Short-Term Effects of Adding Carbs to Very Low-Carb Diets

In my last post, I noted that

So far, all the negative experiences [from adoption of our diet] I am aware of have come from low-carb dieters who had difficulty after adding carbs and/or cutting protein….

It’s interesting that the same dietary change – adding “safe starches” to a low-carb Paleo diet – made some people feel better and others worse.

In thinking about why adding starches can cause short-term trouble for some people, my first thought was a fascinating post from two years ago by Peter Dobromylskyj of Hyperlipid. Peter noted:

Bacterial endotoxin is a breakdown product of the cell wall of gram negative bacteria. It’s a lipopolysaccharide and even quite small amounts of it are extremely unpleasant….

Now the scary thing is that eating a high fat meal, probably based on any fat which generates chylomicrons, markedly increases your uptake of endotoxin from your gut, which is obviously full of gram negative bacteria. Eating short chain fatty acids or carbohydrate [1] does not have this effect.

Endotoxins are fat-soluble, and so fat carries them into the body. The paper Peter cited actually found an increase in blood endotoxin levels after people were fed a high-fat meal:

In humans, no significant relation was observed between cardiovascular disease risk factors, carbohydrate and protein intakes, and plasma LPS concentration. Conversely, positive correlations were observed with fat and energy intakes. [1]

The same effect was found in mice:

Compared with the control mice, mice fed a high-energy diet showed an increase in plasma LPS. However, in mice fed a high-carbohydrate diet, the increase in plasma LPS was blunted compared with mice fed a high-fat diet.

The conclusion:

Experimental data suggest that fat was more efficient in transporting bacterial LPS from the gut lumen into the bloodstream. [1]

Does this mean that one should avoid dietary fat?  No, because it turns out the body regulates the amount of endotoxin entering the body. So a high-fat diet causes the immune system to exert greater control over gut bacteria. Peter writes:

Then came a fascinating random paper [2] through my wife’s journal club meetings … It’s about superinfection with resistant bacteria when broad spectrum antibiotics are used. This is a routine problem for anyone in medicine, especially patients. The concept is very simple, you kill off the susceptible commensal bacteria in the gut and resistant pathogens have no competition, so they have a field day and superinfection causes severe problems for the unlucky patient.

Simple, straightforward and wrong.

It turns out that the immune system, that is the innate immune system (of course), continuously monitors the contents of the gut by looking at endotoxin production. Lots of bacteria mean lots of endotoxin and an active, on-guard innate immune system. Kill off 99% of your gut bacteria and exdotoxin production drops. The innate immune system goes on vacation and clostridium difficile gets in and wipes out your granny.

Simple administration of oral endotoxin to the experimental mice stopped this effect completely.

Apparently, the human body evolved to favor having a certain population of commensal gut flora. When the population is too low, immune defenses are lowered to allow gut bacteria to multiply. When the population is too high, antimicrobial peptides are released into the gut to control pathogen numbers.

Thus, during gut infections adding probiotic bacteria may help defeat pathogenic infections by causing the body to increase its immune defenses. The body is actually trying to control the numbers of probiotic bacteria, but in doing so it makes compounds that kill pathogens.

Removal of tiny numbers of probiotic bacteria can lead to a huge multiplication of pathogens:

Administration of the broad-spectrum antibiotic combination metronidazole, neomycin and vancomycin (MNV), to which vancomycin-resistant Enterococcus (VRE) is resistant, markedly increases colonization of the small intestine, caecum and colon with VRE…. It remains unclear, however, why elimination of the relatively sparse microbial flora of the small intestine increases the number of VRE by over 100–1,000-fold. [2]

It’s possible that this effect may be able to work in reverse – that addition of the small number of bacteria in a probiotic capsule can diminish the much larger population of an acute infection by 100-fold. I’ve noticed that swallowing probiotic capsules can be extremely effective against food poisoning. If you ever get diarrhea from a bad meal, take handfuls of probiotics every few minutes. You’ll be cured remarkably quickly.

The Gut of a Zero-Carb Dieter

On a zero-carb diet – especially an entirely plant-free diet like the one Charles Washington eats – lack of food will cause the population of gut bacteria to dwindle.

As in a gut depopulated of bacteria by antibiotics, this diet will cause the gut to let down its immune defenses. The body will reduce its production of antimicrobial peptides in order to help gut bacteria survive.

Perversely, this may make any pathogens that enter the body with food more likely to enter the body. It also may allow pathogens to gain a foothold in the gut. Thus, heightened infectious disease risk could be another long-term danger of zero-carb diets.

What Happens When A Zero-Carb Dieter Reintroduces Starches?

When a zero-carb dieter starts eating plant foods, suddenly gut bacteria have a lot of food, and can multiply many-fold. Bacteria can double their numbers in 20 minutes, and yeast in a few hours. That means that bacterial populations can increase 8-fold in an hour, 4000-fold in 4 hours, and ten million fold in 8 hours. Yeast can increase 4000-fold in 24 hours.

So it doesn’t take long – the very first day – before gut bacteria have multiplied by huge proportions. In the course of their fermentation, they’ll release a lot of gas, causing some bowel distress.

And along with greater numbers comes greater endotoxin release. Any dietary fats carry these endotoxins into the body. This rise in endotoxin load triggers an immune response that includes release of antimicrobial peptides, killing gut bacteria and releasing more endotoxins.

This rise in endotoxin levels and the resulting immune response may resemble a brief illness. Some known effects of a sudden rise in systemic lipopolysaccharide levels:

  • Depression [3] and depressive-like behavior [4].
  • Impaired athleticism [5]. 
  • Reduced appetite [6, 7].
  • Fever, vasoconstriction and endothelial dysfunction. [8]

Of course these effects would be only temporary. In a matter of days to a week, the immune system should re-establish an equilibrium with the gut flora and the new diet. Gas and bloating in the gut should be reduced (unless pathogens have been able to establish an enduring infection first). Endotoxin levels in the body should return to the evolutionary optimum. Higher production of antimicrobial peptides will maintain a limited gut bacterial population, even though carb intake has increased.

