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. I would like to understand something,
    If we use coconut oil to avoid tissue wasting, how would Autophagy take place if we still have energy from the coconut oil?

    Many thanks!

  2. Hi Ljayne,

    Autophagy is triggered by more than just a shortage of energy – a shortage of protein for instance. Fasting will pull down circulating amino acid levels, triggering autophagy, and coconut oil won’t interfere with that.

  3. WOW, this is amazing! Once i start this Diet i will inform you of my progress,

    Many thanks!

  4. Hi Paul,

    This is a bit off-topic perhaps, but I wonder if you have any thoughts about how to grapple with the rare swallowing disorder called achalasia. My significant other has just been diagnosed. It’s a tough predicament, with every bite of food or sip of liquid a drama since she doesn’t know if it will go down or get stuck and have to come back up. We’ve had to flee restaurants when eating suddenly stops working.

    The underlying problem isn’t really understood, but seems to involve damage to or death of nerves in the esophagus that control peristalsis. The conventional medical treatments aren’t very good and usually involve intentionally paralyzing (botox) or surgically damaging the lower esophageal sphincter muscle to make it easier for food to get through it.

    I can’t help wondering if there could be an infectious cause, and it seems researchers have uncovered at least a little evidence to support that idea. There may also be an autoimmune component, perhaps related to infection, perhaps not.

    But, unlike more common problems such as MS or rheumatoid arthritis, I haven’t had any luck turning up doctors or protocols that confront achalasia with antimicrobials, diet, offbeat immune modulating strategies (LDN, helminths?), etc. I’ve considered asking for an empirical trial of antibiotics, but it seems like a shot in the dark, and without some evidence to support it, probably a tough sell even for my holistic doc.

    Considering the extremely unpleasant symptoms and resulting weight loss, there probably isn’t time for long-term experimentation (unless, as we hope will happen, the recommended oral medications—repurposed blood pressure meds—combined with mind-body work such as hypnosis gets it under control enough to buy us some time before turning her over to a surgeon).

    One interesting anecdote: after her endoscopy, we were incorrectly told that an esophageal ring had been observed and addressed and was the likely cause of her problem. Thinking she’d been fixed, she had a lot less trouble swallowing the next few days, though it didn’t last. That suggests to me that there is at least a potential for this to get better and that there is a substantial mind-body component.

    I couldn’t resist asking if you had any thoughts. I have a lot of respect for your work.


  5. Hi Bill,

    I haven’t heard of this before. My first reaction is it probably has parallel causes with GERD, which I think is usually attributable to “reverse peristalsis” in the small intestine driving chyme etc backwards through the digestive tract. Achalasia sounds like something similar in the esophagus. I think the cause of GERD is usually infectious. Obviously achalasia is far more rare.

    Chris Kresser did a good series on GERD and we’ll have one coming up. Here are some supplements a Brazilian doctor found helpful against GERD:

    I think with antimicrobials you’d like to find clues as to the pathogen before taking a guess. I know Candida can cause GERD and also esophageal diverticulosis. But it could be anything. Does she have other health problems? Did it originate after an acute infection?

    Best, Paul

  6. The supplements recommended in that Brazilian study can be very helpful for GERD. My 81 year old dad suffered from GERD for decades, and in recent years only got some relief by taking one of those high test acid blockers on a daily basis. Last winter I persuaded him to adapt a paleo style diet. That improved some health parameters but didn’t touch the GERD. Adding probiotics and fermented foods did not help. Found a reference to that study and sent it to him. He decided to try those supplements and his condition has improved quickly and significantly. He is down to one acid blocker about every ten days, and is feeling much better.

  7. Hi Paul,

    Thanks very much for your response. I think that achalasia is actually quite a different problem than GERD even though the symptoms can be similar and achalasians are often misdiagnosed with GERD. In achalasia, peristalsis ceases due to nerve disfunction and the affected part of the esophagus becomes more like a passive, inert tube than an active organ. I don’t think anything like that happens in GERD.

    Most crucially in achalasia, the lower esophageal sphincter (LES), which separates the esophagus from stomach, ceases to get the neural signal to open and allow swallowing and simply remains closed all the time (unless gravity and the various odd maneuvers achalasians learn are enough to force food through). In GERD, it’s really the opposite problem since the LES stays open (relaxed) when it shouldn’t, allowing stomach contents to head north.

