How to Recognize and Fix a Brain Infection

I thought I’d pull up an interesting tale from the comments. It is a great illustration of what we’re trying to accomplish on this blog.

Thomas first commented here on December 31:

I just got your book from a relative for Christmas (I told them to buy me it!) and am reading through it now. Very interesting, although some of it is beyond a simple layman like me.

The part of this blog post that starts “Thus common symptoms of a bacterial infection of the brain are those of cognitive hypoglycemia and serotonin deficiency” and continues for several paragraphs describes precisely the mysterious changes I have experience over the last decade of life (I am now 33), with the one variation being that I suffer extreme fatigue rather than insomnia or restlessness. Every other sympton, including the odd mental state you mention, is a perfect match, and I experience them all to a marked degree….

I have been diagnosed with general anxiety but never depression. I do not feel sad ever, just irritable and anhedonia-ac, if I may coin a word. Anti-depressants, and I’ve tried a bunch, do absolutely nothing for me.

Brain infections are widespread – I wouldn’t be surprised if 20% of the adult population has a brain infection of mild severity – but they are hardly ever diagnosed or treated.

Fortunately, there are some symptoms that are almost universally generated by brain infections, so it’s not necessarily that difficult to diagnose them. But I think no one knows the symptoms. Infections are generally allowed to progress for decades.

One of my crucial steps forward was when I recognized that I had the cognitive symptoms of hypoglycemia when my blood sugar was normal. I could relieve the symptoms if my blood sugar became highly elevated. Thinking about why that might be led me toward the idea of bacterial infections.

Thomas went on to describe the origin of his symptoms:

I began to decline after suffering the second subdural hematoma of my life at age 20 when I was in Italy, followed by a 5 year binge on alcohol.

This was another clue. Traumatic brain injuries, such as hematomas, often initiate brain infections, because they breach the blood-brain barrier. Alcohol is also a risk factor, as I pointed out in my reply to Thomas:

Alcohol abuse depresses bacterial immunity and would be a risk factor for a brain infection:, Subdural hematomas frequently show infections, e.g.

We next heard from Thomas on February 22, when he had been on our diet for 7 weeks and had just tried his first ketogenic fast:

I’ve been doing PHD for about 7 weeks now, and tried a ketogenic fast this past weekend. I ended up going 33 hours with some coconut oil and cream. It was a bit tough having to eat a bunch of oil on an empty stomach, but nothing too bad.

I can’t say there was any improvement cognitively or with anhedonia, but there seemed to me to be a pronounced calming effect after about 24 hours of fasting. I often stutter or stumble over words (again, for about 10 years now), which usually goes away only with two or three alcoholic drinks. But the speech problems stopped almost completely during the fast, which makes me thing that there is some link to anxiety and stuttering.

Positive changes in brain function during ketosis suggest that the brain isn’t functioning normally when it relies on glucose as a fuel. There are several possible causes of this, but one is a bacterial infection. Another clue.

I generally recommend getting on our diet and supplement regimen, and reaching a stable health condition, before starting antibiotics. There are several reasons for this, which I’ll elaborate on later, but briefly:

  • Antibiotics work well on a good diet but may fail on a bad diet.
  • Pathogen die-off toxins can cause significant neurological damage and this toxicity may be substantially increased on a bad diet.
  • There is considerable diagnostic value in being able to clearly discern the reaction to antibiotics. Rarely is it certain that a brain infection is bacterial, or that the antibiotic in question is the correct one. To judge whether the antibiotic is working, it’s important that health be stable and as good as possible.

I therefore recommend being on our diet and supplement regimen for 3-4 months before starting antibiotics.

Thomas seems to have followed this advice, since he has just reported starting antibiotics:

I’ve been on PHD for a few months, and about a month ago went to the low-carb therapeutic ketogenic version of the PHD. After reading some of Paul’s posts, I believe that I might have a brain infection as a result of a head injury from more than a decade ago (Paul, if you recall, my condition has a lot of similarities to the one you once had). I started taking doxycycline a few days ago, and I have already noticed pronounced improvement (whether due to the diet or the antibiotic or both) in controlling the irritability and anxiety that have plagued me for years….

I definitely feel great since making the diet changes. My blood pressure, which has been creeping upwards over the last few years to 135/80 or so, is back down to 110/70. My testosterone is 824, and I am pleased to see that I maintaining my strength in the gym despite being on a ketogenic diet.

Pronounced improvement in the first days of doxycycline is quite possible, because doxy acts as a protein synthesis inhibitor. It essentially blocks bacterial functions and switches them into a state of hibernation. The bacteria are still there, but they are not interfering with brain function as much as before.

This improvement is confirmation that Thomas has a bacterial infection of the brain. If there were no infection, he wouldn’t notice an effect from the antibiotics.

Over a period of months, the doxycycline plus ketogenic dieting should help his innate immune defenses clear the brain of most bacteria. Combination antibiotic protocols may be even more effective.

In a follow-up comment, Thomas mentioned Ben Franklin and the blessing of good health:

Thanks for the response Paul, as well as all your help. If this works, I owe you my first-born child and then some! Ben Franklin (I think it was him) might have been right about health being the greatest blessing. The improvements I’ve seen recently have done more for my well-being than anything in the last decade, and I am profoundly grateful to you for all your excellent advice.

It’s comments like this that make blogging and book writing worthwhile.

It’s probably hard for those who have never had ill health to appreciate how enjoyable it can be for those with chronic diseases to recover good health. I’ve blogged on this before (Of Recovery, Hope, and Happiness, July 13, 2010 – don’t miss Ladybug’s painting).

Thomas, antibiotics and ketogenic dieting will work, I’m pretty sure. May you come to perfect health, and always remain grateful for the many blessings that are yours.

Leave a comment ?


  1. Paul,

    Thanks so much for your thoughts.

    I expected you to blame it on the fish oil!

    I am reluctant to take all of this as a sign of eukaryotic infection or of ketosis being otherwise inappropriate because I have not felt worse overall; only the nighttime disturbances (and nighttime numbness) have worsened. Furthermore, as I write this I have not eaten anything in about 48 hours and feel fine — including, significantly, a better than usual sleep last night with no major episodes — so it would not seem that carb restriction per se is the problem.


    Thank you! In fact, the first thing I did yesterday was buy a glucometer. So far it has revealed nothing out of the ordinary (though I have not yet had a chance to test after food or supplements as I have not taken any), nor have I noticed significant correspondence between how I am feeling hour-to-hour and the meter reading, but I am eager to see what I can learn with time.

  2. Hi MM,

    Well 12 g fish oil is much too much as a regular thing, but as a 1 day dose it shouldn’t do you harm. Some people do have sensitivities to fish oil, for poorly understood reasons, so if the problem repeats whenever you take a high dose of fish oil then that would be significant evidence.

    Over-eating is a more likely cause. If you have gut dysbiosis, the symptoms will be more severe after a very large meal.

    I’m glad you’re tolerating fasting. That’s good, it suggests problems are not so severe.

  3. MM’s nighttime numbness made me think about a similar mystery that I experienced. I have had for the last several years, not exactly numbness, but a strange burning sensation in feet and/or legs only at night when I would wake. not every night, but frequently. If I moved my legs a bit it would go away.

    It started after being VERY low carb for over six months.

    I hadn’t noticed, but now that I think about it, it seems to have dwindled significantly, perhaps completely. I have been eating 200 C safe starches for a three and a half months now.

    Chalk up another one for PHD!

  4. This is a useful article, and though I have come late to it, I hope you might still be taking questions from the floor.

    I note your advice, when taking necessary antibiotics, to take pro-biotics during and after.
    Q1. How long after? What are the best, easiest to access, indicators that your gut biota has returned to health after a course of antibiotics.
    Q2. Do you know if taking antibiotics by an injectable route, rather than orally, would be more sparing of the gut biota? I have done a pubmed search to see if this has been studied, but my key word selection does not seem to have turned up anything much.

  5. Hi Scotlyn,

    It can take 1-2 years to replenish gut bacteria. However, fermented foods (fermented vegetables, yogurt) are probably more effective. If you eat fermented foods you needn’t take probiotics very long.

    There are no good indicators of a good flora; a good flora protects you against a bad flora. If you have bad digestion then you know you have bad flora, but if you have OK digestion you don’t know what you have. You could be vulnerable to the next bad bug that comes by.

    I haven’t seen any evidence on injected antibiotics vs oral. It’s a good question.

    • I’m a dedicated believer in the diet. I tell everyone. Almost all take no action ( I have purchased 8 books so far ) I would pay for tests if I knew which ones.

      What tests would u recommend for:
      – gut health
      – thyroid health
      – brain health

  6. Thanks, Paul.

    Maybe some professional researcher who reads here might take up the question and run the study. I would hypothesise that oral antibiotics affect the gut bacteria first, before being absorbed into the blood to travel to whereever else there is an infection. Whereas, it would seem reasonable to believe that injectable antibiotics should largely bypass the gut, accessing it only via the blood/gut membranes, but not enterically.