My Experience

My own experience is consistent with some of these expectations. When I went from zero-carb to including carbs – in my case, the change was adding fruit only, starches didn’t start for another year – my abdomen became bloated and I had gas. It was remarkable:  the very first day I ate fruit, my belly bloated up. It seemed to leave me with a lasting infection, because both the bloating and various digestive problems lasted several years. Probably the scurvy that I also had at that time was a big contributor; until I fixed the scurvy I also had gallbladder problems, and developed diverticulitis during this period, diagnosed by a barium enema.

I believe the main factor in the bloating was a colonic yeast/fungal infection that may or may not be completely gone today (it is certainly much diminished). The bloating was increased whenever I developed fungal skin infections. I suspect the yeast took over my colon while my immune defenses were depressed on the zero-carb diet and vitamin C deficiency, and multiplied immensely as soon as they had access to plant foods.


This hypothesis matches some but not all of the first-couple-of-days symptoms experienced by Don Matesz and his commenter SamAbroad when they cut protein and increased starches. SamAbroad became “hungry and cranky”; Don noted “decline in mood and … increase in hunger and intestinal gas and a disruption of bowel function.” In short:

  • Gas, bloating, intestinal distress.
  • Cranky mood.
  • Hunger.

The first two are consistent with a rise in endotoxin levels. The last isn’t.

However, I can imagine a few reasons why a shift from meat to starches may have made them hungry:

  • Protein is notably satiating, one reason why high-protein diets are often effective for weight loss. Mixed carb and fat, on the other hand, makes a good dessert. As we have all witnessed, many people say they are stuffed after dinner but get hungry again when they see desserts.
  • Or maybe the calories lost from the reduction in meat were not fully replaced. Plant foods have far fewer calories per pound than meat, and many people overestimate how many calories are found in plant foods. In cutting meat from

The body should adjust appetite to the diet, but this may not happen in the first few days. In short-term (3-day) trials of food mix alteration, people who increased carbs ate more food than people who increased protein. [9]

I don’t know if these explanations are correct in the specific cases of Don and SamAbroad. (Indeed, I was very surprised Don had any trouble at all, since he already eats our safe starches and I am pretty sure he also eats within our recommended optimal range of macronutrients — hat tip to commenter Beth Mazur of for a link to one of Don’s meal analyses in which he ate our recommended calorie ratio.) However, I think many people who have been on zero-carb diets can expect short-term gut distress when they first restore carbs to the diet.

In people with healthy gut flora, this should disappear in a few days. In others, like me, who have pathogenic gut populations, a gut infection may become entrenched and take longer to get rid of. Still, overall I think the inclusion of dietary carbs, and the resulting enhancement of intestinal barrier immunity, is likely to lead to long-term improvement in the body’s protection against infectious diseases that enter through the gut.


[1] Amar J et al. Energy intake is associated with endotoxemia in apparently healthy men. Am J Clin Nutr. 2008 May;87(5):1219-23.

[2] Brandl K et al. Vancomycin-resistant enterococci exploit antibiotic-induced innate immune deficits. Nature. 2008 Oct 9;455(7214):804-7.

[3] Weidenfeld J, Yirmiya R. Effects of bacterial endotoxin on the glucocorticoid feedback regulation of adrenocortical response to stress. Neuroimmunomodulation. 1996 Nov-Dec;3(6):352-7.

[4] Fu X et al. Central administration of lipopolysaccharide induces depressive-like behavior in vivo and activates brain indoleamine 2,3 dioxygenase in murine organotypic hippocampal slice cultures. J Neuroinflammation. 2010 Aug 2;7:43.

[5] Sparkman NL et al. Effects of intraperitoneal lipopolysaccharide on Morris maze performance in year-old and 2-month-old female C57BL/6J mice. Behav Brain Res. 2005 Apr 15;159(1):145-51.

[6] Stengel A et al. Lipopolysaccharide differentially decreases plasma acyl and desacyl ghrelin levels in rats: potential role of the circulating ghrelin-acylating enzyme GOAT. Peptides. 2010 Sep;31(9):1689-96.

[7] Rorato R et al. Prostaglandin mediates endotoxaemia-induced hypophagia by activation of pro-opiomelanocortin and corticotrophin-releasing factor neurons in rats. Exp Physiol. 2009 Mar;94(3):371-9.

[8] Feng SY et al. Acute and chronic effects of endotoxin on cerebral circulation in lambs. Am J Physiol Regul Integr Comp Physiol. 2010 Mar;298(3):R760-6.

[9] Coelho JS et al. Selective carbohydrate or protein restriction: effects on subsequent food intake and cravings. Appetite. 2006 Nov;47(3):352-60.

Leave a comment ?


  1. so my questions is then: how to really heal the cause – gut dysbiosis? whether its fungus/yeast/candida/etc… can a healthy diet truly cure these issues? certainly it seems that even long term a healthy diet only minimizes the symptoms, though many people claim herbal medicine or similar “detox” strategies work.
    and in defining a healthy evolutionary diet: how much does cooking increase healing difficulties? would eating a more raw and/or fermented evolutionary diet work better/faster? and i’m speaking of raw and fermented animal protein & fat – a taboo subject to be sure.
    looking forward to more discussion of these sorts!

  2. interesting post. probiotics have never done much for me, although fermented foods have offered me some improvements in my digestive health. wondering if you could share a little more regarding your probiotic of choice and how much (and long) you took it to help your gut health.

  3. Hi Steve,

    I don’t take probiotics, except for food poisoning. Works great for that. I experimented with them but they didn’t noticeably help my gut problems. In my bowel disease series I mentioned that I think they rarely solve bowel diseases because the number of species is just too few. (Thus our discussion of fecal transplants as a much more effective therapy.)

    I would recommend fermented foods for most people.

    Hi Darius,

    I think a healthy diet is often essential to curing these things. However, the diet may need to be tweaked in different directions depending on the nature of the infection. Sometimes fiber is helpful, sometimes you want to starve the beasts; some foods can be toxic to the pathogens and promote probiotic competitors.

    I’m not aware of evidence that raw or fermented meat is helpful. Do you know of any? The subject is not taboo here but I’m afraid I’m ignorant of any evidence.

    Best, Paul

  4. My own experience of “to die for” desserts has always included sucrose and cream, as in strawberries and whipped cream or a trifle with the thickest layer of whipped cream. It has always been cream plus sweetness plus a little acid contrast.