    Some of the treatments for GERD are very bad for achalasia precisely because they oppose relaxation of the lower esophageal sphincter. The supplement studied in the article you linked is a good example: the melatonin it contains interferes with the production of nitric oxide, a promoter of LES relaxation. That’s the last thing you want in achalasia. In fact, nitrates are a frontline pharmacological treatment for achalasia!

    It seems that achalasia results from nerve problems in the esophagus, leading to loss of normal muscular responses there and in the LES. I do think that, like GERD and so many other problems, infection could be a factor. But as you say, it’s hard to know what to do when one has no idea what the infectious agent may be, or if indeed infection is even involved. I just haven’t been able to turn up enough information to go to a doctor with.

    You asked if my significant other has other health problems or had an acute infection that could have precipitated the achalasia. Her only other known problems are diverticulosis/diverticulitis and hypothyroidism. She now feels that the achalasia has been coming on for years. It’s an example of what doctors call “insidious” diseases, since the symptoms are so subtle at the beginning and often progress slowly at first, so the condition is accepted as normal and diagnosis is delayed a long time. If there was an acute infection involved, any memory of that would be lost in the sands of time by now!

    Thanks for giving this a little thought. I’m trying to make sure we don’t overlook any possibilities for real healing before considering the surgical options, which are only palliative, destructive, nonreversible, and come with risks and complications that can be serious.

    I’m only absolutely sure of one thing here: I will never take swallowing for granted again!

  8. Hi Paul,

    I’ve been doing ADF for about 2 years now and I stumbled on your website looking to improve what I am eating on my eating days. A couple months ago I started having attacks of severe vertigo, dizziness and anxiety, a doctor diagnosed me with viral labyrinthitis.

    Also, a couple weeks after that started I began implementing some of your advice. After a month I was up to 4 tbsp’s of coconut oil a day, even on my fasting days. Around then I started developing very severe anxiety and daily panic attacks. I’ve since cut back down to 1 tbsp of oil per day, which has cut back my anxiety a lot.

    I really would like to eat a more ketogenic diet, as I also seem to feel very depressed lately. Could I have a coconut allergy? Or what’s your opinion as to my extreme anxiety with higher doses of coconut oil?

  9. Hi Maggie,

    There are several possibilities. One is that you have a eukaryotic (protozoal, fungal, or worm) infection and ketosis causes pathogen activity to increase, flaring symptoms. However, I’m not aware of pathogens that produce your symptoms.

    I would try to experiment to gather more data. For a start you can rule out coconut allergy by trying MCT oil.

    Next, I would try adding more carbs. Try eating around 400 carb calories (no fat or protein) on your fast days and 600 on your feeding days. Try the coconut oil or MCT oil along with it. If you now tolerate the coconut oil, it’s probably excessive ketosis that’s the problem.

    If that’s the case, too much fasting and ketosis may be doing you harm. You might try regular eating, and a less ketogenic diet.

    Is it your experience that ketosis relieves depression for you, or is that just your expectation? If your problem is a eukaryotic infection then ketosis might make your depression worse.

    If these experiments indicate that ketosis is a problem, then I would find an infectious disease specialist and try to determine what infection you might have and get treatment for it.

    Best, Paul

  10. Thanks for the quick reply Paul!

    Reading up some more on coconut oil I doubt it’s an allergy, I don’t seem to have any of the symptoms that I’ve read about.

    I am now thinking I have candida, in which case you don’t recommend ketosis right? What would be the best treatment in your opinion? A google search turns up so many treatments. I’d really hate to give up ADF, it’s improved my life so much! I’m at a healthy weight and have felt much better up until a few months ago. If I eat some carbs on my fasting days would it be a bad idea to fast most of the day, and have just a late carb meal? Or do you mean just eat some carbs on my fasting days right now until I figure out if it is candida or some other type of infection and get it treated?

    Before the viral labyrinthitis ketosis was great at improving my mood, but now I just seem anxious and depressed all the time. That’s why I was hoping an even more ketogenic diet would make me feel better.

  11. Hi Maggie,

    Candida is very common, and does flare on ketogenic diets and fasts.

    For Candida I think antifungal medications are needed. Everyone I’ve tried has helped. Also the fat-soluble detox aids greatly reduce side effects, which would be intolerable without them. Ask your doctor for cholestyramine, fluconazole and nystatin.

    I’ve done intermittent fasting 16/8 throughout my Candida recovery. It’s probably suboptimal for Candida but like you I believe it’s good in other ways. So I think one carb meal on your fast day would be fine.

