paul

    What do you think of this study showing SaFAs increase visceral and liver fat in humans vs PUFAs? http://diabetes.diabetesjournals.org/content/early/2014/02/11/db13-1622.full.pdf

    I can see both groups were fed “muffins”, which are hardly healthy, but even if SAFAs are only problematic in the presence of other poor nutrients, it still makes me question their safety. Why would PUFAs be much safer in the presence of poor nutrient intake/toxins?

    I know you think saturated fat intake is healthiest on a diet which includes intermittent fasting but I wonder whether this is the only circumstance under which high SAFA instake is safe?

  31. Hello Paul,
    I’ve read your book and am trying to implement a ketogenic diet for depression, anxiety, OCD, ADHA, and binge eating disorder. So far the classic ketogenic diet (<20g total carb's) has made my depression and energy worse. I've read your book and the chapter on PHD ketogenic diet, but was wondering if there is any place with more info. The ketogenic diet chapter was very short. Thanks!

  32. Hi Paul,
    My boyfriend has been on vit k and the dr recently put him on a blood thinner, should we discontinue the vit k.
    Thanks, Sylvia

  33. Paul,

    I am very intolerant to certain food chemicals such as saliylcates, amines, and oxalates as I am on the autism spectrum. I also have digestive issues with certain hard to digest starches like plantains and have issues with FODMAPS.

    What would your opinion be if I consumed something on the order of say 150 grams of white rice two times in a day (giving me about 100 grams of carbs) and one meal of enough white potatoes to get me another 50 grams of carbs at a third meal?

    I would get my protein from beef, pork, chicken, and eggs and consume a decent amount of beef tallow for fat.

    Would the toxin dose from the rice be too high? My concern is over-consuming arsenic.


    • Hi Brian,

      You should also note that white rice has much less potassium than the other safe starches, and safe starches are a major source of potassium on PHD. So this plan may necessitate supplementation of potassium, or being very careful about obtaining enough potassium (you need 4700 mg total) from other sources.

      If you only eat white rice (the arsenic concentrates in the bran), and avoid rice grown in the southeastern united states (which has higher arsenic levels in the soil), then I doubt you will need to worry about arsenic.


      • Yeah, I realized that. I use a potassium chloride salt along with my regular sea salt to make sure I get enough.

        I assume white Jasmine rice is pretty safe since it is grown in Asia, correct?

        Thanks for your response!

  34. Hi,
    I have had my gallbladder removed and wondered whether the PHD would need some tweaking because of that. I have been trying the diet for about 2 weeks and have gained 7 unneeded pounds. Also have hard to pass, small bowel movements.

  35. Interesting article here about circadian rhythm and bi-phasic sleep.


  36. Hello Paul,

    Is it problematic to take Vitamin K2 if one is taking blood thinning medication such as Warfarin? Or is it only Vitamin K that would cause issues?

    Thank you

    • Actually the one my friend is taking is Plavix (Clopidogrel), not Warfarin

    • This is discussed in the book. Generally, one should not take K1, but should take a bit of K2 when on warfarin. You will likely have to increase the warfarin dose slightly, but it is a good exchange. However, you should discuss with your doctor.

      Best, Paul

      • Thank you very much for your answer. I found some information online that says that Vitamin K interferes/interacts with the actions of Warfarin, but it does not interact with Plavix (the one my friend is taking) because Plavix uses a different mechanism, and therefore they are saying it is safe to take Vitamin K or K2 with Plavix. Do you agree with this?

  37. curious if you would know where to begin with painful lumps under the skin in thighs? pencil eraser size, tender to touch and multiples. all bloodwork normal, no other symptoms

    • laceygirl,

      I presume you have seen a doctor about the lumps (because you said that you’ve had bloodwork done),

      but I thought I’d mention a condition that I’ve heard of recently — it can cause tender lumps under the skin in multiples… it’s apparently a form of autoimmune disease, and it affects more people than one would think (since it’s not mentioned very much).
      It’s called hidradenitis suppurativa.
      “Hidradenitis suppurativa (HS) is a chronic skin disease which causes painful, boil-like lumps that form under the skin…. Symptoms occur in places where skin rubs together such as the armpits, groin, buttocks, and under the breasts. …In the mild stage, people with HS have a single or a few lesions in one area of the skin. In this stage, the disease is often misdiagnosed. HS will eventually progress to moderate disease which includes repeated cycles of lesions that enlarge and break open. …the disease is often misdiagnosed in the early stages.”