    When on a low CHO diet (30-40gm/day) I whip my cream and add to strawberries mashed with sucralose. The non-CHO sweetener provides me with the flavour of freshly picked fully ripened berries. I treat raspberries similarly.

    My palate responds to the sweetness with fat, not the fact of delivery via the fructose mono-saccharide.

    I wonder if this is common?

  5. Paul,

    Since you say you’ve had continuing problems with gut bacteria, have you considered a fecal transplant, as you speak of in the book?

    Just wondering!

  6. Hi Paul,

    I’m the SamAbroad you mentioned previously. Just want to clarify a few points.

    I’m still following the diet, I eat circa 100g carbs from starch a day not including veg and this has been one of the best things I’ve ever done for my health along with including a vitamin C supplement. My low-level depression and anxiety have completely disappeared and the diet is considerably more varied and easier to stick to than VLC.

    But I have tried to restrict protein to <80g a number of times, each time with the same result, ravenous hunger and low mood. I'd say I eat about 120g a day and that feels best for me, so who am I to argue. Could it be that it's just best for me to eat 880cals a day from protein and carbs? I still make up the rest (about 1,000 cals) with mostly sat fat. Is a 25% protein diet really that bad?

  7. Great post and a lot to think about. I wonder if people eating traditional diets became briefly symptomatic based on seasonal food availability.

    I also wonder though, how much of the consternation about macronutrient change is psychological in origin. Something I never see mentioned on paleo/trad diet blogs, is that many people attracted to these diets have some form of food obsession or eating disorder. I know of at least one recent paleo diet book author who was hospitalized for an eating disorder earlier in life. Also, many of those promoting paleo now were staunch vegans when that was fashionable 15 years ago, including myself. Diet unfortunately lends itself to obsession, especially in our current cultural food environment.

  8. Wow, that was a great post. Thanks!

  9. Excellent post! So if you’re theory is correct, it seems that a Zero Carb diet combined with ample probiotics over a long period of time should significantly dilute any pathogens, no?

  10. Hi Leon,

    Yes, I think that’s normal. It’s sweetness as much as calories.

    Hi Richard,

    I think if I have a problem, it’s probably Candida/fungal. My doctor thinks I’m cured. I have no symptoms – digestion is great, health is great, no signs of anything except my colon is larger than it used to be. My doctor thinks that is diverticulitis I got when I had scurvy. I’m dubious because when I had the fungal skin infections, the colon would increase in size and get hard, and then shrink and soften when the fungal skin infections left. So I wonder if there is a residual fungal infection in the colon that has increased its size.

    If I’m right a fecal transplant would help. But without any symptoms, no doctor would treat me and I’m not going to self-treat. I’ll just go the natural way, eat fermented foods to pick up bacteria and eat healthy anti-yeast foods like my “Neo-Agutak” to try to displace any residual yeast.

  11. Hi Sarah,

    Thanks for letting me know! I’m glad the carbs have helped you.

    I would definitely eat the amount of protein you need to feel well. Nothing wrong at all with 880 calories carb+protein. Remember that our “optimal ranges” are 200-600 calories carbs, 200-600 calories protein, 600-1200 calories carb+protein. So you’d still be roughly midrange.

    Very interesting that you need more than our lower limit of 600 carb+protein calories per day. Could it be you’re eating fewer carb calories than you think? Or that you have some kind of infection or illness which is consuming glucose?

    You might experiment with whether increasing carbs to 600 calories per day allows you to reduce protein to 200 calories per day. That would help us figure out whether this is a carb requirement (with protein getting converted to glucose) or a protein requirement.

    I’m very glad to have you on our diet and hope you’ll keep sharing!

  12. Hi Robert,

    I think people are often tempted by extremes. I think I’m psychologically normal but I tried zero-carb for a while. It’s easy to think “if less is good, zero is better” but of course biology doesn’t work that way.

    Hi Evan,

    I don’t think probiotics can fix a zero-carb diet. I typical capsule has a few billion probiotic bacteria but a normal gut has trillions. So you’d have to take a huge amount of probiotics to keep the gut immune defenses up.

    I think it’s better to eat some carbs and let a normal gut flora help maintain a healthy gut.

  13. The book “Probiotics 2: Application and Practical Aspects” recommends you take Saccharomyces Boulardii to rid your self of bad bacteria in the gut. It is a yeast that will overwhelm any gut pathogens that you may have.

    Take it for a month and then switch to a probiotic so that the good bacteria can reestablish themselves.

    The book also suggests taking Saccharomyces Boulardii a week before and during and a week after a visit to any country where hygiene is suspect. I do travel to third world countries and it works for me.

  14. Hi Jake,


    I’ve known people with bacterial gut infections who got much better taking S. boulardii.

    I’ve also known people with chronic fungal infections who got much worse after taking it. Fungi may be able to exchange DNA – they certainly influence one another. One person with a chronic illness like mine got a bad fungemia after supplementing S. boulardii. She was on antibiotics at the time.

    It may well be therapeutic for many people, thanks for the information and reference to the book which I hadn’t heard of.

    Best, Paul

  15. hi paul

    have you ever considered doing a DNA stool test, which would show a qualitative AND quantitative analysis of your flora, incl. quantity of candida? would be very interesting to know if your suspicion is right, and this would also produce an excellent blog post.. 😉 is offering such a test via a lab in georgia (also available as a mail in kit).

    also, you say typical probiotics are too weak. i agree, but those were never designed to cure pathologically disturbed floras. tehy are just for “maintenance” of an otherwise healthy flora. for serious problems, one needs to take a “prescription strength” product like the well known one who has 450b colonies. or, as i just did very successfully, just take 3-4 of these for example (-> ~100b)

    going from my usual 5b to >100b made a huge difference, and i’m now symptom free (!) after just one week. i now can eat all the stuff again i couldn’t for the last half year or so if i want (e.g. eggs, bread, etc). this already worked once with a different probiotic (primal defense ultra), but only for a few days, most likely because it is too weak.

    however, the much higher probiotics dosage was not the only change. after an even closer examination of my diet and all the supplements i take, i found out that the digestive enzymes from vitamin shoppe contained MILK (wtf!), and also one of my fav canned fish meals contained milk powder (duh). needless to say, that after removing these, everything improved and stabilized rapidly. i believe that the constant low-grade milk contamination prevented my gut from getting rid of the inflammation, and therefore kept all the other secondary allergies (eggs, nuts, etc) going. now as the inflammation is gone, all secondary allergies are gone too.