    I think once you clear whatever infection this is then ketosis will help again, but you should be on mild ketosis, not extreme. High levels of ketones only benefits pathogens.

  12. Paul,

    I’ve always been hesitant to take any kind of medication. Coconut oil is an anti-fungal isn’t it? You don’t think that or something like garlic or oil of oregano would be enough for the candida?

  13. Hi Maggie,

    Coconut oil is a very weak antifungal, it’s actually a better antibacterial. Turmeric, garlic, oil of oregano are good antifungals. Spinach supports immune function.

    But I think those dietary factors are great for preventing Candida but not so effective at reversing an entrenched infection.

    The good part about antifungals is that they don’t kill probiotic flora, so they tend to promote gut healing rather than dysbiosis as antibiotics do.

  14. Paul,

    What do you think of taking curcumin capsules as an antifungal?

    For me, implementing all the dietary measures you list did greatly reduce my facial rash. But it was only when I started taking the curcumin caps that it completely cleared up. I tried it because I didn’t really care for cooking with turmeric.

    I continue to take it, along with your recommended supps, as I seem to be reaping benefit from my present regimen.

    Do you know of a downside?

  15. No, I don’t know of any downsides, it’s a remarkably healthy spice. You may need to take it with black pepper for it to enter the body, without pepper it only works in the gut.

    There is probably a dose where it causes problems, but I don’t know what that might be.

  16. I am curious about the Earthworm Enzyme Ljayne mentioned earlier that has helped her so much with her infection. Have you heard of this application and is it something worth trying if one does not have access to a doctor willing to experiment with anti-biotics?

    Also, like Maggie, I become overly stimulated by coconut oil, and had a few days of what I would describe as mania/insomnia when I was taking 2T a day. I had to back off. Someone told me it could be the very high levels of salicylates in coconut oil, and that this could also explain why my tinnitus has also flared up with the use of coconut oil. Depression is another symptom of salicylate intolerance. ~Susan

  17. Hi Susan,

    No, I am not familiar with earthworm enzymes. (Ljayne’s comment was here: Here is a story about lumbrokinase:

    If you can’t get a doctor to help, I’d say it’s worth trying. I would be careful not to overdo it, and do it intermittently so you can better judge if it’s helping.

    Salicylates is an interesting idea for why coconut might cause problems. Hadn’t thought of that.

    Best, Paul

  18. Thanks Susan,

    I’m going to switch out the coconut oil for palm oil, see how that works for me. Unless palm oil is also high in salicylates?

  19. How to Recognize and Fix a Brain Infection | Low Carb Daily - pingback on August 4, 2011 at 12:06 pm
  20. Hi Paul,
    I’ve written to you once before regarding a very complex, mysterious, and disabling constellation of problems that I’ve been dealing with for almost five years.
    I have a couple of specific questions, and I’ll try to be as brief as I can. I’ve radically altered my diet over the course of the past year, and at present it’s fairly orthodox paleo/PHD fare. I’ve also made a series of additional changes to my lifestyle that seem to have produced some mild improvements, but I’m still struggling significantly (the most disabling of my symptoms are nearly identical to the ones you experienced–namely, virtually every cognitive/psychiatric/neurological problem imaginable). The next step for me, I think, is to try the interventions you recommend for a brain infection and see if they help. My questions about this approach:

    1) When I first started tweaking my diet, I cut my carbohydrate intake down to around 50 grams per day (and sometimes even less) for about two months. This didn’t work for me at all. I had a lot of difficulty sleeping (I would wake up after 4 or 5 hours, feeling wired but not rested), assorted symptoms of hypoglycemia, constipation, etc. Could these problems be prevented by adding more MCTs and thus inducing ketosis more reliably and consistently? How can the problems associated with very-low-carb dieting be prevented on a ketogenic diet?

    2) Considering that a course of antibiotics was the original precipitating factor in your illness, weren’t you reluctant to use doxycycline for any extended period of time? Wouldn’t long-term use of doxycycline have a detrimental impact on gut flora, and thus render you more vulnerable to future infections? Finally, have you continued taking doxycycline indefinitely? Is this necessary, or can the infection eventually be permanently eradicated?