      I have seen several mentions of this condition in relation to nightshade vegetables — apparently many sufferers of HS report dramatic improvement when they avoid eating some or all of the nightshade plants.

  38. Hi Paul, unsure if you check this still, but worth a try: after a few TSH readings of 3-4.5 I went on 25mcg of levothyroxine last year. I subsequently had two readings of 2.6 and 2.5, but just this week pulled a 3.6 again. (No antibodies.) I’d hoped of course to be going the other direction. (My cholesterol though has come right in-line since taking the levo.)

    I’ve been lower fat and higher protein than official PHD would recommend over the past six months, but plenty of carbs; all the supps; etc. Very high stress. Poor sleep.

    Anyway I’m wondering if not enough fat / too much protein could be an issue here. Or if there’s any reason to think I need to drive TSH below 2 — i.e. with an increased levo dosage — before it can go on its own. All I know is that while on a more perfect PHD (higher fat, lower protein) it climbed in the years prior to the levo.

  39. Hi Paul,

    I have heard that taking certain minerals together (minerals that balance each other, such as copper-zinc) might cause competition between each other for absorption, and therefore prevent proper absorption of both minerals. Is there any truth to this? Should I not supplement zinc when I’m eating liver and supplement it later?

    Thank you

  40. Hello Paul,

    Could you please check out this link? The guy sent several homemade bone broth (with different cooking methods), and the lab reports show that bone broth is not rich in minerals.


    • I just checked the bone broths of Bonafide Provision brand and realized that their Chicken bone broth has much more collagen (12 g protein) and much more calcium (200 mg) per cup than their Beef bone broth, which has 5 g of protein and almost 0 calcium per cup. I wonder why?

  41. Hello,

    I have a question about your recommendation of Cod Liver Oil for people who does not eat liver. You recommend that the CLO should provide 50,000 IU per week. But if one consumes CLO to get that much vitamin A, they will also consume an excess of Omega-3.

    For example, 1 teaspoon of Rosita brand Cod Liver Oil will provide 1293 mg Omega-3, and at most 2962 IU vitamin A. So one has to consume about 16 teaspoons of CLO a week to get 50,000 IU. And if one consumes 16 tsp of CLO per week, it will provide 20,688 mg Omega-3. But your recommendation on Omega-3 intake is up to a pound of fatty fish per week, which will provide about 6000 mg Omega-3. Also, for the Rosita brand, you would need 2 bottles a month because of the high dose, which would be $100/month.

    So my question is, is the regular synthetic Vitamin A (retinol) in supplements really that bad? We should definitely not take it? If the answer is no, then there is no other option than forcing ourselves to eat liver.

    Rosita CLO (if you want to check):

    Thank you,

    • Hi Daniel,

      There was a readily available brand of cod liver oil made by TwinLab that had 5000 IU of vitamin A per teaspoon. Our recommendation is about 35,000 IU vitamin A per week so only 7 teaspoons per week would optimize A. That is not far off on omega-3 if you don’t eat salmon.

      However, if you inspect our Recommended Supplements page you’ll see we don’t recommend taking cod liver oil, and haven’t for a long time. Rather we recommend salmon for omega-3 and liver or supplements for A. No CLO or fish oil supplements.

      Best, Paul

      • Thank you for your reply.

        Few months ago you updated the Optional Supplements list, it now shows this:

        “FOR PEOPLE WHO DO NOT EAT LIVER: Vitamin A from cod liver oil, 50,000 IU/week”

        There is no mention of supplemental Vitamin A (synthetic retinol), only liver or Cod Liver Oil for those who don’t eat liver.

        I’m guessing your recommendation of 35,000 IU vitamin A is the ‘minimum’ weekly intake, since I have read from you many times that you recommend 45,000-50,000 IU weekly.

        Strangely enough, TwinLabs CLO does not have to be refrigerated after opening, and according to an article on Weston Price website, TwinLabs CLO contains added synthetic Vitamin A.

        This is what is says:

        “As of 2015, we recommend the following brands of cod liver oil. Sources of high-vitamin fermented cod liver oil and high-vitamin cod liver oil with natural vitamins are in the BEST category; sources of processed cod liver oil with synthetic vitamins in the right proportions (ten or fewer units vitamin A to one unit vitamin D, and with at least 2,500 IU’s of vitamin A and 250 IU’s of vitamin D per teaspoon) are in the GOOD category. We do not recommend brands of cod liver oil that have low levels of vitamin A and/or low levels of vitamin D.