    i had the feeling, that the high-dose probiotic also was extremely efficient in toning down the gut inflammation directly. i usually could feel the “cooling” effect within half an hour or so. must be some kind of gene signaling from the probiotics to the gut or so *g*

    so for now, this is my conclusion:
    initial triggers: removal of 11 mercury fillings + several days strong antibiotics within one year.
    a few months later, crash of gut flora, manifestation of primary sensitivity, which most likely is milk. a few weeks later, appearance of dozens of secondary allergies, possibly all cross-reactions to my preexisting pollen and grass allergies.

    solution: ultra-strict elimination diet (incl. supplements!), if needed even fasting for a few days (only coconut fat and maybe some fish), combined with high-dose (>100b) probiotics complex taken with each glass of water until gut inflammation and symptoms resolve. continue for two weeks or so, and the re-introduce paleo compatible foods. avoid primal trigger for a while, or forever (i guess).

    notes: in the past 20y i had a few episodes with milk/whey intolerance, but could resolve it by simply leaving out the whey protein. i never realized that dairy as such could be a fundamental problem, which probably also is a major cause of my worsening CFS and FM symptoms during the last few years. -> always WATCH and REMEMBER food intolerances, eliminate/re-introduce, and observe. never think it’s just a coincidence..

    also, my chronic throat infection (still there, but not very active) is probably just a bystander in all this. still would like to get rid of it long term of course *g*

  16. Hi qualia,

    That’s great news! I didn’t know about “prescription strength” probiotics and it’s great that they along with milk elimination have cured your problems.

    Your prescription sounds like a good trial technique for bowel conditions. Very good.

    As for me, I had some testing done years ago but my doctor didn’t believe in treating yeast/fungal conditions so I went the diet/nutrition route and that has worked in that all my disease symptoms are gone. I am a perfectionist however and my concern is that infections may still be present, just at a sub-observable level. It would be interesting to get tested again, I would definitely want it to be a PCR DNA test like the one you linked. It would have to be easy and inexpensive for me to do through the mail.

    Congratulations again on your fix! Are your CFS/FM symptoms resolving?

    Best, Paul

  17. thanks! yep, all the acute CFS/FM and brain fog symptoms i periodically, or sometimes constantly, had seemed to have been caused mainly by the milk sensitivity. also, during the inflamed, and therefore leaky gut phase, acute exorphin effects from milk and gluten also have been a huge problem. those are now gone too.

    it seems that the immune response that gets triggered by some food sensitivities puts the body in some kind of “self protection” mode, just as with a systemic infection. in fact, it indeed often felt like the severe lethargy and brain fog one experiences during a salmonella or flu infection. in addition to this immunological response, there also probably is an “colon lining/mucus emergency rebuild” response, which sucks up all of the free glutamine in the body, which then causes severe exercise intolerance and very slow muscular recovery. this is at least my suspicion, because my response to supplemental l-glutamine during this time was always very positive. i could pretty much silence my muscular symptoms temporarily just by taking an ass ton of glutamine. HMB also helped a lot. now, that i’m milk and food allergy free, my protein and glutamine need has dropped massively while i’m still as muscular as before, and muscle aches, even after a strenuous workout are very limited, and don’t induce the kind of “i need protein NOW!!” panic reaction as it was the norm before. i’m now completely fine with around 1g/kg

    so: food indolerance -> inflamed gut lining -> increased glutamine turnover -> breakdown of muscular performance and recovery

    and: food sensitivity (prob. mainly dairy and gluten) -> immune system goes into emergency and recovery mode -> lethargy and brain fog + AI symptoms

    i’m not saying all CFS/FM is caused my these mechanisms, but at least for me it seems to be that way.

    now, without dairy (and gluten), i have much better performance and recovery, and don’t even need a protein supplement anymore. muscle aches are only slight if at all, and don’t bother me at all (like it should be when healthy and fit).

    currently i’m still taking some of the mytochondiral boosters and some other supportive supplements which proved to be extremely valuable during the lethargy phases, but i don’t think i actually need them anymore. but hey, they just feel so good.. 😉

    btw, this is the “prescription strength” probiotic i mentioned:
    i din’t try it though – but i guess it’s easy to find some user feedbacks on the net if you’re interested.

  18. Dear Paul,

    Could you write something about PREBIOTICS.

    I’m truly interested into knowing if it is more important to use PRE or PRO -biotics.

    The gut is of extreme importance. I’m impressed how human strains of probiotics like LGG and LP 299v provide an array of benefits to the host, like reducing systemic inflammation, reducing endotixin levels, rising antioxidant capacity of the blood, etc.

    I have a bottle of Larch Arabinogalactan, but not sure if I should use it. What I’m doing is trying to consume berries to modulate my gut flora.


  19. Hi Enrique,

    My prejudice is to use foods, like berries … I think that’s the most natural way and I have most confidence in it. That’s what I do myself.

    Prebiotics are food for gut bacteria and they could help or hurt — probably they would help some and hurt others, depending on the state of their gut flora.

    I have a little more confidence in probiotics. They’re at least unlikely to do harm. I use probiotics in cases of acute bowel conditions, like food poisoning. I eat fermented foods regularly also.

    I don’t think the science is adequate to give us definitive answers, but this is what I do.

    Best, Paul

  20. Yes, I agree that high intensity interval training is great. However, Gary Taubes has stated many times that exercise does not help with weight loss. I’m not sure I agree with him on that, but he does provide some good evidence to back up his claim.

    BTW, If anyone is interested in testing for food intolerance, I used and was very happy with their service.

  21. to qualia: i have never heard anyone describe my symptoms so accurately – please let me know what mitochondrial support you used – i would love to talk more about this – my email is superbadasswhatever at gmail

  22. @darius check your spam folder if you haven’t received my email yet..

  23. I have been on a very low carb (nearly zero) for about 4 months and while I lost about 20 pounds (initial motivation to change my diet was to lose weight) I found myself with a continual cold that I couldn’t shake. I started taking vitamin C which helped but didn’t solve the problem (milder/shorter colds).