    Thank you so much for your time–it is deeply appreciated by all of us who are trying to sort out this monstrously complex riddle of health and illness.
    Best wishes,

  21. Hi Brendan,

    1) It’s not a surprise that low-carb diet would exacerbate symptoms from a bacterial brain infection. Many of the symptoms are a result of brain hypoglycemia, and further reducing glucose levels would aggravate symptoms. Usually in these cases glucose consumption temporarily relieves symptoms.

    The solution, as you suggest, is to eat more MCTs and thus increase ketone levels. Ketones relieve symptoms by sustaining neuronal energy levels.

    If MCTs don’t work, then we have to revisit the hypothesis that you have a bacterial brain infection.

    2) Antibiotics are risky but the better your diet, the less risky they are. You definitely want to take probiotics and fermented vegetables while on antibiotics, to maintain some kind of gut flora throughout. I took doxy for 3 months. No, you shouldn’t take it indefinitely, hopefully you will be cured in a reasonable period of time. Infections cannot be completely eradicated but they can be reduced below a “tipping point” which gives the immune system dominance over them, and may prevent return of the infection for decades – or even delay it past your natural death.

    Best, Paul

  22. Hi Paul,
    Thanks so much for responding. I might be nagging you about this issue periodically for a while, so please don’t be afraid to tell me if and when further questions aren’t welcome. I know I’m imposing on your time and attention, and any advice you can give is really, really appreciated.

    A couple of follow-ups:

    –The hypothesis that I have a brain infection is just that–a hypothesis, with very little concrete evidence to support it as of yet. However, I do have a couple of pretty good reasons to believe in it. First of all, I took azithromycin for an (apparently) unrelated infection for about a week a couple of years ago, and I felt DRAMATICALLY better during that week. It felt as if the lights had suddenly come back on after a power outage. Interestingly, the improvements also continued, more mildly, for several additional weeks, after which I got steadily worse. Would this experience suggest a brain infection? Or could it be explained in some other way? Does azithromycin cross the blood-brain barrier?

    Also, I’ve found (like you) that spiking blood sugar by eating a large bowl of ice cream after my normal dinner, for example, makes me feel slightly better than usual. Many of my symptoms, especially impaired fine-motor coordination, seem to improve the more carbs I eat. But this is obviously not a very good long-term strategy.

    So, in short, I seem to be finding all sorts of empirical evidence to support this hypothesis, but this could just as easily be explained by confirmation bias. Is there any way to objectively confirm, with some certainty, that this is a problem, and that the risk of a long-term antibiotic protocol is worth taking?

    A thousand thanks, again, for your time. You’ve created a wonderful resource on this blog, and your personal accessibility is a great blessing.


  23. Hi Brendan,

    Yes, azithro does cross the blood-brain barrier, and azithro and doxy together are the core of the leading protocols for C. pneumoniae brain infections. See (and the whole “Getting Started” guide) for more.

    Yes, your experience is startlingly similar to mine and is dispositive: I will virtually guarantee you have a bacterial brain infection. The reason the “lights come on” is that azithro is a protein synthesis inhibitor that shuts down bacterial activity while it is present. They stay on for a week extra because the bacteria shift into a hibernating “cryptic” state in response, and only come out slowly.

    Since good diagnostic tools are lacking, you’ve done about all the diagnosis you can. The next step is to begin a combination protocol such as that at Don’t neglect detox aids such as cholestyramine and salt.

    Best, Paul

  24. Dear Paul,

    I am ocd sufferer and I am using antidepressants from last few years. I am 31 year old male living in finland. I would like to ask that why I become sound and touch sensitive after eating certain foods like nuts or cheese? How to avoid these issues? I tried coconut oil but it makes me anxious and as I said become sensitive to touch or certain sounds. Rest I am doing fine with prozac,I dont have any symptoms of ocd anymore. Please help me in this regard. Thanks

  25. Hi imran,

    That’s a good question. I don’t know.

    Hypersensitivity to sound and touch is a common symptom in various neurological disorders including autism, ADHD, and anxiety/panic.

    From this site,, it is associated with various infectious diseases: Lyme, TMJ (usually caused by infections), and Meniere’s (often infectious in origin, see

    Nuts and cheeses have a variety of compounds which may induce immune function or neurotransmitter changes. For instance, tyramine which is found in cheeses, coconuts, and some nuts ( Tyramine and its metabolite Octopamine ( induce neurotransmitter changes. Nuts and dairy are common allergens.

    I don’t know what the mechanisms are, but I think between the OCD/anxiety and the hyperacusis there are hints of some sort of neurological infection.