        GOOD (and available in Stores):
        -Carlson soft gel Cod Liver Oil Super 1,000 mg capsules
        -NOW Foods double strength Cod Liver Oil capsules
        -Sonne’s Cod Liver Oil
        -Swanson double strength Cod Liver Oil capsules
        -Twin Labs non-emulsified liquid Cod Liver Oil”

        Here is the link to the article:

        So, I am still not quite sure if you recommend synthetic Vitamin A (retinol) or not? Could you please clarify?

        Thank you,

        • Paul- this is still an issue. I am sorry I know you are busy but it is true that in the ‘Optional Supplements’ section of this website you recommend that if you do not eat liver you should obtain your vitamin A from cod liver oil, yet up above you just stated that you prefer a person to take Viamin A supplements instead of cod liver oil if they do not eat liver. Please update this section to reflect your current recommendation. Thanks! Just looking out for you friend! 🙂

  42. Hi Paul,

    I felt the need to ask about this since the information you gave about this is not clear and somewhat contradictory. In the book you do not recommend Vitamin A supplements, but you just told me “Rather we recommend liver or supplements for A.” And also you just told me that you do not recommend Cod Liver Oil, but it is included in your Optional Supplements list for those who don’t eat liver.

    Would you mind clarifying this?


    • Really? Am I not making any sense?

    • We don’t recommend vitamin A supplements or cod liver oil because we recommend liver. If you don’t eat liver, next best is vitamin A supplements. If you don’t eat liver or salmon, then cod liver oil becomes an option. But it is not the recommended option.

    • Daniel,
      I can see how it was confusing.

      It’s now January 2019, and the Supplements page on this site still says what you saw in October 2016:
      “FOR PEOPLE WHO DO NOT EAT LIVER: Vitamin A from cod liver oil, 50,000 IU/week”
      “Vitamin A (Only If Liver Is Not Eaten)
      Target of 50,000 IU/week”.

      There is no mention of a 35,000 iu target for Vitamin A per week, no mention of salmon, and no mention of fish in regards to Vitamin A.

      Fish is mentioned in one place, but in regards to selenium:
      “fish, shellfish, eggs, and kidneys, weekly (for selenium)”

      I am pretty sure that the supplements page here once did give the range of 30,000-50,000 a week for Vitamin A, because that is what is in my notes that I took of this website’s supplements page that I wrote down several years ago.

      Like you, I had also found the Weston A. Price article about Vitamin A a couple of years ago (around the time in 2016 that you wrote your comment here and mentioned it), and I recall that their advice was a bit confusing and also that it may not have mentioned the specific Vitamin A that I was taking at the time (and that I still take).

      [I also think that I recall reading on Chris Masterjohn’s own website that he had an article about Vitamin A and/or cod liver oil that had different conclusions/recommendations from the Weston A. Price Foundation’s article, or something like that. Chris was working for the Price Foundation then, I think, or prior to that – maybe he still works for them now, I don’t know. Maybe he even wrote their Vitamin A article too; I don’t remember. Anyway, that is just tangential…]

      The Vitamin A that I take is: Swanson Vitamins Cod Liver Oil

      Per softgel, it has:

      1250 iu Vitamin A, which of course is now expressed in RAE (retinol activity equivalents), so the RAE is 375 mg. The label says that this amount of Vitamin A is “from ecoMarine Norwegian cod liver oil”.

      It also has 3.4 mcg of Vitamin D per softgel, which I believe used to be expressed as 135 iu. The label says that this amount of Vitamin D is “from ecoMarine Norwegian cod liver oil”.

      I know that the Weston A. Price Foundation article cautioned that some companies put synthetic versions of Vitamin A and D into their cod liver oils, and in my notes I quoted them as saying, “Most cod liver oils these days replace the naturally-occuring vitamins D and A with synthetic ones. Those are better than nothing, but it’s more preferable to use a cod liver oil that still contains the natural compounds. Dropi, Sonne’s, NutraPro, and Rosita’s cod liver oils all contain the natural vitamins.”

      Even though the Price Foundation didn’t mention Swanson in that quote, I concluded from what the label of my Swanson Vitamin A says that the A and D it contains are “from” the actual cod liver oil, and not synthetic additions to the cod liver oil. (But I might be wrong and giving them too much trust; I don’t know.)