    Thankfully an acquaintance introduced me to your book. I added safe starches into my diet, increased healthy fat, and decreased protien. I felt miserable the first two days (lethargic, gassy, bloated)! Good news is that today is day 3 and I feel great.

  24. Welcome, cheryl! Let me know how things go from here.

    Best, Paul

  25. very intersting!

    i’ve been dealing with an annoying case of heartburn (maybe GERD) for several months now. it began when i switched to a VLC diet (about 20-40g per day) and has persisted for months. initially i wiped out almost all foods and was eating a very narrow diet. over time, i have introduced many new items and eat a very rich and balanced diet now. my carb count is now around 100g per day or so and all foods consumed is whole and healthy.

    my doc put me on nexium and i took it for 3 days but stopped when i found chris kresser’s series on heartburn/gerd. the bottom line is nothing helped me until i ordered a jar of active manuka honey 16+ UMF. i’ve been taking it now for 3 weeks daily, and it’s been extremely helpful. my symptoms are not 100% gone, but maybe 80%? i have always felt though, that my radically new diet seriously altered my gut flora and threw it into a whirlwind of sorts. i eat a high fat (mostly from pastured dairy and pure meats), moderate protein, semi low carb diet now with carbs coming from potatoes, whole fruits like blueberries and bananas, veggies, and active manuka honey. i was eating a fair amount of fully sprouted breads but i’ve haven’t had that now for over a month.

    i will continue on with the honey doses, as many testimonies claim it takes up to 2 months to bring things back into balance. but do you have anything to add with regards to me drastically shocking my gut flora and how that may have played a part in my development of heartburn?

    jack k

  26. Hi Jack,

    I believe that GERD/reflux generally results from small bowel infections. This leads to irritation and spasms (“reverse peristalsis”) which shoot chyme from the stomach back up. In severe cases pancreatic enzymes and bile also go up to the esophagus, which confirms that the problem is in the small intestine rather than the stomach as most doctors believe.

    As this post argued, I think very low-carb diets will let pathogens get a foothold in the gut. Pathogens in the small intestine interact with intestinal cells and may often decrease mucosal secretions (see the photos of what H pylori does in this post, making the gut more likely to be irritated by stomach acid.

    So your experience doesn’t surprise me.

    Manuka honey has some antimicrobial compounds. I think your current diet sounds excellent, and let’s hope you clear the problem very quickly. If not, you might want to read our bowel disease series for further ideas (

    Best, Paul

  27. Great article Paul,

    I personally have a wide range of health problems linked to chronic exhaustion, an irritated gut and sluggish liver/gallbladder so trying to optimise my gut somehow is of upmost importance to my recovery.

    I’ve kind of felt ‘trapped’ into a low carb diet due to suffering from previous sugar addiction and hypoglycemia, which ultimately led to destruction of my gut, food sensitivities and liver dysfunction.

    The chain of thought thus far, which you do touch on is that a predominantly meat and fat diet can heal the gut for some. I’ve never quite gone this far, and in fact wonder if I should by removing the remainder of my veg.

    I’m hoping a slight reduction in fats and slight increase in carbs may both boost my energy levels and take a little strain off the liver. I’ve been practically 80/20 (fat/protein) for a while now and not seen many improvements with my gut. I am incredibly carb sensitive so I’m trying to increment by 50g of sweet potatoes (around 10-15g of carbs) around every 4 days to see how I do. Is already a bit of a warzone down there so I hope the introduction of starches won’t aggrevate the problem.

    Do you have any thoughts on minimising/reducing inflammation in the colon/small intestine within and/or beyond the scope of this diet?

    Many thanks! Love the blog!

  28. “This rise in endotoxin levels and the resulting immune response may resemble a brief illness. Some known effects of a sudden rise in systemic lipopolysaccharide levels:

    * , vasoconstriction and endothelial dysfunction. [8]”

    Hi Paul,

    This symptom in the form of sharp jabbing pain in the left chest area (different places) was what first drove me to the doctor. I was thoroughly checked for heart attack with over night observation and they proclaimed no heart problems and that I was healthy. An Ultrasound did show a leaking mitral valve which was a recent development.

    The jabbing pains, almost always occurring at rest, never went away however. That was over a three year period then I went paleo low carb, meat and vegetables…basically what PHD says is VLC. The pains disappeared completely for the 3 or 4 months I was strictly low carbing it.

    I was elated until I ran into other problems…typical low carb stuff like severe energy problem, weight loss, looking like cr@p, etc all on over 3000 calories a day.

    My gut had shrunk way, way down. My hip bones protruded and my stomach and lower gut were concave. This all happened fast as I now realize my bacterial gut population must have crashed.

    I added back starch, rice and potatoes which reversed things but the what I assume is endothelial pain, came roaring back.

    This post might explain the source of the pain (the endotoxin derived from bacteria.

    Paul, do you have any idea for an experiment I could do in order to test this idea from your post? Should I try commercial probitics to see if pain is abated by endotoxin changes they might induce?

    I am following your general guidelines right now after reading your book with the exception of NAC and k2 supplementation…they are on the way though.

    Also, reintroducing safe starches has brought the joint pain I had back as well I have mentioned this before and have taken your recommendations. I currently am trying to correct for any deficiencies, then I will play with protein and carb ratios to see if I can lower glucose intake without suffering a deficiency there again.

    I have to be careful with IF, keto and fasting because a chronic fungal infection I have and knew about flair and i get a sinus and cold lasting months

    Ironically, I am back to feeling very much like I did before starting this whole affair, excepting a few war wounds for my troubles!

    In my mind I have to blast the fungus, kick out the bad gut bacteria and get some new good ones, and determine if any deeply embedded virus is in play.
    Thank you.

  29. Hi Matt,

    I think if you’re currently 80% fat 20% protein 0% carb then your carb+protein intake is too low. Read our “zero-carb dangers series for more on that. At a minimum you need at least 600 calories per day carb+protein together. I would try to get at least some of it from carbs.

    You may find that rice or even glucose/dextrose, the easiest to digest form of carb calories, may help you the most. As the least available to gut bacteria, they may be the easiest transition from a zero-carb to higher-carb diet. I would re-introduce fiber slowly.

    Vegetables are not really that consequential for health and if you think dropping them will help you, go ahead. You might as an experiment want to simplify your diet a bit, that might help you figure out what helps and what hurts. However, at some point you’ll benefit by re-introducing vegetables and fermented vegetables.