    It’s interesting that coconut oil makes you anxious, that’s not consistent with a bacterial infection and suggests a protozoal infection. Ketogenic diets are curative for bacterial infections but promote protozoal infections. You might check whether MCT oils have the same effect, to see if this is a ketosis effect or a coconut allergy. If ketosis causes anxiety, then I would ask my doctor to test for Toxoplasma or other common protozoal infections, and pursue appropriate anti-protozoal treatments.

    Toxoplasma has been linked to OCD, see and It’s possible that treatment might clear all your issues. No idea what the odds are, but worth looking into.

    Best, Paul

  26. Thanks a lot for reply. I will try to use MCT oil and will let you know, How I feel after the usage of mct oil.Take care.

  27. Because I tend toward hypoglycemia and suspect brain infection, I got some MCT oil. But after taking a couple teaspoons my brain/mind became very disassociated and depressive. It stayed that way for quite a while. I did not like it and am not eager to experience it again unless this means something good somehow. Any idea what this would indicate? ~Susan

  28. Hi Susan,

    It could indicate a protozoal/parasitic infection like Toxoplasma.

    Basically, a pathogen that has mitochondria and can metabolize ketones, so that its activity goes up when you follow a ketogenic diet.

    If you look into this, please let me know the results. I am as curious as you.

    Best, Paul

  29. I must admit I am feeling very daunted at this point!
    It seems that it’s nearly impossible to figure out exactly what’s going on. All the trial and error and experimenting can get overwhelming. What kind of doctor do you think would be most helpful?

    If you were just going to do one shotgun approach that might have the best chance of doing some good, would it be the doxycycline -will that help a parasitic infection? ~Thanks, Susan

  30. Hi Susan,

    No, doxycycline won’t work against parasites, only bacteria. It probably won’t do any harm to test it. If it helps then you probably do have a bacterial infection; if it doesn’t it adds support to the idea that any brain infection symptoms are probably due to some other kind of pathogen.

    For general care I would look for either a naturopathic doctor or one who specializes in chronic infectious diseases like Lyme. If you can’t find one of those, ask for referral to an infectious disease specialist and ask for diagnostic testing for a parasitic infection based on your symptoms and your response to a ketogenic diet.

    Unfortunately I’m not very knowledgeable about the steps for diagnosis or treatment of parasitic infections, so I would have to defer to doctors there. I don’t know of a single shotgun approach with good odds of success.

    Best, Paul

  31. Just wanted to say how very kind it is of you to take such a significant amount of time to have conversations with your readers who have been strugling with health issues. It means a lot.

  32. Susan, thanks for being here. It’s great to be able to share what we know with nice people.

  33. Hi Paul,
    First of all, I’d like to second Susan’s sentiment. Your generosity really does make a huge difference to all of us.

    Would you be willing to briefly comment on the following aspects of my personal history–that is, do they strengthen or weaken the case for an infection of the brain (bacterial or otherwise)?

    –I seem to feel best with Vitamin D levels in the 60-90 range, rather than the 40 ng/ml that is commonly recommended. In fact, I experience noticeable improvements as my 25(OH) level rises ABOVE 40 ng/ml.

    –Here’s a fascinating (and potentially illuminating) one: supplements and drugs that increase concentrations of nitric oxide (NO) seem to significantly improve my symptoms for about 24 hours after I take them.

    –I have iron levels suggestive of hemochromatosis, but tested negative for common HH genetic mutations

    –I have issues with rosacea and mysterious hair loss (both relatively mild, but present nonetheless).

    –I have pathologically low cholesterol (TC never greater than 125, and below 100 on several occasions), which responds only modestly to changes in diet.

    I have many more questions, and I’m not sure where else to find reliable information on this subject, but I’ll try to keep these comments as brief and manageable as I can for now. I don’t plan to take any action on this information for another month or two at least.
    THANK YOU and best wishes,

  34. Hi Brendan,

    I’ll take each point in turn:

    1. I’ve blogged about this: in certain diseases people do well with 25OHD well above normal levels — up to double normal levels, ~80-90 ng/ml. See

    2. Nitric oxide is involved in immune function. It’s also important for vascular dilation and oxygen supply. Finally, nerves use it. I am sure this is an important clue but I would have to do research before I could venture an interpretation.