  7. Hi Paul

    I really enjoyed your book and thank you for all the info you make available on this site.

    I have been Paleo for about 6 months now and have fiddled with my carb intake quite a lot throughout. My health improved a lot when I made the change but some symptoms still remained (dry skin, psoriasis on elbows, recurrent jock itch, brain fog, poor concentration, dizzyness and drunk feeling)

    I started taking natural antifungals (undecylenic acid, caprylic acid, charcoal) about 3 months ago to try and correct my symptoms Things seem to have improved but my symptoms still have not completely disappeared.

    I seem to get better results on a lower carb diet.

    My questions are:
    1. Would you say my symptoms are fungal, bacterial or both?

    2. How do natural antifungals compare with the pharmaceutical products like Nystatin? And is there a significant health risk associated with taking something like Nystatin for a prolonged time? I just want to know if something like Nystatin might be a better option for me.

    3. Could my brain symtoms be related to a fungal infection / die off? My symtoms seem to be worse directly after eating.


  8. Hi Paul,

    I have had mental brain fog and irritability in the mornings for about as a long as I can remember. About a year ago I tried intermittent fasting (16 hour fasts/8 hour feeds, and every once in a while a 24 hour fast). This seemed to clear up my AM grogginess enormously. Fasting and feeding in this fashion made me feel bright and alert.

    I never gave my diet too much thought in terms of macronutrient ratios until very recently. I decided to lower my carb in take and increase my saturated fat consumption. I really didn’t know what to expect, but the first 5 days were nothing short of pure exhaustion. Looking back, I’m sure I cut my carbs far too much. Things started to clear up (more energy) around day 6 and 7, but from there on in I’ve been irritable with sore lymph nodes in my neck. I have increased my carb in take, but I still feel somewhat irritable with lower energy than normal. Although I practiced regular fasts and felt well, is it possible a more prolonged period of ketogenisis could have aggravated some sort of latent infection?

    I very much enjoyed your book! I couldn’t be without the safe starches.


  9. Hello Paul,

    I am so fascinated with this information on brain infections and mental illness. It’s a theory I never heard before but makes total sense in light of my own experience. I started to experience mental illness in my early teens. I experienced depression, anxiety, hallucinations (horrible ones, like demons entering my bedroom), delusions and other severe psychotic symptoms. I also had “poltergeists” at one point (!). At times my life was truly a living nightmare. Honestly I don’t know how I got through it alive, as I was suffering tremendously and obsessed with suicide. Then somehow around my mid-twenties, it just went away. Not immediately, but slowly over the course of a couple of years. I always wondered what happened. How I could have possibly gone from being that sick to being normal and happy. Now I think I know the answer. Around age 23, I discovered Atkins and started ketogenic dieting. I did it somewhat sporadically, but there were many solid stretches of VLC eating, and even when I wasn’t in ketosis, I tended to go pretty low carb whenever I could muster the discipline. I still tend toward low carb eating and am just now experimenting with adding starches on a daily basis. I’m careful though, because I sense that whatever happened to me may have left some permanent damage that could still cause problems under certain circumstances. I’ve had a few glimmerings over the years, but only under extreme physical or mental strain.

    When I look back, I also recall two head injuries in my childhood and one in my teens.

    This is all pretty hard to talk about still, as there is a lingering sense of shame and regret for lost years. Nobody I’ve ever met has experienced this level of mental illness (They are probably all in hospitals). It’s like something out of a scary movie. And yet there it is. And here I am, probably one of the most mentally healthy people you’ll meet. Anyway, I just wanted to share my experience since it was such an extreme case that seemed to be resolved through ketogenic dieting.


  10. My step-brother has had issues on and off for a few years with regard to depression, anxiety and things like that. He’s been on meds for years now and according to how he’s doing or feeling, they keep tweaking dosages, etc. I feel like it’s a disaster and he never seems to really get better. He’s been in a few car accidents due to drinking and he already knows that when he drinks, things get worse, but he always seems to revert back to drinking even after he’s successfully quit it after several weeks. I remember when he was in high school (10 years ago or so) he was so sweet and kind, he was one of those guys. Now he’s easily irritated, seems kind of angry underneath, things like that– for the last several years he’s become an entirely different person. I know it’s not him. I really feel like part of the answer is his diet for sure. I just feel really bad for him because regardless of how he’s been acting and feeling, I’m sure he doesn’t want to be that way… no one wishes that on themselves. But he doesn’t know the way out, and at this point, I don’t know if he’s even looking for a way out.

    One additional thing- this might be a huge clue pointing toward bacterial brain infection– several weeks ago he ended up in the hospital due to swollen jaw and into his neck area. They thought it was a bacterial infection, probably in his tooth, but apparently they never found a bacteria. I will check on that to see if that’s accurate, but that was the last info I got about that.

    If he were to give PHD a try, do you see any potential problems with his meds interfering? Maybe he can find a new phsychiatrist that is well-versed in nutrition related to mental health, that can guide him in figuring out that balance. In the meantime though, I have to figure out how to convince him to try PHD (once he starts eating healthy, I think the intermittent fasting would help if he’s willing).

    Any thoughts/ advice?
    Thank you so much.

    • Hi KH,

      I think it’s always good to improve one’s diet. I wouldn’t refrain from adopting PHD just because of medications. He might be able to reduce his doses (or get off them) after he changes his diet, so he should be aware that his needs may change.

  11. Justin Dougherty

    You guys are all wrong. Your problems are caused by excess histamine in the blood. You would need to get a whole blood histamine test through Labcorp. If your score is over 70 you have histadelia. Your body is deficient in copper. Your body needs copper to lower the histamine. Take 2 mg of copper. It kills all bacterial infections in your body. It kills fungal/candida in your body. You will see skin eruptions that look like bug bites. Inside is massive amounts of bacteria that will come out of your body. It’s disgusting and painful but it must come out. Take VSL 3 to replace the destroyed flora in your intestines. You will feel like a million bucks after the detox. Email me if you have any questions. I’m an expert.

    • Justin – if you know about histadelia I assume you also know about pyroluria? If so, advising someone to take copper without first having pathology testing to assess zinc:copper balance is irresponsible.

      Additionally, you can’t pin every individual’s problems on histamine. Of course, that will be a factor for some people but not everyone. Please don’t generalise.

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  13. Hello Paul,
    Can C- reactive protein provide a clue for brain or intracellular infections?

  14. Hi imran,

    It is a marker of certain kinds of inflammation so it is a clue, but it is not a specific clue.

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  17. Paul,

    Do you have an opinion on beta glucan? I can’t find what effect it may have on IFN-g. I dream and sleep better when on it the past few weeks. My only concern is if it simply suppresses that function of the immune system and makes things worse in the long term. It has proven to be very effective for my allergies:

    Do you think inducing a tryptophan deficiency short term could be an effective anti-bacterial strategy? I.E only eat gelatin as a protein source for a while. I am shifting more and more towards gelatin away from typical animal proteins. Effects are uncertain with regard to cognitive spectrum, but otherwise I notice a lot of benefits in other areas (skin, exercise, body composition). I would like to try a full blown gelatin only trial for a week if I can manage it.

    Third thought – I seem to feel good drinking alcohol. While I see that too much alchol can actually be a risk for brain infection, can bacteria metabolize alcohol or it’s byproducts? Is alcohol a way to feed the brain without feeding bacteria?

    (Alcohol causes brain to shift from using glucose:)

    • I think if beta glucan helps you, then it’s worth taking. It’s a natural compound that we’re normally exposed to in small quantities. I wouldn’t recommend it for healthy people but it does stimulate certain immune responses which may be beneficial in certain health conditions.

      I do think a low tryptophan diet can help against bacterial infections.

      Bacteria can metabolize alcohol. I’m not sure how alcohol consumption affects infectious disease risk.

  18. Paul, thanks as always. Do you know of circumstances where beta glucan is contraindicated?

    I didn’t find any info on the blog about ‘mitochondrial cocktails’ for brain disorders. I was interested in Coq10 for migraines but was disappointed to find it feeds candida. I have both tested positive for intestinal yeast and very low coq10 levels. Seems like there’s always a catch 22 with supplementation. I saw mention that you felt vitamin C superseded the benefits you had with coq10, are there other ways of boosting the compound without directly consuming it or feeding pathogens? I haven’t found any info on whether bacteria/protazoa utilize coq10, though most coq10 supplements are created by bacteria.

    • Hi Yves,

      It’s a fungal cell wall component, so it’s a toxin and excites an immune response. You wouldn’t want to overdose it, or add it in to an existing infection. The uses I’ve seen claimed for it are to stimulate an immune response that might attack cancer, for instance. If you have intestinal yeast I don’t see the purpose, your body will be seeing plenty of beta glucans as is.

      Most microbes use CoQ6-9:

      CoQ10 is a fine supplement, just expensive, so nothing wrong with taking it.