    Gut problems are very diverse – they are most commonly caused by infections of various kinds or by food toxins and allergies/sensitivities. As always, malnutrition exacerbates these. Vitamin D levels should be optimized, to help produce antimicrobial peptides in the gut.

    After you’ve been on our diet and supplements for a while it will be easier for me to give you advice, because that will fix some problems and clarify others. I think in general you should go slowly and gradually, giving your gut time to adapt to dietary changes, and focus on being well-nourished. I would not neglect micronutrients as well as the carb/macronutrients.

    Keep us posted as you progress!

    Best, Paul

  30. Hi Perry,

    Nutrition may bear on some of the issues you mentioned. Magnesium deficiency can produce mitral valve prolapse, and scurvy like I had can arise on zero-carb diets and produce a skeletal appearance and weight loss.

    Joint pain suggests a leaky gut and toxin accumulation in the joints and/or some sort of chronic infection. You say you have a chronic fungal infection and possibly viral infections.

    This is a pretty long list of maladies. It’s not really possible to tackle all of these problems at the same time. With so many problems, I think you need to get on a healthy and nourishing diet first, then see which problems go away and which stay.

    You’ve seen that zero-carb isn’t good for you – and if you do have fungal infections, that’s understandable, with fungal infections zero-carb is a disaster. As I mentioned to Matt, when you have gut problems you may find low-fiber, easy-to-digest glucose sources the best way to start. Rice or even dextrose may be a good way to add carb calories at first. Go slowly and incrementally, and experiment to see if you are helped or harmed by fiber. Watch out for food sensitivities. Make sure you are taking vitamin D, vitamin K2, magnesium, and the key antioxidant minerals zinc/copper/selenium/vitamin C.

    If your doctor agrees that you have a fungal infection, then perhaps he’ll prescribe drugs to treat it. It seems sensible to start with what you know to be a problem rather than with mere possibilities.

    With so many problems and symptoms, you should definitely be working with your doctor.

    Until you’re consistently on a good diet with good nutrition, it’s very hard to analyze these problems, since on bad diets so many different things can go wrong in so many different ways. So start there and proceed systematically. And let us know how you’re doing!

    Best, Paul

  31. Hey Paul,

    If I were trying to gain weight on your macro nutrient ratios, which are 65% fat, 15 % protein, and 20% carbohydrate, and I was consuming 3000 calories to achieve this goal I would have to consume about 1950 calories from fat, 450 from protein, and 600 from carbohydrate. If I were to convert that to grams that would give me a total of 216 grams of fat, 112 grams of protein, and 150 grams of carbohydrates. My one question is: how do I this. I have tried out various combinations on fitday, and it seems I would have to consume an awful lot of added fat, which at times I feel is unnatural, plus I just can’t seem to imagine myself eating 150 grams of carbohydrates after being VLC for 5 months now. I would have to eat about a pound in a half of potatoes, just to reach my carb intake. Should I go on a ahead and do it, or do you think this approach is unhealthy.

    I am at times afraid to consume this much food, because I believe it is unnatural for us to add so much extra fat. Did our ancestors really pour mountains of butter on top of there food? I am so desperate to gain weight, and cure myself of all these nasty fungus infections that I am willing to do anything. VLC helped my gut issues, but it failed to cure my fungal infections, so I know something must still be wrong with me.

    Sorry for the long, annoying post. I hope you have the time to answer.


  32. Hi Robert,

    Your post is not annoying and I’m happy to answer.

    It’s fairly simple:
    1) Eat fatty meats and fish such that fats are 2/3 of calories, protein 1/3. This isn’t too hard. Eggs are 68% fat, 32% protein for reference, so you want to average the fattiness of eggs.
    2) Add fats/oils like butter to carbs so that fats are again 2/3 of calories, carbs 1/3. E.g., put butter on potatoes or egg yolks or oil on rice. This is not hard either because fats have so much greater caloric density than plant foods. (e.g. potatoes have 300 calories/lb, oils 4000 calories/lb)

    That ends up with 2/3 fat, and carb+protein adding to 1/3. Adjust the carb-protein ratio to your taste.

    As far as eating a pound and a half of potatoes, yes that is safe. Chris Voigt who just ate the all-potato diet was eating 7 pounds a day. However, it may not be to your taste. If you don’t like eating so much plant food, eat white rice instead.

    Our ancestors ate bone marrow and brain to get pure fat. If you can get access to those, then you can eat those instead of butter.

    It is OK to eat fat and OK to eat extra calories! They will help you add muscle. If you are eating too much, your body will tell you. You have to listen to your body.

    VLC makes fungal infections worse, you need glucose to fight those. So I would definitely encourage you to go forward.

    Best, Paul

  33. Thanks a lot Paul. Your blog is kickass, and you are slowly becoming my favorite “paleo guru.”

  34. Many thanks for the response Paul,

    Everything on the web tells me that white rice should be avoided, both due to the potential insulin spike and it’s ability to ‘feed Candida’. I don’t like labelling myself with Candida specifically, rather just gut dysbiosis, however my problems with hypoglycemia might make working it in tricky.

    Would your research/experience suggest that white rice combined with protein and fat has less of an impact on gut flora than say fibrous veg and protein? There is a school of thought (food combining) that starches and proteins combined in the same meal would lead to greater fermentation, i.e. rice and chicken for example. I don’t have any specific references and I believe it’s more something that is banded round alternative health circles. I guess I can only experiment.

    Will see how I do sneaking starches in in tiny amounts. At the moment I’m just trying sweet potato’s but will also try yams. Having a bit of a stressed liver/gallbladder does complicate the issue and I have a number of chronic symptoms so it’s hard to gauge changes, but it may help slowly moving out of VLC.

    Might a return of hypoglycemia (hopefully temporary) be a problem for some people who have been VLC for a while when adding carbs back in?

    Many thanks,

  35. Hi Matt,

    As someone with long experience with Candida/fungal infections, I couldn’t disagree more with the avoid rice meme.

    Fungi mainly occupy the colon, only in severe infections do they reach into the small intestine. Rice or, even more so, glucose is largely digested in the small intestine and so it doesn’t feed Candida much.