      Also, one of my Swanson softgels contains altogether 350 mg of ecoMarine Norwegian Cod Liver oil, which on the current bottles of the supplement do not say how much EPA and DHA it has, but I have in my notes that it was indicated either on their older bottles or on their website that each softgel contains about 30 mg EPA and 30 mg DHA.

      -The USDA 2013 adult female Recommended Dietary Allowance or Adequate Intake is 2310 iu per day (700 mcg RAE)
      [I am female, so that is why my notes are about the female recommendations]

      -The US Tolerable Upper Intake Level (food + supplements) for adult women was, when I last looked at it, 10,000 iu per day (3000 mcg RAE)

      -The UK 2003 Safe Upper Level or Guidance Level (in supplements only; for a 132 lb adult) was 5000 iu (1500 mcg RAE) daily.

      Some people have genetic variants that make it hard to convert beta carotene to vitamin A, and I am one of those people (according to my 23andMe results).

      Additionally, my skin has a bad reaction to topical vitamin A, so I can’t use anything (like a cream, lotion, soap, makeup, sunscreen) that has retinol or retinyl palmitate in it.

      Whenever I tried to take 2 of the Swanson softgels per day, for a total of 2500 iu, it made me have an unusual and replicable skin rash, so I had to drop back down to 1 softgel a day for just 1250 iu.

      Despite my low threshold for getting a rash from supplemental Vitamin A, because I have the genetic variant that makes it hard for my body to convert beta carotene to A, I think it might be good for me to take the small amount of preformed A that is in the 1 softgel (if I can presume that Swanson isn’t adding synthetic A to that product, and that it only contains preformed A originating from the cod liver oil itself).

      Note that I am allergic to shellfish, and don’t eat liver or salmon, and live far from any ocean, so that’s why I have tried to make sure that I am getting a modest amount of preformed Vitamin A on a daily basis.

  43. Just subscribed again to Q&A. For unknown reason i didnt receive last month comments.

  44. Hi Paul,

    For which root vegetables — including potatoes, sweet potatoes, beets, carrots, and anything else you have an opinion on — do you usually remove the peel? As a rule of thumb, it appears that the peel often contains both a higher concentration of beneficial nutrients like potassium, and a higher concentration of plant toxins, and I’m not sure how to weigh these factors against eachother…


  45. Hello Paul,

    I think you should update your Supplements page and remove Calcium from the list of nutrients that Bone Broth provides (maybe also Phosphorus?) and recommend it only for its extra-cellular matrix/collagen content, since there is enough evidence now that the amount of Calcium in bone broth is negligible. Don’t you think so? What do you think we should do about Calcium since we are not getting any from bone broth?

    Thank you,

  46. Just wondering if anyone can share any specifics about reversing melasma. I started a general low carb diet (<=30 grams per day) to lose weight rather than any health issues. I noticed though that over time the melasma was breaking up, but I dont know what specifically is correcting it, ie increased saturated fat, elimination of wheat etc. I am doing about 90 grams of carbs a day now – safe starches only, but would really like to see some more improvement/reduction of melasma.

    The only medication I take apart from nutritional supplements is sodium valporate for epilepssy – low dose only.

    Thanks in advance for any help/advice.

  47. Hello Paul,

    Is it preferable to eat fermented vegetables (probiotics) with or between meals? Does it matter in terms of probiotics surviving the stomach?


  48. Hi Paul

    I bodybuild and am trying to find a diet that will help me continue to gain strength (strength leads to size). I have been on and off keto, observing how it affects me. I find I’m stronger on keto (more energy because of the extra ATP from eating high fat) and also because of the lack of carbs. Eating carbs within several hours of my workout reduces my strength and there are many bodybuilders on forums who report a better workout while training fasted or that they are stronger on keto (not everyone though). Keto makes my muscles shrink from glycogen depletion but a few weeks in I am stronger and get bigger than on carbs due to lifting heavier.

    Then I have always tried carbs again and filled out better while losing fat. Carbs are good for my muscularity. I can eat 600g carbs a day with little fat gain and lose fat on 400g a day. However carbs soon make me weaker so not good for my long term progression. Even if I eat all my carbs in the evening after my workout so I am clear of them before next days workout, I get progressively weaker as the weeks go by and feel sluggish. I have energy (almost as much as keto) but feel sluggish and muscles contract in a more shaky way. On keto my muscles feel smooth and powerful as they contract. Low carb at 100g carbs a day with refeeds reduces sluggish feeling but I’m very tired and I can’t lift heavy when glycogen depleted. On keto glycogen stores come back after some weeks.

