Dear Mark: IBS and Gluten, Tweaking Calories for Fat Loss

GlutenFor today’s edition of Dear Mark, we’ve got a short but sweet two-parter. First up is the connection between Irritable Bowel Syndrome, gluten, coffee, and alcohol. A reader with a history of IBS triggered by gluten, coffee, and alcohol wonders if giving up gluten really could have solved his intolerances of the other foods. Then, I give my take on the best dietary strategy for losing the last few pounds of body fat for an otherwise lean individual. Believe it or not, I even mention and recommend counting calories.

Yep. Let’s go:


Hi. I have been a long time sufferer of IBS. I always thought dairy, liquor, and coffee were the main instigators of my problems. I just stayed away from all 3, and was only ever semi-fixed.

Recently (few months), and for unrelated reasons I went mostly primal. I definitely gave up refined sugar and flour. I noticed that my IBS symptoms have lessened a considerable degree! Out of curiosity I started drinking some liquor (after all I quit drinking beer) and haven’t noticed any ill effects. I even have had a cup or two of coffee here and there and have been okay.

Is it plausible the whole time gluten was my the main instigator? And if so, why were liquor, dairy, and coffee so involved? I used to not be able to finish a cup of coffee without running to the bathroom – but now if it was really gluten all this time — why did it have such an immediate effect…. how does the combination of these things affect IBS?

Basically, I’m writing you because I don’t trust my own observations? They seem so weird to me, and it seems too good to be true that I can enjoy a nice cup of coffee nowadays…. So am I lying to myself, or is there any known truth to my observations?



These are very good observations, not the deluded visions of a madman. It’s not just plausible that gluten was the main instigator. It’s probable. Check it out:

What about the relation of the foods you mentioned – alcohol and coffee – to gluten and IBS?

In large amounts taken in a short period of time (binge drinking), alcohol can increase IBS symptoms. But moderate and light drinking appear to have no relationship to IBS. If they reduce stress and improve enjoyment of life, they may even reduce the symptoms of IBS, for which stress can be a trigger. Gluten-containing beer may also exacerbate IBS, particularly if you’re gluten-sensitive or celiac.

How about coffee? It can increase intestinal motility, so if your IBS was of the diarrheal persuasion, coffee may have worsened symptoms. Some people also claim that coffee proteins and gluten share cross-reactivity – that the amino acid sequences in coffee and gluten are similar enough to provoke an autoimmune response from both. I haven’t seen any published research showing gluten-coffee cross-reactivity or a comparison of protein composition, just anecdotes, but that’s something to keep in mind.

What about leaky gut causing increased sensitivity to otherwise benign foods like coffee?

In IBS-D, you’ve got increased intestinal permeability across both the small intestine and the colon. IBS-C (constipation) patients have an interesting pattern of leaky gut: permeability is lower in the small intestine than controls and IBS-D patients. Many IBS patients oscillate between both constipation and diarrhea throughout the course of their symptomology, and gluten is a well-known inducer of intestinal permeability via zonulin – even in the absence of celiac – so you likely experienced some leaky gut which could have made other foods problematic.

Removing gluten removes a potential aggravator of general food intolerances, many of which present with abdominal cramping, bloating, diarrhea/constipation, and other hallmarks of IBS. Food intolerances themselves have been linked to IBS for decades.

So no, it’s probably not too good to be true. Enjoy your coffee and alcohol (in moderation)!

Hey Mark,

I forget if you mentioned this in an article or podcast, but you brought up the fact of having to get very strict regarding calorie intake if you want to drop into the single digit body fat range. There are a lot of different calculators and equations that determine TDEE/maintenance calories and the results from the different sources vary (sometimes by up to 500-1000 calories). What source or equation would you use to determine TDEE/maintenance calories? Also, to drop from say 10-12% BF to 8-9%, and assuming the person follows an exercise regimen of lifting 3 days a week + one sprint session + lots of walking, would you recommend eating at maintenance, above maintenance by a few hundred calories, or trying for a small calorie deficit? I know this advice goes against a lot of what you talk about, however, I think there is definitely a time and place for strict calorie counting, especially if all the food is primal.



Ask a dozen fitness heads for their favorite way to calculate TDEE and you’ll likely get a dozen different calculators. What gives? How can such a thing happen? Are they all horribly mistaken?

It all seems silly until you realize that calculators (any of them) work best as a baseline. A starting point. And pretty much all of them will work for that. You might, however, want to check them all out, avoid the big outliers and stick to a calculator that gives similar results as its peers.

The best way is to choose a calculator (any calculator that looks good to you), run the numbers, do a two-week test run based on the results to determine if they’re accurate for you, and adjust up or down accordingly. It’ll take more time than just going with a calculator and trusting it from the start, but you’ll get better results in the long run. And two weeks isn’t that much time if the payoff is worth it.

Once you’ve determined your maintenance calories, you can get to losing. But how?

I think the worst way for most people to lose the last few bits of body fat is to lower calories drastically and keep them that low for days, weeks, months on end.  This is a great way to destroy your will to live and train. This is a great way to depress your metabolism and tank your thyroid. This is a great way to see your body fat losses slow to a trickle.

The simplest way is to eat at maintenance (or even slightly above) on workout days and drop calories by a few hundred on rest days. You’ll usually end up in a slight caloric deficit week over week, and the added training will help you preferentially burn fat rather than muscle.