  19. This is very compelling stuff but how do you guys find a doctor willing to prescribe antibiotics for this kind of thing? I am pretty sure my GP would look at me like I am crazy. ‘Because I read it on the internet’ is not his favorite answer to the inevitable ‘Why do you want that?’ question.

    • Hi David,

      I apologize, but I have little advice re the doctor issue. I had the same problem but I had other signs of infection that gave my doctor reasons apart from the neurological symptoms to prescribe antibiotics.

  20. Hi Paul,
    I’ve been suffering with very strange symptoms for the past 3 years; it all began from a sudden inability to stand upright, fatigue, dizziness, lack of appetite, diplopia etc; tu cut it short, when performing an MRI they could see 3 brain lesions (demyelination). Up to this day nobody knows the nature of these lesions, which, on subsequent MRIs, have multiplied. However, little by little I have regained my ability to have a bearable life – mainly due to a raw vegan diet (for 3 years). Just recently I have come to the conclusion that I might have neuroborreliosis, which was confirmed by dark field microscopy, several antibody tests, together with hemobartonella/haemoplasma as co-infection. In the past year I have followed a high-fat raw vegan diet, which I feel has helped me with my inflammations (due to rheumatoid arthritis – diagnosed 22 years ago) and only recently introduced some animal protein in the form of raw goat dairy and raw egg yolks. Yesterday evening I binged on both fats and sweet fruit and today I’m feeling very well (I have a history of binging and I wonder if it was triggered by bacteria..).
    I haven’t taken any allopathic medication for several years and I’d prefer not to start now with antibiotics, rather with more natural approaches.
    What do you think of my situation?
    What would you suggest for Lyme disease? Is a ketogenic diet appropriate for me? How much protein should be ingested? How about co-infections, do they allow such ketogenic diet?
    Sorry for such a long lithany and for my not so correct English, I’m from Romania. I’ve read your book and I found it very useful, but I’d really appreciate further advice for my specific condition. Thanks so much! Gabriela

    • Hi Gabriela,

      Some nutrients from animal foods are essential for myelin formation and maintenance. Vitamin K2 and B12 are good examples. Also, myelin is derived from lipids and if your diet includes too few fats/cholesterol myelin repair could be impaired. I would eat at least 3 egg yolks per day and supplement vitamins K2, B12, magnesium, vitamin D, and maybe a few others.

      Also I would reconsider the raw vegan diet approach.

      Before considering possible infections I would try to optimize the diet. Our book is our best advice for that.

      Best, Paul

      • Thanks, Paul. I’ve been raw vegan for 3 years now, but lately I’ve incorporated some animal products such as fermented raw dairy and raw egg yolks. I’m still undecided as to the effects of the raw dairy, since I seem to develop some mucus in my throat when eating too much.
        K2, B12, vit D are also part of my daily regimen. I only eat 2 egg yolks per week, so I’ll try to include them more often, they are delicious.
        Thanks again, you do a great job on your blog!

  21. So I have exactly waft you Paul described at the Top. I am 15 years old and don’t know what’s going on in my head anymore.

  22. Hey Everyone! and Paul,

    So for about a year now i just haven’t felt myself. I wake up with a tightness in the back of my head, behind my eyes, and sometimes a stiff neck and back. I have light sensitivity and have intense brain fog. I have no idea what is going on and i feel like the last year of my life has been a blur. I really need some guidance and hep here, cause i have tried with my doctor and have made no progression.


  23. Fixing BrainFog | re.lyable - pingback on March 6, 2013 at 5:03 pm
  24. Hi Paul,

    First of all, I’m a big fan of your book and I recommend it to everyone.

    I stumbled across this post and I’m wondering if you think my condition is possibly related to a brain infection or some other chronic infection.

    I’m 31 years old, male, 5’7” and 140 lbs.

    About 9 months ago I woke up one morning with what I believe to have been a swollen spleen. A few days later I developed a persistent lightheadedness that seemed to get worse immediately after eating (starting with the first bite) or after drinking anything. For several days I was delirious and barely slept. 9 months later I’m still experiencing this persistent lightheadedness all day, every day. It goes away completely when I’m lying down and it’s better when I’m sitting. It’s the worst when I’m walking around or standing for any length of time. I also experience a lack of coordination and will often knock things over.

    I’ve had a barrage of tests done. Below are the things that stand out.

    – A TSH that jumps around a lot (Anywhere from 1.5 to 3.7). Free T3 was low once but in subsequent tests it was normal.

    – A low WBC that bounces between 3 and 4.5.

    – Two saliva hormone tests 3 months apart that revealed consistently low DHEA & low progesterone (but normal cortisol & cortisol pattern).

    – A digestive health panel that revealed an overgrowth of E-Coli (not O157), an absence of gram positive flora, and low intestinal SIgA (14 with the normal range being 400 – 880).

    – Low intracellular selenium levels despite supplementing 200 – 300 mcg a day.

    – High levels of antibodies to Epstein-Barr suggesting a possibly recent but not an active infection. The test was done several months after the symptoms began.

    – Unstable oral temperatures. Day to day temperature averages vary between 97.3 and 98.1.

    – A high A/G Ratio (typically 2.5).

    – Various odd neurological symptoms that come and go – tingling & numbness in hands and feet. Also, stiffness in the neck that exacerbates the lightheadedness when looking down at the floor.

    – Sensitivity to light. Wearing sunglasses, even indoors, seems to improve symptoms.

    – A neurotransmitter urine test that showed high levels of GABA (everything else was in normal range).

    – An allergy panel that showed a severe reaction to the mold species Rhizopus Nigricans and Botrytis. I’m in the process of getting my apartment tested for mold.

    A Brain CAT scan 2 weeks after symptoms began and an MRI 3 months after the CAT scan revealed no abnormalities. Over a dozen CBC, metabolic and lipid panels have been normal (besides the low WBC and high A/G ratio).

    Based on what I’ve read and through some elf experimentation, the lightheadedness and loss of concentration seems to be caused by orthostatic intolerance. So far the only relief I’ve found is in consuming a significant amount of salt (about 4 – 5 grams a day) and limiting water intake to 8 – 12 oz every 2 hours (the goal being to increase blood volume). I also noticed some benefit from taking piracetam and vinpocetine to increase cerebral blood flow.

    I’ve been following the ketogenic version of the PHD for about 5 months. During this time my WBC recovered from a low of 2.6 to a stable 4 – 4.5, which stayed this way for several months. However, in the past month, after two weeks of exercising every other day and increasing carbs to about 100 g/day (vs < 50 g/day before), my WBC suddenly dropped to 3.1. The differential showed that neutrophils and lymphocytes dropped by roughly the same percentage. RBC also saw a significant drop but it's still well within the normal range (4.92) Also, my ALT, which hadn't changed at all in months, shot up suddenly from 22 to 39. I've cut my carbs back to what they were before and have stopped exercising (except for brisk walking 2 – 4 miles a day). I plan on doing a follow-up CBC and metabolic panel soon to see if my WBC has improved.

    It's the chronically low WBC more than anything that leads me to believe I'm dealing with a chronic infection. Once in a while I have a decent day where I don't feel as lightheaded as usual. However, on those days, the lightheadedness is usually replaced by extreme fatigue.

    I've seen three MDs and two NDs. None have been able to provide a definitive diagnosis or help. The naturopaths had me do 4 infrared sauna sessions, which seemed to help slightly and the MDs only wanted to prescribe thyroid medication, which only made things worse.

    Any thoughts?

    • interesting problem/test results…Just curious why you are supplementing so much selenium, as I think too much can cause hypothyroidism, and thus the increase in your TSH… (Paul mentions this somewhere on the blog, that too much selenium caused fingernail issues and hypothyroidism for him and he backed off).

      I have some similar issues to you, and wonder if perhaps adrenal fatigue (i.e. cortisol dysregulation), which could be causing the variations in body temperature and the sensitivity to light. of course, what could be causing cortisol dysregulation or adrenal fatigue besides pathogens? I’m curious to what paul would say, if it’s chronic fatigue you have, perhaps caused by C. Pneumoniae?

      Do you have sleep problems, or depression, as Paul described in the post?

      Have you tried doxycycline?

      Do you have a reaction (flu-like) to NAC (N-acetyl cysteine?)

      Just curious as I have some issues similar to you – although not a light-headedness, just brain fog, day in and day out, and the ability to fall asleep but feeling completely unrefreshed 6-7 hours later when I wake up, no matter what.

      • Hi LJ,

        I only began supplementing selenium because my intracellular levels were extremely low. I retook the micronutrient test a few months later after supplementing and my levels did improve but they are still low. Besides, 200 mcg is really not that much considering the upper limit is twice that. Another consideration is that going into ketosis frequently (as I do) can rapidly deplete selenium.

        I do believe that several of my symptoms are related to adrenal fatigue, but as you suggest, there may be an underlying chronic infection causing it. I’m curious why you think it may be C. Pneumoniae? I had never heard of this pathogen until now.

        I don’t really have sleep problems. I fall asleep fairly easily and sleep through the night.