    I would like to be strong while eating carbs but they make me feel sluggish. Is there a solution or an explanation for what I am experiencing? I am considering trying zero carb to see if it makes me stronger even though I have read of its dangers. This is a dilemma for me as I value health as well as bodybuilding. I haven’t done much keto so my carb intolerance shouldn’t be too bad yet.

    Thanks Ben

    • Hi Ben,

      It’s an interesting set of experiences. I might look to alternative methods of achieving the growth hormone push you are getting on keto. If you aren’t already, tend more carefully to circadian rhythm entrainment and intermittent fasting, then feast at mid-day and after workouts. Focus workouts as much as possible in the late morning – late afternoon window. I know this is hard to combine with a job, but it’s possible that the problem with the carbs is that they are coming at the wrong time of day. Ketones/fats are better tolerated outside the daytime and it could be keto is mitigating a disrupted circadian cycle.

      Best, Paul

  49. Hello Paul! And PHD Readers 😀

    I have been following standard PHD recommendations for a while now as well as dabbled with the Keto version of the diet. Overall I feel great on the diet, but I notice a few symptoms that seem to appear with higher carb intake that definitely sounds like some sort of dysbiosis. I get very little gastrointestinal distress overall, my energy levels are pretty great, sleep quality pretty good i think. The main thing that I notice is after having a more carb heavy meal, I feel like I produce a lot of extra saliva and/or mucus in my mouth, nose, and throat. Mainly, my nose will get a bit stuffy and I’ll get the feeling of constantly having to clear my throat from fluids (Im guessing excess saliva or mucus). This will last about an hour or two after finishing a meal. And on less frequent occasions I will notice along with it, a warm flushing of my cheeks and what feels like a slightly elevated heart rate that lasts about as long as the oral/nasal symptoms. My question is, does this sound like more of a oral/nasal microbiota issue? Or is it still likely gut-related?

    If anybody else gets the same symptoms please let me know if anything has worked for you!

    Happy Holidays!

    – Mike

  50. Hi Paul,
    I just finished reading your book and I already started to implent some of your recommendations. I’ve been struggling with some disordered eating for some time as well as some mild hypothyoridism. I’ve been on a strict paleo diet for a while but it has been an up and down course depending on my thyroid status and my constantly recurrent cravings.

    Since I just got back to intermittend fasting, I was able to reduce my levothyroxin-dose from initially 25 to 37,5 µg to almost zero. On some days I need a mere 12,5 µg to feel well (somehow I respond extremely sensitive to small fluctuations in the hormone dose). I am absolutely positive that by further improvements in nutrients like iodine as well as living my circadian rhythms I can fully restore my thyroid.
    After avoiding gluten AND adding safe starches, I did not once develop a serious craving for sweets and in cases I ate some sugary nonsense, I never felt the urge to overeat.

    I really seem to be on the right way, but there is one question I have:
    Currently I restrict eating to 12 noon – 8 pm which fits best into my office schedule. You recommend eating during daylight and doing some light exercise in the early morning when the sun rises. However I live in Germany, and now in winter time, sunrise is at 8 am and sunset at 4 pm. I go for a walk outside in my lunch break to get at least some sunlight, but I don’t know how to set my mealtimes the best way. Eating during that sunlight hours would mean eating everything at work, so it would be all without family and all without cooking.

    What would you recommend for optimizing circadian rhythms in areas with such a dark wintertime?

    Best regards,

    • Hi Olivia,

      We recommend having a personal 12 hour “day” that is shifted relative to the sun. This gives you time after work to cook dinner and eat well before the end of day.

      We personally use an 8 am to 8 pm day, 8 pm to 8 am night. On this schedule the best times to eat are between 11 am and 7 pm, the best times to sleep 11 pm to 7 am. Try to obtain most calories in the early afternoon. Try to exercise before eating.

      To implement this, set up bright 5500 K color temperature white lights throughout your home and office (or use a light box such as the one here, http://perfecthealthdiet.com/shop-circadian-rhythms/) and another set of orange-filtered bulbs for use in “night”. Switch to the orange bulbs about 3 hours before your bed time and after all eating and exercise is done.

      Best, Paul

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