    3. Since iron is necessary for metabolism in all cellular organisms, pathogens included, it is sequestered in the immune response to infection. Also pathogens may utilize it, both intracellularly and in biofilms. Commonly treatment of such infections may produce a porphyria.

    4. Rosacea is typically infectious, mine seems to be fungal but others have bacterial forms. There may be other kinds of pathogens that can cause it too.

    Hair loss is most commonly due to hypothyroidism; have you had thyroid hormones tested? Danny Roddy has been doing a lot of neat blogging about hair loss.

    5. Low cholesterol is a very strong indicator of a protozoal or worm infection. Probably protozoal. Malaria, Toxoplasma, many others are candidates. You should definitely be checked out for parasites.

    I definitely think you have a systemic infection of some kind, probably protozoal, possibly with co-infections. It needs an infectious disease specialist and good diagnostic testing.

    I would try to fix whatever is infecting your body and worry about the brain second, as the body is easier to diagnose and treat, and what you learn will give you clues about what’s going on in the brain.

    Please keep me posted!

    Best, Paul

  35. Hi Paul,
    Would it be easier for you to conduct this exchange via email? If so, let me know.

    The most promising clue that I’ve found to the nature of the relief that I get from NO-increasing substances is this study:

    Unfortunately, I can only access the first page. Also, this doesn’t seem to help me ascertain the identity of the infection–it merely confirms that some sort of infection is probably present.

    Hypothyroidism of unknown cause has been a problem for several years (another clue?), but I am currently being treated with replacement thyroid hormone, and my TSH is normal.

    Based on the symptoms I exhibit (fatigue, cognitive and neurological problems, skin problems, low cholesterol, etc.), do you think an infectious disease specialist would be willing to evaluate me, and would they know what to look for? Should I ask for any specific diagnostic tests?

    Thanks again and very best wishes,

  36. Hi Brendan,

    While NO has antimicrobial properties, it’s hard for those to account for immediate improvement and loss of the improvement after 24 hours. More likely it’s the endothelial, immune, or neural signaling effects of NO that improve your symptoms.

    I do think an infectious disease specialist should be willing and able to evaluate you. They would know better than I would what tests to order. If you can find one who is familiar with protozoal diseases, that would be best. Those are more common in Africa / the tropics than in the US.

    Best, Paul

  37. Hi Paul,

    I’ve been a long time reader, and I’ve been interested in your ideas about brain infection. I recently began using mct oil, BCAAs, and lysine to aid with ketosis. However, whenever I go into ketosis the back of my kneck becomes uncomfortably tight. Is this a common response? I have been unable to find any information about this.

    As well, I’m curious about your thoughts on using stimulants such as Ritalin or Adderall to help with brain fog.


  38. Hi PT,

    First, I’d drop the lysine and use leucine if you want an amino acid for ketosis. Limit it to 5 g/day. Although lysine is non-toxic, I think it can promote some infections.

    Neck stiffness can sometimes indicate a throat infection, eg it often accompanies a sore throat. Or it could indicate some sort of nervous system effect. I’m not really sure what’s going on.

    If the neck tightness is infectious in origin, and ketosis makes it worse, then it would indicate a protozoal, parasitic, or fungal infection, as those are the pathogens that can metabolize ketones.

    I don’t really have thoughts about Ritalin or Adderall, as I leave drugs to doctors, but I generally consider drugs a last resort, and primarily for mitigation of intolerable symptoms rather than as cures.

  39. Dear Paul,

    Thank you for all of the time you dedicate to this wonderful site, which I discovered only a few weeks ago. I have been working through every post and comment.

    Thank you also for pointing the way to My reading there raises a question about porphyria.

    First, as very brief background, I believe that I have been suffering from a brain infection for 12 years — perhaps Lyme, perhaps Cpn, perhaps a mess of coinfections. I had been fairly stable for a decade when an experiment with tryptophan, 5-HTP, and glutamine late last year triggered severe deterioration. A few months later, at a celebratory feast, I ate gluttonously of foods I normally avoid: wheat, dairy, beans, nightshades. That night MS symptoms began.

    I have studied my decline from every angle I can find and have seen my face reflected in a great many disease websites. Descriptions of porphyria attacks resonate closely with my recent experience.

    My question, with porphyria specifically in mind, is how to proceed in terms of diet and supplements. The dietary advice on and elsewhere stresses very high carbs, low protein/fat/cholesterol/iron (limiting most animal foods), low sulfur (limiting most of the best vegetables), absolutely no fasting, and avoidance of a long list of specific foods believed to contribute to porphyria attacks.