        I have not tried doxycycline yet. I want to but I’m not sure how I can convince my doctor to let me try it.

        I track how I feel day to day and I tend to feel better, not worse, after taking NAC.

        • Hi Kevin – sorry for replying late! C. Pneumoniae is a pretty commen pathogen paul has talked about a lot on this site, and it even has a website completely devoted to it – (also the pot belly diet is an interesting book about how common pathogens can cause chronic symptoms – wonky cortisol, a pot belly, as the name implies – which antibiotics can temporarily help but it’s difficult to kill the pathogen in all its life forms in the human body).

          Just out of curiosity, are you following paul and shou-ching’s ketogenic diet? why are you ketogenic?

    • Kevin
      Where did u get all that testing and what tests?

  25. Diana Durnford

    Hi Paul
    David and I have been on your PHD diet for 3 months now. So far so good! I have also read pages and pages of your blog and am still working at it. You have already healped my health (Lyme disease). Our question relates to David.
    We think that David has a brain infection. There is a clear link between excessive carbs and
    or exercise and bouts oftotal amnesia , or severe brain fog and memory loss. His brain function, including memory is way better on your 200 cals a day of safe starches.
    Two weeks ago, David had a seasure. He also had one 8 years ago. So far all the tests have come back normal.and the neurologist has no explanation to offer. In your opinion, could the seizure(s) be in any way related to the amnesia, possible brain infection. if so how. And what should we do about it.
    Many thanks for all of your hard work. We feel so fortunate to have access to research of your calibure.
    Diana (+David)
    P.S. Do you ever offer telephone consultations. If so what is your rate.

    • Hi Diana,

      I’m not a great believer in coincidences so I think it’s likely that the seizures and the other neurological symptoms have overlapping causes, if not the same cause.

      It sounds like he would do well on a ketogenic diet. Circadian rhythm tactics are also important for brain health (see chapter 42). Intermittent fasting is helpful.

      As far as medical treatments, it is difficult to say. It is impossible to diagnose brain infections so you would have to test antibiotics to see if they improve matters; and then interpretation is often difficult, sometimes it’s hard to tell whether antibiotics are helping or hurting. A good rule is that if you don’t have an infection, they will produce minimal effects. Another good rule is that you should improve health as much as possible naturally before starting antibiotics.

      He might also get a stool test to look at the microbial population of the gut (see Metametrix microbial ecology profile), as there are many gut-brain interactions and the gut is more amenable to diagnosis and treatment.

      I’m afraid I don’t do consultations. But you can ask questions here and make a return by recommending our book to friends, leaving Reader Results stories, Amazon reviews, etc.

  26. Diana Durnford

    Hi Paul,

    Thank you so much for your helpful reply. We will fallow up on your recommendations and let you know how it goes.

    Can a brain infection be viral or fungal in origin, or are they always bacterial ? Presumably antibiotics would have no impact on at least a viral infection . What about a fungal infection ?

    For a strict ketogenic diet , are coconut oil, ghee and bone broth acceptable during fasting , or just MCT oil as per page 158 of your book ?

    Is aerobic exercise contraindicated on a ketogenic diet ? It is strange that David’s seizure and at least one bout of amnesia were preceded by a day of vigorous aerobic activity .

    Yes , we will of coarse happily and enthusiastically recommend your book , etc .In fact we already have . One of my doctors was so impressed , he asked me for further recommendations !

    Many thanks once again

    Diana ( & David )

    P.S. We apologize for the presentation of our first email . Our computer stubbornly refused proper punctuation and we finally gave up , trusting to your good humor and interprative skills . Perhaps things will work better once our brains are working better !

  27. Diana Durnford

    Hi Paul,

    Some interesting things have been happening. First, David significantly increased consumption of MCT oil, and got stricter about intermittent fasting. To our astonishment, on Day Two, he got up, said he felt himself for the first time in months, and sat down and read the newspaper. Still lots of brain issues, but a significant improvement.

    Second, his naturopath diagnosed the brain infection as Borrelia (Lyme.). Whatever the validity of this, this would be consistent with problems associated with aerobic activity. Lyme is known to more easily cross the blood brain barrier with vigorous exercise, exacerbating any brain symtoms. Lyme, of course, also gets worse with excessive carbs, etc.

    Finally, we learned that Lyme can cause seizures! Many things can, of course, cause seizures, but given your June 4th post, we were particularly interested to learn this.

    So what do you think? Any pointers on how we could test and/or treat a Borrelia brain infection?

    Many thanks,

    Diana (and David.)

    • Hi Diana,

      That’s great news!

      Well, I think the response to ketosis and fasting does seem like strong confirmation that he has a bacterial infection, and that suggests a course of antibiotics along with the ketosis and fasting.

      Unfortunately there is no way to test for brain infections and the blood/serology tests that are available are of somewhat dubious reliability. I personally don’t try to keep up with clinical matters so the various tests and possible treatments are best discussed with a doctor who has worked with Lyme and other chronic infectious disease patients.

      I would just emphasize that a good diet will be an important adjunct to any treatments you pursue, it will make antibiotics work better and diminish side effects.

      Best wishes and let me know of David’s progress!

      Best, Paul

  28. Could you tell me what are the cognitive symptoms of hypoglycemia and how did you relieve your blood sugar when it became elevated?

    Also, would diet pepsi or coke be harmful to hypoglycemia and to gut bacteria balance?

    And last, I bought your first book last year and just started reading it. Is the newer edition much different?
    Thank you.

  29. Paul,

    you said antibiotics may fail on a bad diet. But as a trial on antibiotics, would you feel better at least temporarily while on it?

  30. Hello there. I am suffering from all of the symptoms of a abscess in the brain. And I have pain in the temple vein and the top of my head. It came on slowly ….at first forgetting things, and clumsiness. Then one day everything LOOKED different . I couldn’t explain it, but it was off. I was trying and being hopeful. It got so bad one night, I couldn’t function at all and I took off to the ER. CAT Was fine and so was MRI according to them. I suffered for li ger but tried to tell myself it was nothing like they td me. i took matters into m own hands bc it was sad feeling my mind and my body go while i was trapped inside :/ i borrowed anti iotics from a feiend with a thyroid condition. i was functional! i was so happy, but the sec i ran out of the. The feeling slowly came back. if i go to the ER now How do I find this infection? How do I stress to them that the antibiotics cured me ! They don’t listen to me and I am on garlic now it helps but not like the anti biotics. Am I a lost cause? Will I need brain surgery? Please help. … help 🙁

  31. Paul I would appreciate if you could give me your opinion on something I’ve been dealing with. Please. Doctors where I live don’t really have an explanation for what was happening (same doctors who adviced me eating low-fat and whole grains 6 times a day so I’m not surprised.)
    I’m 20 and I’ve had severe reactive hypoglycemia after being without my period for 2 years. (I think there’s a connection). My fasting blood sugar was always normal (80). I did a 72h fast in the hospital and they didn’t found anything wrong (they were suspecting an insulinoma, which I always knew it wasn’t the case). Later in that day when I got home I ate dinner and my blood sugar crashed to 35… (like it used to). I almost died!!! But if that happened after being 3 days without any food I believe (from what I’ve been studying) maybe cortisol is involved. I also have hashimoto’s since I was 14 years old but my thyroid labs are normal and I never had any issues since I started taking levothyroxine, so I believe that’s not the main culprit. What I did was to eat only fat and protein for a couple of days and every 2h… that really helped me. Now I don’t have hypoglycemia one hour after eating but if I eat something with more than 10g sugar my blood sugar spikes and still crashes. (insulin resistance) but to 60… I’m not in a life threatning situation anymore like I was 3 months ago.. and the fact that I managed to avoid such intense and stressful hypoglycemic episodes made me regain my awareness of them (which saved my life) but I still would like to understand what was going on with me and what tests do I think I should ask my doctor. This is a very important issue for me because I am going to college next week and praying that I don’t have to go through that again and that I can finally live without having to measure my blood sugar all the time. (since I was not aware of when I got values like 35 or 40 and I am not diabetic).
    Please if you could help me understand this I would be thankful for the rest of my life

    If you could answer me or write an article that could help me I would be thankful for the rest of my life.

    • Hi MK,

      Usually blood glucose regulation issues result from infections of the small intestine that spread to the pancreas. Hashimoto’s is usually caused by gut infections too. I agree that this infection was probably connected to your loss of period.

      Going zero carb will help in the short term if you have a bacterial infection, but it’s not sustainable and in time you’ll tend to acquire other infections that flourish when carbs are absent, and then you are really in trouble.

      The first step is to supplement vitamins A, D, C, zinc, and iodine to support immunity. You can take 5,000 to 10,000 IU of preformed A per day, enough D to optimize serum 25OHD, vitamin K2 (100 mcg/day MK-7) to support those, vitamin C to near bowel tolerance as ascorbate powder in water, ~20 mg zinc per day (150 mg / week), and 225 mcg iodine per day.