    Meanwhile, the immune response to fungi is a large consumer of glucose, in order to generate reactive oxygen species. Too much carb restriction shuts down anti-fungal immunity.

    My fungal infections always became severe when I zero-carbed and receded when I ate starches.

    Fructose was a problem for me, I think it is best avoided.

    It’s possible that food combining may slow digestion, let more food reach the colon, and promote infections, but I’m not aware that it’s a major effect.

    I’m doing a post on sweet potatoes today. It’s relatively high in fiber so the concerns you expressed about feeding a fungal infection would apply much more strongly to sweet potatoes than to white rice.

    Rice and carbs are easy to digest and would help the gallbladder issue.

    Hypoglycemia — I’m not advocating a huge carb intake. Most diabetics can handle a modest carb load. Have you been diagnosed with a named medical condition that causes your hypoglycemia, like hepatitis or diabetes?

    Best, Paul

  36. Thanks Paul,

    I haven’t been diagnosed a medical condition beyond ‘reactive hypoglycemia’. Seems pretty common these days even in the absence of diabetes due to the SAD diet causing a blood sugar rollercoaster.

    Would you ever recommend brown rice? Would I be right in thinking white and brown are at opposite ends of the spectrum when it comes to digestibility? Is white rice still regarded as a complex carbohydrate?

    Interesting about the fiber and will be something to bear in mind. I assume yams have a similar amount.

    Apologies for asking questions I could probably google!



  37. Hi Matt,

    I think white rice is healthier … the brown part doesn’t add much but some starch that can be had more safely from the white part and some protein that is more toxic than other protein sources.

    So the only reason I see to eat brown rice is if you like the taste.

  38. that is so contrary to what most people believe regarding rice (even the popular Paleo bloggers themselves). most either say avoid rice altogether, or choose brown if you’re gonna choose one, and if you choose to eat brown rice, it’s probably best to soak it in raw whey overnight before cooking.

    yet you say to just eat white rice straight up, and ditch the brown rice completely. i know eating brown/white rice is probably not going to be the main determining factor on ones overall health, but sometimes it’s pretty tricky to figure who’s got the handle on certain things.

  39. Perfect Health Diet » What’s the Trouble With Sweet Potatoes? - pingback on January 11, 2011 at 3:48 pm
  40. I’m so glad you guys are discussing kinds of rice. Today at lunch the only non-grain carb choices to order with the salmon were wild rice or french fries. I chose the wild rice because I don’t like french fries, but I wasn’t sure exactly what “wild” rice means, so I didn’t really eat much of it.

    Is there a rule of thumb for situations when none of the choices are appealing?

  41. Hi Jack,

    The “brown rice” recommendation is part of the “whole grain” (over refined/milled grain) recommendation. That recommendation lacks a scientific basis in our view. It is supported mainly by epidemiology – people who eat whole grains tend to be healthier – but analysis reveals that the people who eat whole grains are the same health-conscious people who exercise, don’t smoke, don’t do drugs, don’t engage in risky behaviors, earn more money, etc. So there are a million confounders and the epidemiological evidence is not convincing.

    Whereas it seems incontrovertible that the whole grains have more toxins, so if the big concern with grain is toxicity then it must be best to avoid brown rice.

    Hi erp,

    Thanks for asking, I didn’t even know that “wild rice” is in a different genus from true rice until I just now looked it up:

    It sounds like it’s probably safe but unfortunately we don’t have a billion Chinese and 12,000 years of consumption to vouch for it. It is related to Asian rice and so I guess I would consider it presumptively safe. According to Wikipedia its Ojibwa name was “good berry” and shouldn’t we trust the Ojibwa?

  42. Paul this Candida/Rice talk is very interesting, as I battle it too (confirmed via Genova CDSA). Using low fruit version of the specific carbohydrate diet along with Nystatin and optimizing other supplements (k2,fish oil, enzymes, betaine HCL, b complex, probiotics,zinc) I saw huge improvements and for all practical purposes returned to perfect health for 5+ months.

    However, 3 months after ending the Nystatin and bringing back some carbs but still on SCD my tongue and bowels are telling me the Candida is back. No where near the level it once was. But after I experienced such awesome levels of health I’m rather annoyed with this.

    Any thoughts on the long term battle with Candida? Your making a strong case for glucose/starch to fight it (I did fine without the first time), are their any other specific nutrients that are depleted in a fungal infection and should be monitored?

    Thanks for the help!


  43. Hi Steve,

    For me it seems like getting many small things right has added up to slow but steady improvement.

    For instance, the immune response begins with glucose but also relies on iodine and antioxidants. This is discussed in the book. So selenium, iodine, C, zinc, copper are all important. So is chromium (for unclear reasons, possibly related to glucose entry into immune cells).

    Another issue is antimicrobial peptides for which you need D and magnesium.

    Berries and coconut oil both have some antifungal activity, that is why I ate that here: Probably I should have left out the baby spinach due to oxalate, but I thought others might like the spinach to make it more salad-like. You probably know about oregano and other antifungal herbs.

    Eliminating fructose and getting sufficient glucose was a big step forward for me. The last time I had tongue or skin symptoms was during my first six weeks on antibiotics in 2009.

    The diet and supplement regimen set out in our book is really the best I think for fungal infections. It’s not a cure-all but it certainly gave me a leg up – it’s only been progress ever since.

    Best, Paul

  44. paul- you said its not a cure-all – what is your definition of a cure-all? and what do you speculate would be even better?

  45. Hi darius,

    By cure-all I mean that one step causes eradication of the infection. E.g., antibiotics can be a cure-all for some acute bacterial infections.

    Fungal infections tend to be slow to progress and slow to disappear. Also, when they’re not presenting symptoms it can be hard to tell whether you still have them. I’ve been symptom free for a year but I’m not quite prepared to declare a complete victory until I’m totally clear of my rosacea and I know my gut is perfect.

    I don’t know that there is anything better, in terms of diet and nutrition. I could do more of course, I could take antifungal drugs and probiotics. Since I have no symptoms I don’t think either is necessary.

  46. Paul (wasn’t sure the best place to toss this), have you given any thought to whether or not carbs + fats ought to be ingested separately? Or if at least there woud be any benefit, weight- or fat-loss-wise, to separating them?