    Clearly it is difficult to reconcile this with PHD — but I know that you developed PHD after much personal experience with these issues! Everything you have written about ketogenic diet and intermittent fasting for brain infections makes sense to me and I am eager to experiment — indeed, over the last few days I have been increasing my coconut oil consumption — but perhaps this is a good idea in relation to the infection itself but a bad idea in relation to the porphyria? And if porphyria is in fact the immediate cause of my most serious daily symptoms (including, recently, the feeling that I am alarmingly close to seizures and psychosis), I am wary of making matters worse.

    I am willing to endure anything to heal, but it is far from clear whether the daily, even hourly, roller coaster I have been on is taking me in the direction of healing at all.

    I am grateful for any thoughts you have.

    Thank you again for this site and your time.

    p.s. You may well ask why I do not have a more solid diagnosis. For financial reasons I have little access to doctors or laboratory diagnostics. This is not ideal, I know, but I must do the best I can.

  40. Hi MM,

    Yes, the diet advice on is not that good. Much better to use our diet and their antibiotic protocol. I recommend the four steps of our book.

    For porphyrins, I believe the key is to use detox aids. Cholestyramine, activated charcoal, and bentonite clay should all work. This should reduce your symptoms and make therapy more tolerable.

    Since you don’t know your pathogens, you will need to experiment a bit to optimize everything. But I think you should treat our diet as your base from which to experiment.

    Please keep me posted!

    Best, Paul

  41. Thanks so very much for your help, Paul!

    At risk of belaboring the point, do I understand correctly that you see no reason to limit any of the PHD-compliant foods that are commonly viewed as the worst porphyria triggers? Given what porphyriacs have written on the web, eggs, organ meats, and high-sulfur vegetables seem to be of particular concern.

    For what it is worth, goat liver severely exacerbated my symptoms a few weeks ago, the only time I have eaten liver in my life. I learned afterward that the amount I had eaten, not knowing anything about liver, was far more than people would normally eat at once. But I still wonder what specifically it was about it that messed me up.

  42. Hi MM,

    I would be reluctant to make the diet less healthy to accommodate a porphyria. I would focus on detox methods first and turn to dietary changes only as a last resort.

    Goat liver – probably copper, possibly vitamin A. The ruminant livers have high levels of copper. Zinc might be a partial antidote.

  43. Thank you, Paul!

    Copper has been a concern, and I wonder how much significance to read into the symptom exacerbation I experienced after eating goat liver.

    When my problems first escalated, one of the things I investigated was metal toxicity and Andy Cutler’s work in particular. Since hair tests are very cheap, I performed one, but it did not reveal anything dramatic except for lithium so low as to be off the chart (which is why I asked about lithium elsewhere).

    These results caused me to turn largely away from the metal toxicity angle but not to write it off entirely. As you doubtless know, there is extreme disagreement on the value of hair tests and the specifics of how to interpret them.

    In any case, Cutler claims that copper toxicity can mimic mercury toxicity.

    He also claims that alpha lipoic acid — which I have been taking for months now, reasoning that it could potentially be helpful from a variety of angles — causes copper accumulation and so is contraindicated if copper is already causing problems.

    I welcome your thoughts and would also like to ask about another issue which may have a partial connection to the copper question. For about a week I have been following the ketogenic version of PHD and so have been eating a lot of coconut oil. Unlike some of the posters here, I love coconut, so taste and smell are not a problem, though I still find it challenging to squeeze that much oil into the day.

    In the last couple of days I have been experimenting with true coconut butter products (that is, pureed whole coconut meat) such as Coconut Manna from Nutiva. No challenge here: I enjoy eating this straight and can do so all day long.

    My question is whether this is a good idea. On the one hand, the fact that it is a whole food would seem to be a good thing. On the other hand, even though the proportion of oil in whole coconut is high enough that I cannot imagine that the goal of ketosis would be threatened, I nevertheless wonder whether eating it in sufficient quantity for fat might result in too much of other things: fiber, carbs, plant protein — or perhaps copper!

    I would be most grateful for your thoughts.

  44. Hi MM,

    The whole coconut is good. It’s still largely fat, and it has substantial fiber which is also ketogenic.

    It is possible to measure blood levels of ceruloplasmin and copper. Here are tests with symptoms of copper excess:

    If tests are too much trouble, you might just try zinc supplementation and copper reduction for a few months and see if that makes you feel better.