      Best, Paul

  32. Plz help me …plz my sister in brain infection. ……

  33. Any body help me …she is too much weak and disabl…….

  34. Doctor said she sufring varial brain infection.after 4mount she is not her condions is no good so weak and disabl …pls ans me ……

  35. Plz help me my sister in vairal brain infection. .her condition is not well .day by day she let down…doctors her tratment but she doesn’t improve. ..plz u help me plzzzz .I am in so much painn….

  36. Hi Paul,

    The good news is that we have found a neurologist who is open to the possibility that David has a brain infection. The bad news is that, in his opinion, David’s MRI is not normal. We will learn more in our next appointment.

    So our first question is: how would a brain infection manifest in an MRI?

    Second, would you recommend treating biofilms or would this be too dangerous when dealing with a brain infection?

    Third, and unrelated, even after several months of MCT oil, I still get a burning sensation in different areas of my digestive tract. What is this? Is this of concern?

    Thank you so much once again,

    Diana (and David.)

  37. Hi Paul,

    Would a lumbar puncture show anything related to your kind of bacterial brain infection?

    Our neurologist is willing to do a lumbar puncture for David, but we don’t want to do one if it would be a waste of time. He says that for the type of bacterial brain infection that he is familiar with (one that is fatal unless treated very quickly), there would be signs of inflammation, etc. in the test results. He also says that if David’s brain is being affected by a bacterial infection elsewhere in his body, that nothing will show up.

    What do you think?


    Diana (and David.)

  38. Hi Paul,

    Thanks so much anyway. I really appreciate your responding.


  39. Hi Paul,
    all those symptoms are what i’ve been feeling for what seems like forever. i had a concussion as a 12 year old and pneumonia in my early twenties – wonder if they lead to this possible brain infection….

    My 5 year old also experiences hypogylcemia and irritability, difficulty finding pleasure, low self esteem etc. I suppose it’s possible we have the same root problems which i now suspect is a bacterial infection in the brain and fungal overgrowth. I know young kids can often clear things more efficiently (e.g. controlling SIBO through diet alone). DO you know of this being the case for brain infections and candida?

    Also, can you point me to any literature i can present to my doctor to help me persuade her to investigate this with us?

    thanks, you have made a huge difference for us. i now see a brighter future.

  40. Eugene Trileski

    Is extreme fatigue after carb–heavy-meal a sign of infection?

  41. Hello Paul,
    I have a question about yerba mate. I have been drinking it for years thinking that it helps to boost the immune system, provides a steady source of energy while managing blood sugar. Recently I have had some trouble with a systemic fungal infection which was exacerbated by a change in diet (I am now eating a mixture of the GAPS and PHD diets, but also very low-carb). It seems that the internal symptoms (brain fog, fatigue, depression) are now manifesting on the surface of the body (i.e. skin infections); that is something I am grateful for. However my skin infections persist. While I have read that yerba mate has anti-fungal and anti-viral properties, I just came across the following study that suggests that yerba mate may actually contain fungal colonies:

    What are your thoughts on yerba mate?

    Thank you,

  42. “Positive changes in brain function during ketosis suggest that the brain isn’t functioning normally when it relies on glucose as a fuel. There are several possible causes of this, but one is a bacterial infection.”

    What are other possible causes?


  43. Hi Paul,
    Thanks so much for these insightful posts on brain infections.

    Could you elaborate on the concept of “cognitive hypoglycemia?” I haven’t seen this mentioned in a medical context elsewhere, but your description of a brain infection matches my experience exactly. I feel horribly brain-fogged, fatigued and anhedonic almost all the time, when my blood sugar is normal at ~80-100. If I consume high amounts of carbs, I temporarily feel significantly better while my blood glucose is elevated

    I am in my early 20’s, and my symptoms began about 3 years ago. My problems also include gut issues, high cortisol/low T3/low testosterone, and autonomic nervous system issues. I followed a nutrient-dense paleo diet for most of this time and use most of your supplement recommendations, so micronutrient intake wasn’t likely a factor. I got a positive Lyme disease PCR result, so I was treated with several different classes of antibiotics, including IV Rocephin for several weeks. All of these failed to fix my symptoms, so I began to doubt that an active infection is causing my problems. Most recently, I’ve been trying to treat SIBO and heal my gut to reduce endotoxemia.

    However, your posts about brain infections are a spot-on description of my symptoms. When I did a 60-hour coconut oil fast and then transitioned into a ketogenic diet, my energy and neurological symptoms improved drastically for about a week, but I then started to feel worse again, so I added carbohydrates back into my diet. I usually feel worse when I add MCT oil to my diet, so I can’t really follow your protocol for increasing ketone production while on a moderate-carbohydrate diet.

    Do you think it’s likely that I have a brain infection, even though antibiotics didn’t help? Is there any way to find out for sure, and do you still recommend following a ketogenic diet?


    • Hi Greg,
      I can’t respond to all of your questions, but I did get this response from Paul when asking about brain infections. He said: “Possible causes of doing better on ketosis are gut infections whose activity is suppressed when deprived of carbs, or genetic mutations that impair glucose metabolism.”

      If you feel better with increased blood glucose, that’s probably an important clue.

      From reading this post, and the comments and responses to comments, I get the feeling that Paul would recommend trying doxycycline and if you feel better, great. and if you don’t, go back to the drawing board. He says on other places on the site that doxycycline is less worse when it comes to destroying gut flora than other antibiotics, but I’m not sure where that comes from (have been trying to find a paper or study that would support this)

      It’s strange that you can do coconut oil for 60 hours, but not MCT oil? I think they’re pretty similar, and perhaps someone could jump in if I was wrong, but for a ketogenic diet (i.e. one that includes carbs and PRO), I don’t think you have to use MCT oil. I think you could also use the branched-chain aminos, MCT, or coconut oil.

      I believe coconut oil or milk (bc 3 tbsp of coconut milk = 1 tbsp of coconut oil) are just as good as MCT oil. I think MCT oil is just a refined coconut oil and slightly richer in ketones, albeit a more expensive way to get ketones. I found the branched-chain amino acids to taste horrible and so don’t use them.

      But anyway, the ketogenic diet helping is probably a good sign.

      Unfortunately, most people don’t have just one infection but multiple. seems to be another recurring PHD theme unfortunately.

      Paul also told me “If you clearly do better on a ketogenic diet, then I would continue it while taking doxycycline. However, in your case that is not so clear. In general I favor intermittent ketosis with intermittent fasting, not continuous ketosis.”

      So, in summary: you could try doxycline with a ketogenic diet, and see how you do, but it sounds like you have other infections to worry about as well, and this might not be the panacea.

      have you had any stool testing? I would recommend BioHealth Labs 401H + Doctor’s data as the metametrix test for parasitic infections is now O & P (i.e. they examine the stool for ova and parasites, but no longer check for DNA of parasites)…
      Good luck!!!

      • Hi LN,
        Thank you for your thoughtful reply.

        I have already tried doxycycline, and I’ve also tried minocycline, along with more than 10 different other antibiotics at some point. However, these didn’t help my symptoms significantly, and I’m sure that they’ve destroyed my gut flora. Do you think that antibiotics might help if I tried them concurrently with a ketogenic diet, even though they didn’t help before?

        When I said that I generally don’t respond well to MCT oil, this also applies to coconut oil. However, this effect isn’t that significant, and it only applies when I am not in ketosis. When I started the fat fast, I felt even worse until I went into ketosis and started feeling better.

        I can’t practice intermittent ketosis with intermittent fasting, because I have symptoms of “adrenal fatigue” that worsen when I do intermittent fasting. For me, I only get the benefits of ketosis when I follow a ZC diet. MCT oil, coconut oil and BCAAs don’t make me feel any better when I take them at other times.

        As for stool testing, I got the Genova Diagnostics CDSA a while ago. I believe we found some evidence of parasites, but the antibiotics didn’t help my symptoms.

        At this point, I don’t know what is causing my symptoms, because they have gotten even worse over time. I recently found out that I have SIBO and gut inflammation, so I’m trying to treat that now. However, I doubt that this could have caused all of my neurological and hormonal symptoms for the last 3 years. Some sort of brain infection would explain my illness, but I don’t know what to do now since I have already run the gamut of antibiotics. I might try starting a ketogenic diet again since it temporarily improved my neurological symptoms so much, but I would like to find some way of preventing any downsides. For example, I already have high cortisol, low T3 and “adrenal fatigue” symptoms, so this might be an issue.

        I think that if I am to have any chance of getting better, I would have to find some way of determining exactly was is causing my illness. I think you’re right that it might be a good idea to repeat the stool testing, but I don’t know if this will turn up anything useful.

        • Greg,

          The reason you may feel better with an increase in blood glucose may have to do more with insulin’s effect on water retention and therefor blood volume. People with adrenal issues tend to have low blood volume. Have you tried sleeping on an incline? This can help increase blood volume. Avoid the temptation to just prop your head up with pillows. The entire head of the bed needs to be elevated 6″-12″.