    I’m about 2 months into fully legitimate PHD (inclusive of starch, which I’d eschewed for nine months) and after some nervousness around weight gain (3-5lbs over the past few weeks) which I can’t confidently attribute to muscle — much as I’d like to think my lifting is that productive — I’m wondering if the composition of meals is anything to think about.

    Typically I have my serving of starch (rice, potatoes, etc.) alongside eggs/cream/cheese midday. Any benefit to spacing those components out?

    Reading this at CarbSane prompted the query here:

  47. Hi John,

    That’s an interesting idea. For healthy people I don’t believe it matters – or matters only in terms of a few pounds, not some progressive weight gain. Remember that with just a few extra pounds, leptin increases and suppresses appetite. So combining starches and fat wouldn’t produce progressive, continuing weight gain unless it was constantly damaging weight regulation and making it worse. I don’t believe safe starches with safe (sat and monounsat) fats can do that. Sugar and omega-6 might.

    I personally haven’t seen a big change. I’m a bit heavier, but I think that’s all or nearly all muscle and bone mineralization. Still wear the same clothes, but my shoulders fill them out better.

    I do however do intermittent fasting now, and I think that helps control food intake. Perhaps that cancels out the effect from eating fat and carbs together.

    I wouldn’t have any problem with a decision to eat carbs in a separate meal from most fats. If you try it, let me know how it goes. It sounds inconvenient, but maybe it would help some people lean out.

    Best, Paul

  48. I will keep you posted!

    Started today — eggs, macadamia nuts and coconut milk at noon; rice I will enjoy separately, a few hours after. OK I had some 99% dark chocolate too at noon.

  49. Hello Paul

    I’ve been on a VLC diet (20 g. or fewer carbs, from non-starchy vegetables plus 1 oz. nuts/day) for two months. I started eating ‘safe starches’ five days ago after reading your book. On a typical day I have 4 to 5 oz. sweet potato, mashed with butter, for breakfast, and maybe 4 oz. white rice or butternut squash later in the day. I immediately found myself experiencing digestive discomfort (a feeling of being extremely and uncomfortably full), loss of appetite and ‘cranky mood’, all as described in your post on side effects. I seem to be feeling worse, not better, as time goes on, and have also become very constipated (a problem I did not suffer from on my VLC diet after the first two weeks).
    You say in your post that people coming to your WOE from a VLC diet may experience these symptoms for ‘a few days’. Please can you tell me what is the maximum amount of time you would expect it to take for a VLC-er to adjust to ‘safe starches’ and what I should do if I do not start to feel better soon? Should I just stick with the diet and hope that I get used to it, or should I get tested for gut dysbiosis (and if so, how?)
    (BTW while on my VLC diet I did not have any of the symptoms which would suggest a fungal infection, and you say that fungal infections get worse on VLC diets, so can I assume I don’t have one?)

    (From London, England)

  50. Hi elima,

    At this point it could either be gut dysbiosis of some kind or a food sensitivity. There’s definitely some significant immune activity. It’s not just an adaptation to carbs.

    The first thing I would do is experiment with different types of carbs to if you have the problem with all carbs or just some. Some people have trouble with sweet potatoes, for instance (see

    The other diagnostic aspect of this experimentation is seeing where in the digestive tract the problems occur. Quick digesting sugars (e.g. rice syrup) would indicate a dysbiosis close to the stomach; bad reactions to fiber indicate a dysbiosis in the colon.

    It’s a little premature to rule out any particular pathogens, but I would associate your symptoms more with bacteria than with Candida/fungi.

    As far as carbs go, you should find the best tolerated carb source, eat so you have minimal symptoms, take probiotics and eat fermented vegetables and give your gut some time to adjust the gut flora. Make sure you have enough vitamin D, C, and selenium. Eat bone broth soups to support collagen formation which supports gut barrier integrity.

    If it persists for a long time, then I would have a doctor test for gut pathogens. Personally I would favor starting with a fecal pathogen profile like this one: However, doctors have their own favored ways of going about diagnosis and treatment.

    Best, Paul

    • Hi Paul,

      I finally found this article, and I am much encouraged. As I have commented elsewhere on your blog, my family embarked on a GAPS-type diet four years ago, to heal our then-six-year-old’s very terrible gut issues, autism-spectrum-style symptoms, and severe anorexia.

      It has been a long nearly-four years.

      Starting over a month ago, I began introducing various starches to our meals, as per your fascinating suggestions. I had been thinking, just prior to that, the ways in which our years on “GAPS” were sort of like an antibiotic – which our son clearly needed, since all the food he ate (especially carbs) were going straight through him at that point, and even now, after all these years, his gut is super sensitive. To my surprise, he is not getting diarrhea from rice! Sweet potato, on the other hand…shall we just say that that didn’t go well.

      I will be very interested to hear about research in the near future, because I am convinced that diseases such as autism and OCD and depression will become hugely linked to the state of our kids’ gut flora…

      My husband and I are experiencing symptoms just as you describe in this article. Which gives me hope, since you say the situation is temporary. However, I am just a little concerned that four years of an essentially low-carb diet may have given us this new set of problems, even while it addressed some huge issues for all of us (perhaps I can view it as a therapeutic protocol?).

      We are obviously not simply “adjusting” in a few days or a week, nor do I expect our son to respond favorably that quickly (although our two youngest are doing great with your PHD recommendations! And digesting fantastically, after only a couple days of slight Complaints).

      My main questions:

      * Do you see heightened reactions in people who are coming off many years on a lower-carb diet?

      * How about reactions in people who had moderate to severe gut dysbiosis to begin with?

      * How should we attempt to quell some of the heartburn and indigestion and exhaustion and depression that has been happening over the past month, if these are all indicative of “endotoximia” (if that’s the right word)?

      * Would activated charcoal be helpful?

      Thank you so so much for your research, and for your dedication to Learning New Things.


      • Sorry, but I have another addendum question: after reading the sections in your book where you discuss intermittent fasting, and diets higher in carbs that still include many SCFAs to induce ketosis…I had assumed that these things would both be good for me (my history is a history of luteal phase/”female” hormonal dysregulation, and depression.

        Basically, I adopted your recommendations for two meals per day, and added a lot of coconut oil to our food. But now I am wondering if this might be a harmful approach?

        I would so appreciate any thoughts on this.


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