  45. What factors do you think can initiate chronic brain infection?

    Do you think orthodontic/dental treatment could be one of the contributing factor?

    Does it depend what kind of infection you get, some could easily reach the brain while others not?

    You’ve suggested that I might have brain infection which I find plausible. I just wonder how I might have gotten it. Bad diet along with orthodontic treatment is what I can think of.

  46. Hi A,

    I haven’t heard of that, but I guess it’s possible. Teeth and gums often harbor pathogens and the orthodontics might promote movement up the nerves.

    Most of the time, however, we’ll never know a cause. Some infections can reach the brain by establishing a vascular infection in the brain, and passing through endothelial cells to cross the blood-brain barrier.

  47. Thank you again for all of your help, Paul!

    A follow-up question on charcoal. I gather that your personal experience is with cholestyramine, but do you have a sense of what sort of charcoal dosing schedule people have needed for good effect?

    I have worked up to 8 x 280mg capsules before bed each night. I have no idea if this is excessive or nowhere near enough. Ideally I would take it during the day also, but I have had a hard time squeezing it in where it would not potentially interfere with all of the supplements and herbs that I am taking, and food.

  48. An update on my progress with PHD.

    Sleep disturbances, perhaps due to nighttime hypoglycemia, have haunted me for a while, but they have worsened since implementing the ketogenic version of PHD. Last night was the worst yet. After finally falling asleep around 4am, I awoke shortly thereafter with what seemed like a true blood sugar emergency: sweating, shaking, tension, racing heart, headache, nausea, intense thirst, and the certain feeling that I was on the verge of seizure.

    Less alarming but still problematic, nighttime limb numbness has also been rising in frequency and severity.

    Any thoughts on how to stabilize blood sugar so that I can avoid harm and improve sleep?

    I adopted PHD in the spirit of experimentation and want to continue the experiment. And I know that advocates of low-carb/ketogenic diets claim that reactive hypoglycemia is not uncommon and will pass. But if it is true, as I believe, that I was about to lose consciousness or start convulsing, the stakes are growing awfully high.

    I must admit that all the other arguments that have held my attention at different times over the years — especially “too much fat, not carbohydrate, is what causes diabetes” — are echoing back to me and challenging my confidence that all this fat is good. I have not yet eaten anything today as I am suffering a loss of conviction about what is safe. I am also at a loss as to whether I should move in the direction of more frequent eating — perhaps including right before bed — or more fasting. (After last night’s scare, part of me is inclined to stop eating entirely for a week, though of course conventional wisdom would consider this crazy given these blood sugar issues.)

    Any help would be deeply appreciated.

    p.s. I take alpha lipoic acid, which I know affects blood sugar, as well as other supplements and herbs of unknown impact. But this has been true for many months. Yesterday there were a few confounding variables which may be important:

    1. I overate. I took in more calories than usual and more than I needed, including coconut butter equivalent in fat to 14T coconut oil. Beyond this: 11oz sweet potato (with 3T red palm oil) for lunch; 8oz salmon and 6oz spinach salad (with 1T olive oil) for dinner.
    2. I tried a gram of taurine with dinner and another gram an hour or two before bed with the hope that this would help me relax and sleep. Again, I know that taurine can affect blood sugar.
    3. I took a fairly large amount (12g) of fish oil as an experiment. (Although I am persuaded against fish oil supplementation and avoid it as a general rule, I am not convinced that it has no value as a short-term intervention when certain disease symptoms are unbearable.)

  49. Hi MM,

    There are various reasons why a ketogenic diet may be unsafe. Any infection by protozoa like Toxo gondii, malaria, etc makes a ketogenic diet untenable. Also, some people have severe fluctuations in blood glucose levels when fasting.

    If it doesn’t work for you, stop and eat ~600 calories carbs per day. Give yourself time to heal, and try again in 6-12 months. If you have any evidence of protozoal infection, seek diagnosis and treatment.

  50. HI MM,

    Just curious if you have done any blood sugar testing with a glucometer?

    People often find that what feels like hypoglycemia is not in fact dangerously low blood sugar, but high blood sugar that is dropping into normal or even still high numbers and it is the drop itself that is affecting you.

    It is worth knowing exactly which it is and easy to find out with home testing. Then you can use the glucometer to get a fix on the range of safe carbs that work best for you. Or if certain supplements are having an impact.

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