          • Hi Kevin,

            That’s an interesting idea, but I don’t think it has to do with insulin’s effect on water retention. I took fludrocortisone for 2 weeks at one point to try to raise my blood pressure, and it made me retain about 10 pounds of water, but I didn’t feel any better during this time. This makes me think that retaining more water doesn’t really help, although I still make sure to use a large amount of sea salt in my diet. Also, when I spike my insulin with protein but without carbohydrates, I usually feel worse. The same thing happens when I use an insulin mimetic like alpha lipoic acid. The effect of feeling better from high amounts of carbs also is much more pronounced and sustained if I consume the carbs at night, when insulin sensitivity is lowest and blood glucose levels will likely remain elevated longer. This all points to the increased blood glucose making me feel better, and not the insulin.

            I haven’t tried sleeping on an incline, but I’ll look into this since I do have low blood pressure and heart rate. Thank you for the suggestion.

        • hi Greg,

          I think this might be useful for you? Genova and Metametrix merged. So when you try to buy the Metametrix GI Effects or Ecology Effects (which Paul recommends on other places on the site), or a Genova CDSA, I’m not sure if they tested everything that needs to be tested.

          With that in mind, can I ask if you got the GDX 2200 stool panel with pathogen add-ons?

          I think a lot of the pathogen testing they used to include in the Metametrix GI Ecology Effects test you now have to add on to the Genova diagnostic test. With the add-on, then and only then will they (merged Genova/Metametrix) test for the following: C. difficile, H. pylori, Shiga Toxin E. coli, and Campylobacter spp

          Those are key to test for, in my opinion, and from the research I’ve done. It seems like you, with your background, would be more susceptible to those pathogens than others.

          Do you read That’s where I obtained this information. Here’s a link to the comments discussing the proper tests to take:

          (you can search for 2200, or EIA and that will take you to the points I was talking about in the comments, because it’s quite far down – some information in the post as well about testing)

          3) Dr BG also recommends ordering the GDX ONE urinary dysbiosis panel.

          Another test, you say?

          My 2 cents: I worked with a functional MD and he also ordered a stool test as well as the urine dysbiosis/nutritional status panel.

          The urine test looks for fungal and bacterial compounds in your urine, and also based on urine metabolites can indicate if you’re deficient in any vitamins or minerals.

          These were metametrix tests at the time my doctor ordered them, but I think these Genova tests Dr BG recommends are the same or very similar to what I took.

          The urine test helped show that I still had a Magnesium deficiency despite supplementation, as well as fungal overgrowth and L. acidophilus overgrowth that my stool test did not pick up.

          So, my stool test on its own wasn’t complete to help diagnose me.

          I also supplemented more magnesium for a while. If paul had scurvy – a deficiency of Vitamin C – I definitely had a BAD magnesium deficiency from eating Primal/Paleo.

          I noticed a difference after treating all these things – I had a parasite, the mag deficiency, supplementing bifidobacter – but then I started to feel tired again. It’s better then it was, but still working on it. Progress was slow.

          Unfortunately, my doctor was quite expensive and so I tried to retest my stool on my own via Unfortunately – I hadn’t realized that Metametrix and Genova had merged and so I think I paid $350 for a useless stool test that didn’t look for any pathogens! (Beware 100% self-treating, basically)

          And I guess my gut bacteria are in fairly good shape, but the stool test was pretty useless as it didn’t test for pathogens or parasites that were all I really wanted to know about.

          There’s a 3rd website, (or something like that) that actually now recommends BioHealth Diagnostics 401H and Doctor’s Data with Parasitology x 3. Jordan Reasoner and Steve Wright talk about how a lot of times one stool test will miss what another picks up. So that may be your case as well.

          With respect to parasites, I’ve read that you want several days of sample as parasites can intermittently shed. Again, you’ve taken so many antibiotics that it seems like you may just want to refocus on leaky gut and rebuilding your gut flora. Paul, any thoughts?

          I think the important thing to keep in mind is that no stool test is perfect and a practioner, IN THEORY – should be more well versed in which tests you should take – but keep in mind as well that even functional docs may have a very strong interest in which company’s tests they use.

          I’m so sorry that you have taken so many medications and still have not seen results, but although they are not perfect. But don’t give up! I think PHD works great wonders, but I think for some of us it could take longer than others. For me the hardest part is definitely getting the bone broth made and finding interesting ways to use it. Second hardest part is finding the energy to exercise for 30 minutes a day. If I get 30 minutes of light walking in with the dog, I’m lucky.

          Two more tips for PHD-living:

          1) A bowl of bone broth with tomatoes (can you withstand those?) or even broth with just herbs, lemon, salt and pepper is a good fasting breakfast or fasting meal. Remember – you can eat during fasting!

          I found I had worse cortisol and adrenal fatigue symptoms with VLC, despite other symptoms getting better. I would definitely recommend getting some carbs back in – maybe dextrose? – even though I understand how VLC can help a lot.

          2) which parasites did you find? Blasto? B. Hominis?

          • Looking back at the Genova CDSA, they did include the pathogen testing. However, my stool tested negative for all of these. I had remembered that one of my stool tests showed evidence of parasites, but now I don’t see this. I’ll ask my doctor why he had me take antiparasitic drugs, because I assume he based this off of one of my test results. As of right now, I don’t think I was diagnosed with any parasitic infection.

            I do read drbganimalpharm sometimes, although her SIBO protocol made me feel worse from the resistant starch/soluble fiber/probiotics. I found some of her posts on the APOE-4 genotype useful, and I suspect that this genotype is involved in my susceptibility to neurological problems from infection and toxin exposure. My hair and provoked urine mercury levels both tested very high, but I react badly to chelators and read that I shouldn’t attempt chelation therapy until I fix my gut problems. Anyway, I’ll look into Dr. BG’s lab panel recommendations and ask my doctor about them. Have you heard of a type of stool testing where you take a high dose of laxatives to “clear you out” and increase the likelihood that any sign of parasites will be present in the stool sample? My doctor mentioned this, so I’m going to ask about it tomorrow.

            I’m very glad that PHD has helped you feel better, as it has for many other people. I’ve been eating this way for a long time too, but at this point, I know that my medical issues persist even on a balanced, nutrient-dense diet. I’ve been taking high doses of magnesium and vitamin c for a long time along with other micronutrients, so I don’t think nutrient intake is a problem.

            I was eating grass-fed bone broth with all meals for a few months, but it didn’t make any noticeable difference in my symptoms. Now I just eat grass-fed gelatin and trace minerals, because I don’t have the energy to make bone broth. With me, intermittent fasting exacerbates my “adrenal fatigue” symptoms even if I eat a light meal like bone broth. My body temperature drops even lower than normal, along with a slowed heart rate. I always feel much worse after I eat, but intermittent fasting messes with these other symptoms too much to continue.

            I already added carbs back into my diet a while ago. Currently, I only get carbs from dextrose because I started an elemental diet to treat SIBO. I eat most of them in my last (liquid) meal of the day, because my tolerance for carbs increases at night. However, I still don’t like that I am consuming ~80g of pure glucose at once, as I’m sure this causes a very large insulin spike. Again, I wish there was a way of doing a ketogenic diet without messing with my cortisol and thyroid.

            Thanks for sharing your knowledge and experience and trying to help. I agree that I need to try to fix my gut immediately, but I still don’t know what is causing my severe neurological and hormone problems. I developed these medical problems before I tried the antibiotics, so I don’t think that healing my gut (if this is even possible) will fix my all of my problems. If there was some way of verifying that I do or don’t have a certain type of brain infection like Paul described in his posts, then this might at least point me in the right direction. Also, I would like to know whether it’s worth continuing a ketogenic diet for its neurological benefits even though it has some other adverse effects, and ruling out certain types of pathogens would help me figure this out.

  44. Greg
    I guess if it makes you feel better, you could follow the PHD ketogenic diet. (Ie induced by scfats and still eating carbs?).. That is basically the advice paul gave me. And he said to me that if I did have improvement that I should continue while on AntiBx.

    It’s tough bc gut symptoms will cause brain symptoms, and which came first-from what I understand- is kind of like the chicken and the egg. You might find that healing the gut will help brain symptoms, but I understand too it is a long road for either, and you are in pain now.

    I have heard that you want to take something to have loose stool to get the parasites to shed… I get diarrhea from too much mct oil or coco oil so I got that in one sample naturally.

    If I may, what are your thyroid results? Are you taking thyroid hormone to help your gut heal? (Paul talks about that on a post on the website) it may also help with brain fog symptoms. From what I understand you try it and go for the lowest possible dose…


    Keep in touch, let us know.


  45. Unfortunately, the PHD version of the ketogenic diet doesn’t work for me. When I use large amounts of MCT or coconut oil when I’m not in ketosis, it doesn’t improve my energy. I seem to only experience the benefits of ketosis when I eat almost zero carbs, and anything that spikes insulin makes me feel fatigued again. I’m considering going back on a ketogenic diet, but I’ll try adding 25-50g dextrose after a brief high-intensity workout every day, and I’ll also try doing refeeds with 200-300g dextrose once a week. However, I suspect that even this amount of carbs might be enough to prevent the neurological benefits of ketosis in my case.

    It’s possible that gut problems preceded the neurological symptoms and hormone problems, but I’ve never read about anyone with problems as severe as mine that resolved with treating the gut. However, I do know that my gut is very messed up, so I’ll see what happens if I manage to fix GI function. Currently, I’m starting an elemental diet to treat SIBO along with glutamine and DGL to heal the gut lining. I might also add LDN at night to decrease inflammation.

    My thyroid results are consistently low T3, borderline-low T4, and TSH ranging from low to high. I also have a low pulse rate, low body temp and often low BP. I’ve tried many different forms and doses of thyroid meds including Cytomel, sustained-release T3, T4, T4/T3 combo, and Armour Thyroid. All of these make me feel more fatigued/brain-fogged and make my heart pound, and my blood tests show that these medications suppress TSH significantly without improving T4 or T3 concentrations. Thus, I’m currently off all thyroid meds, although I was on them for a while. I also have high AM cortisol and secondary low testosterone. I’m currently treating the testosterone with low-dose Clomid, although my free testosterone levels are still low-normal.

    My sleep is usually not very deep or restful. I always take melatonin because I can’t fall asleep without it, and I also usually wake in the early morning and have trouble falling asleep. When I’ve tried supplements to reduce cortisol like phosphatidylserine, they make my sleep worse and give me heart palpitations. Circadian rhythm therapy has helped a little, but my problems are still there. I think that getting good-quality sleep every night would go a long way in improving the likelihood of a positive outcome from my treatment, but I might not be able to fix my sleep until I fix the other problems. This is another chicken-and-the-egg problem that I haven’t been able to figure out.


  46. Right, it would be too simple that thyroid hormone would fix all your problems, right?

    I’m no doctor, but definitely sounds like you have a brain issue. The problem, I think, is that you probably need multiple doctors to kind of deal with all your problems. One to run functional medicine tests, another to run traditional medicine tests.

    This was an approach I picked up from others on PHD. Neither doctor is always 100% right, but can give you helpful information as you navigate through your own symptoms.

    Did you retest gut flora after taking antibiotics? Do you still have significant amounts of “good” bacteria? Did you have die-off symptoms while taking them? Were you on PHD while taking the ABX?

    Prior to ABX as well as now, do you have any other symptoms that might lead you to conclusively say you have a bacterial infection more than say, fungal or protozoal? (Foot fungus, rashes, etc.? sometimes come up when VLC versus LC, things like that and would say you have a fungal infection, versus a symptom when your blood sugar is high (BTW are you measuring your blood sugar?)) Have you tried charcoal/Bentonite to absorb circulating pathogens and see if you feel better? That can be a clue as to what type of infection as well.

    I was eating low carb but had symptoms of adrenal fatigue/burnout like you and I think I couldn’t withstand low carb because of a parasite and mild fungus. On the other hand, VLC was probably suppressing some SIBO/SIFO so VLC was helpful in suppressing my symptoms for a while.

    Also, even though the glutamine supplements may help initially, after Paul posted about supplementing specific amino acids causing bad after-effects in mice, I became very cautious of supplementing with amino acids. So, for example, this is a paper I found with respect to dangers of L-Glutamine:

    Basically, L-glutamine, not glucose, was the major agent responsible for Vaccinia virus replication. Likely, you don’t have this virus, but there are other viruses and pathogens which you may have and likewise, supplying L-Glutamine in excess could encourage those pathgens to grow. On the other hand, you may see significant benefit with L-Glutamine – it probably wouldn’t kill you to perform an experiment, and the improvement may be enough to convince you start making your own bone broth! (I throw bones in a slow cooker with water to cover and leave the thing on for three days – super easy!)

    Finally, one last tip on the melatonin – the more I take, the earlier I wake. I found out if I take only 0.5 mg before bed that I can usually sleep through the night. Your body only makes 300 mcg on its own, and a huge drop-off may be what wakes you up.

    Don’t lose hope! There’s a lot of information out there, just keep trying things, and observe the result. Try to spend as much time outside as possible, and even if you can’t fast, try to eat at almost exactly the same time everyday. The zeitgeibers as Paul calls them.

    The progress will be slow, but it’s worth it to be able to live normally with a clear head.


    • I actually am seeing several doctors, and I have seen many others since I became sick. My experiences with most of them made me very skeptical of listening to doctors, as pretty much all of them gave conflicting diagnoses and medical advice. Obviously, none of them have succeeded in figuring out how to treat my condition either. I’ve seen both functional and traditional medicine doctors who have run extensive lab testing. Currently, I’m trying to find new doctors, because I’m at a loss for what to do otherwise.

      I did not retest gut flora after taking abx, because I already know that the bacterial balance in my gut is very messed up so I’m not sure what this would tell me. When I try most probiotics, the make me feel worse, which might be because of the SIBO. I didn’t notice pronounced die-off reactions while on the abx, but it’s hard to tell because my symptoms fluctuate often, and some days I feel much worse. During this time, my diet contained high amounts of vegetables, animal protein and good fats, along with some rice, nuts/seeds, and whey protein isolate.

      During the time since I became sick or when I was on a ketogenic diet, I don’t think I noticed any new rashes that would point to a fungal infection. While I was on antibiotics, I did develop oral thrush, but the tongue coating went away after I used Nystatin. I don’t know how else I could distinguish between the signs of a bacterial and fungal infection, but maybe there are some other differential criteria that I’m not aware of.

      I am measuring my blood glucose, which is how I found out about the cognitive hypoglycemia. My blood glucose levels are generally normal and drop back down fairly soon after consuming carbs, except I feel better when BG is at least ~120.

      I have tried various binders including charcoal and bentonite, and it’s possible that some of them improved my brain-fog, but I couldn’t continue any of them because they all made my constipation much worse.

      I agree with your advice to be cautious with glutamine, but I’m unsure about whether it’s essential that I use it to heal my gut. I saw Paul mention that it can feed certain types of pathogenic bacteria, so I decided against using it for a long time. However, pretty much every other gut expert makes it seem like glutamine is essential for repairing leaky gut, and I haven’t seen evidence of any other treatment that is as effective at decreasing intestinal permeability. That’s why I tried adding it to my regimen while I’m trying to heal my gut. Do you think that bone broth is as effective as glutamine for this purpose? My understanding is that the benefits for leaky gut come from the gelatin content, and I have already been consuming grass-fed beef gelatin for a while. However, gelatin contains glycine and proline but not glutamine, so I assume that its benefit against leaky gut is by a different mechanism.

      I completely agree that higher doses of melatonin wake me up earlier in the morning, and I try to take physiological doses of only 300mcg for this reason. However, I often find that I can only fall asleep if I take 1-3mg, so I take more in order to fall asleep. I’ve tried various other sleep aids, but none of them work well enough. Valerian root seemed to improve my sleep quality and make me feel significantly better the following day, but its effects wore off with continuous use and then my sleep worsened after I stopped.

      Thanks again for your detailed and rational responses.


  47. Hi Greg, sorry that this has turned into so many questions. I understand your predicament and that many of the supplements don’t work for you. I am the same way with the Bentonite/charcoal – it gives me constipation and drinking more water like you’re supposed to when you take it, well it makes me sick to do that too.

    On sleep – I used to have many of the same sleep problems you have and they have taken me about 9 months to fix them. I was so fortunate in that I was able to take off of work for a while to focus on sleep and health. I had had insomnia on and off for 10 years. But I felt until I fixed my sleep and was able to sleep consistently, I would have no baseline for fixing anything else.

    I wasn’t sure if my fatigue/foggy head were caused by being unable to sleep through the night. and I was tired of getting dismissed by doctors that thought that restless sleep/waking early was the cause of everything.

    Are you at all able to spend multiple hours outside during the day, especially now that summer/warmer weather is coming? Or if you cannot spend multiple hours outside, would it be at all possible for you to go camping for about 1 week, without bringing any electronic devices? (or bring them, but only use them during the day?) I think even being in the shade outside can be beneficial, but I found it took me 3 months of being outside for ~3 hours every morning before my circadian rhythm was set and melatonin began to really help.

    Sometimes there was someone to talk to outside, sometimes there wasn’t (I went to the dog park with my dog). I think talking to someone is supposed to help a lot – morning faces and all for hypothyroidism.

    But if I had been able to get away for a while then camping would have been my first choice of “medicine.” It usually helped with sleep problems for me before, and there was a study showing camping without electronic devices helped people with seriously disturbed circardian rhythms when they camped for about a week.
    (The medicine prescription of the future I hope!)

    Re retesting gut flora – you’re right, it takes a long time to remodel and change gut flora. But eventually I think you want to do it to find out which “beneficial” species you are low in, or if you have any bacterial overgrowths from lack of good bacteria. or fungal overgrowths as well…

    In the meantime, I do think there is benefit to bone broth versus Glutamine. Depending on how you cook the bones, the bone broth can have magnesium and calcium, plus other bone matrix material, and perhaps other amino acids which gelatin or even gelatin+glutamine might not have.

    Again, probably litte danger in trying glutamine + bone broth for a while? But because your immunity is likely suppressed (indicated by brain issues), that’s where I see the danger in your trying glutamine.

    Dr. Kharrazian has written a book called “Why isn’t my brain working?” and he talks about the deal breakers for him with brain issues. Iron levels (i.e. anemia), glucose issues, and there may be a third – are deal breakers for him. But for glucose issues I think he means people with wild swings – like from 70 to 140 or something.

    Are you iron levels ok?

    PS one supplement my functional MD recommended was Zinc Carnosine – there are two versions, a metametrix one (really expensive) and a Swanson one, and Zn Carnosine has a medical study showing that it will help decrease intestinal permeability. That was the great thing about my Functional MD – I don’t think he was recommending supplements willy nilly as many will do.

    The swanson one costs about $15 and it might be worth a shot, in addition to the bone broth. You could take 50 mg of zinc carnosine per week as opposed to other zinc supplements and balance that zinc out with your liver intake. I would guess you would need vitamin A for immunity and to help improve intestinal permeability as well, so liver or lots of egg yolks would be in order!

    Here’s the article on zinc carnosine, take it for what you will – the reviews on amazon for Zinc carnosine are also good:

    Finally, are you able to stand at all during the day – when you work, use the computer, etc? I understand you may be too fatigued to do exercise like I was, but I found standing really helped, as well as very, very light walking. I lean on something while I “stand” so I’m not perfect. But it helps my body know it’s time to be awake.

    All in all, I’m not sure if anything helped me improve my health more than having a dog. Made me exercise, talk to people, stick to a schedule, and provided some play, in spite of chronic fatigue, brain fog, insomnia, hypothyroidism, randomly a low serum iodine level, etc. that took (and are taking) their own sweet time to resolve.

    I don’t know if my health issues will ever be 100% resolved – I still get some stomach troubles every now and then, and every so often a bad night of sleep, but mine follow a cyclical pattern, and now I’ve come to expect when my health will fall of the rails a little (basically around that time of the month)

    I guess, I would say that if you feel like things are that bad, maybe try the perfect health retreat on the beach? A little vacation (albeit an expensive one) might be good medication, even more so than researching, trying new doctors, or new supplements.

    Hope I don’t sound like I know best, but I definitely would have gone to the PHD retreat in Austin if I could’ve. I think 30 days there was probably equivalent to the 8-9 months I took off trying to fix things, so which would have been more expensive in the end, it’s hard to say.

    I’m subscribed to this thread, so let me know if you have anemia/how the zinc carnosine/whatever other supplements work out for you.


  48. A lot of good advice again, although I’m already doing much of what you said. Sorry that I didn’t list more of the treatments that I’ve tried, but I didn’t want to make my comments even more wordy.

    I’m currently on leave from college because of my medical issues, so most of my time is dedicated to my health, although this hasn’t helped at all yet. I spend most of my time in a well-lit room with plenty of windows, but I’m trying to spend more time outside too. I don’t think I have the energy to go camping, but I try to disconnect myself as much as possible, and wear amber glasses after sundown.

    As for the bone broth, I think that it does probably have health benefits beyond the gelatin and minerals. However, as far as I know, most of the benefits for leaky gut come from the gelatin. If I find out otherwise, then I’ll try to put in the effort to making bone broth again, but for now I’ll probably just stick to using plentiful gelatin/hydrolyzed collagen.

    I haven’t gotten my iron or ferritin levels tested in a while, but last time I checked my ferritin was 72 with a reference range of 30-400. I don’t think I have anemia, because my RBC count is always normal. My WBC count is always a little low, but I don’t think that has to do with iron.

    I’ve also heard of zinc carnosine helping intestinal permeability, and I’ve been taking Doctor’s Best brand every day for a few weeks now. I don’t think it has as much evidence supporting its efficacy as glutamine, but I figure it’s at the very least benign. I’ll probably go above Paul’s recommendation of 50mg/week of zinc while I’m using it, in order to match the amount used when it was studied.

    I have my laptop set up on a treadmill, so I’m usually standing when I use the computer. I have to sit or lie down a lot of the time when I’m feeling too fatigued, but I try to stand as much as possible. I also walk as much as I can and do brief high intensity weight lifting every few days. Exercise is one of the only things that makes me feel clearly better, although it usually only lasts for about an hour after.

    Interesting that you had a low iodine level, because I had that too for some reason. Now, I’m supplementing with Lugol’s solution, so my serum levels are probably better.

    Did you ever diagnose a specific cause of your health problems? Did you find that any treatment really helped you get better other than circadian rhythm therapy, diet and activity? Do you now feel significantly better and at least have relatively normal energy on most days?

    I’m not sure how much I could benefit from the PHD retreat, since I already read the PHD book and follow the blog, and I implement the changes to support circadian rhythms. I think the main benefit would be from getting a chance to consult with Paul.

    I know at this point that following “ideal” practices for general health and getting plenty of rest just isn’t enough to resolve my medical issues. I’m pretty sure that in order to have a chance of getting better, I would need to find and treat whatever is causing my illness.


  49. Hi Greg,

    The things that helped me the most were going outside each and every day for light activity (I mean LIGHT walking); tracking how much I was eating, because I think sometimes it’s easy to not eat enough; melatonin; and the combination of bone broth + coconut milk + herbs once I was able to fast really helped with my fatigue and head/brain fog.

    Monolaurin helped a little, and I’m on a lot of the PHD vitamin and mineral supplements which helped with a random skin rash. I don’t like taurine, for example, and didn’t find much benefit from lithium, so for example, there are things I don’t use.

    Like you, I wanted to find the source of all my problems. I did go to a Chronic Fatigue doctor, and I was tested for all kinds of viruses, fungi, and bacteria – Mycoplasma, H. Pylori, Herpes viruses (1,2 and 6), C. Pneumoniae, Cytomegalovirus, Epstein-Barr, and maybe others?. I was positive or had antibodies for all of them in some way or another, which was pretty expected. Some were higher IgG/IgM than others, like Epstein-Barr, but none of them high enough, in my doctor’s opinion, that he wanted to focus on treating them exclusively. Plus anti-virals for viruses stop working once you stop taking them he told me.

    I had a positive result for H. Pylori, which I’m not sure should be treated or that it could be the source of all my problems, but the doctor seemed to think it was.

    The other thing which was high was something called ECP, Eisonophilic cationic protein, which can either indicate high allergy load to foods(conventional MD would say this) or high parasitic load (chronic fatigue doctor said that that seemed likely).

    Unfortunately, my chronic fatigue MD doesn’t put much stock in stool tests. But, he’s generally pretty supportive of supplements and PHD.

    Finding that I had a pretty high viral load, in spite of the other stuff, I actually stopped eating so much protein and found bone broth to help with that – i.e. keep me full without OD’ing on meat/eggs/seafood. Also I find fasts to help, when I can do them. Again, I know that they cause you adrenal fatigue, so build up your health so you can do them. It took me about a year a half after starting PHD (granted, incomplete PHD) to be able to fast.

    I’m female, so for me, my time of the month is the worst in terms of fatigue, which is my main symptom, and some insomnia and digestive issues and brain issues. But the rest of the month, I’m able to function and I think I could go back to school or hold down a job again. So say, 70-80% of the time I can think clearly and do things and function like an almost normal person, versus 25% of the time before (or less – I was honestly afraid I was going to get in a car accident from falling asleep or just being fuzzy at the wheel). I’m aiming for 100% but like I said, I might never get there.

    I could probably work an office job at this point, but say, an amazon or costco worker – I don’t think I could cut it.

    I’m going to try a small dose of T3, as my RT3/FT3 ratio is a little on the low side. My MD said that this is kind of like the gas pedal. It might help with energy, I hope so just because I think all my other nutrition has been optimized.

    I think it’s likely that it’s multiple infections causing your problems, which is why PHD is your best bet. You can’t possible attack or find ONE source – there may be multiple things to attack, and without proper nutrition, how do you know that won’t let other pathogens take over? (i.e. candida/other fungus from antibiotics, or viral pathogens when you OD on glutamine). after reading all the information on this site, I think spices are really important for the Quorum sensing; human contact and activity during the daylight hours; and having some sense that you’ll get through this. But of course, some days are darker than others and then I think a nap is in order. I’m lucky in that I’m able to attack this with time off from work, and I remind myself of that every day. And I feel blessings to have found PHD.


  50. Hi Paul,

    You mentioned that you were on doxycycline for a 2-3 month period? I was wondering what dosage you were taking. I want to ask my doctor about getting a prescription as I suspect a similar condition. Also, would you consider being on a ketogenic diet a necessity for antibiotic success?


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