The most effective way might be to try alternate day fasting, or ADF. ADF as they show in human studies needn’t entail complete abstention from food. Sometimes it does, but not always. Instead, you can eat significantly less than you normally would on the “fasting” days – I’m talking like 50% of your maintenance calories – and eat more normally the next. In humans, fully fasting for one day doesn’t necessarily result in overeating the next. So if you’re like most of the subjects in the ADF literature, you don’t make up the missing calories the next day. You may eat more, but not enough to replace the food you didn’t eat. It also works equally well with high-fat or low-fat dieting, so you can go a bit higher carb on training days and higher fat on rest days if you’re into that kind of macronutrient apportioning.

You sound pretty active, so even just two days, maybe three of the “fasting” should do the trick. Make them your rest days, or days where all you do is walk. You still need to eat to support your training.

I wouldn’t even worry too much about fasted training. It’s nice if it happens, but don’t stress out about doing a workout after having eaten something. Training is still effective if you’ve eaten and it’ll still help you lose body fat especially if your overall calorie intake is below maintenance.

Hope that helps! There are lots of ways to do it. Whatever method lets you stick to the calorie deficit without going crazy is the one that will work best.

Thanks for reading everyone!


About the Author

Mark Sisson is the founder of Mark’s Daily Apple, godfather to the Primal food and lifestyle movement, and the New York Times bestselling author of The Keto Reset Diet. His latest book is Keto for Life, where he discusses how he combines the keto diet with a Primal lifestyle for optimal health and longevity. Mark is the author of numerous other books as well, including The Primal Blueprint, which was credited with turbocharging the growth of the primal/paleo movement back in 2009. After spending three decades researching and educating folks on why food is the key component to achieving and maintaining optimal wellness, Mark launched Primal Kitchen, a real-food company that creates Primal/paleo, keto, and Whole30-friendly kitchen staples.

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31 thoughts on “Dear Mark: IBS and Gluten, Tweaking Calories for Fat Loss”

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  1. I also enjoy a cup of coffee every morning after not being able to tolerate it for over 20 years. Its a lovely way to start my day.

    1. I stopped drinking coffee 10 years ago because it caused too many GI tract problems for me. l switched to tea, which, for many of us, is much kinder to the gut.

  2. Counting calories can make it difficult to stay in a primal mindset, but I’ve found it helpful for losing the last couple pounds. In my experience, it’s best to decrease my intake less than I think I should. I have had a tendency in the past to go too low which is not sustainable and then causes my metabolism to slow down, so I stop losing weight after a couple weeks. Lately I’ve been successful with adding sprints to my routine once a week and a kettlebell circuit workout while only slightly lowering my food intake. PLUS I cut out alcohol. Thats been a big factor!

    1. Right on–I’ve had similar experience. Although instead of counting the calories really, I do a 16hr IF three or four times a week and keep other meals about normal; it’s an overall reduction. And that glass (or two) of wine which I was having every night does add up!

      1. I like that 16hr IF! I’ll do that a few times a week as well. I can see how incorporating that with alternate day fasting could be effective and easier to adhere to. It’s amazing how easy it is giving up alcohol. I usually do it for a month or so at a time, and even though I usually enjoy red wine it’s become so easy for me to just say no.

        1. I play with the macro breakdown rather than the overall calories. As a peri-menopausal Grokette (47), I’ve found shifting up the protein and down the fat helps to lean out. However, going super lean in this age bracket isn’t necessarily so great as oestrogen is related to fat stores. The hormonal balance for me now is different than 10 years ago when being 5% leaner made no difference to my cycle or sense of well being. Also varying the macros through the cycle can help too, going higher carb (still within low carb) in the second half and dropping back in the first half.

          Tracking using fitday really helps me see what’s going on and gives me the chance to look back and make comparisons.

  3. Brian, I could have written your letter. I went primal about 3 years ago, on the premise that it made sense, and no one had ever died (or even been harmed!) from a wheat or grain deficiency. So, I did it for about 30 days, and felt better, so I kept it up. I was primarily looking to lose weight (and I did – about 40 pounds after about 1 year!). However, one of the other things I discovered was that had I previously had IBS. I mean, it wasn’t anything I had ever thought about going to visit the doctor about (heck, I thought it was normal!), but a week or so after eliminating grains and gluten I realized that was how my digestive system was supposed to work!

    Mark says (above) “Many IBS patients oscillate between both constipation and diarrhea throughout the course of their symptomology” – well, that was me on grains. Again, nothing terrible, but it definitely took away from my quality of life! I mean really, the idea that I could sit down on the toilet and be done with a bowel movement in a minute or two was kind of crazy. Just like the idea that I might not have to expect diarrhea a couple of times a month!

    So, while the weight loss may have brought me, it was the IBS relief that keeps me coming back 😉

    1. Yes this has been a great adjustment! I really never expected this, so much so its been hard to believe ;).

      It was primarily a weight thing (I’ve lost about 20lbs) but I was probably only ever 30 lbs overweight anyway, so 2/3rds of it in a few months is great!

      But man everytime i look at a piece of pizza and think… damn that looks good and ya know alot of people say you can cheat 20% of the time and i barely do at all… i should just enjoy it….. I stop myself because i dont want horrible IBS issues. This now means more to me then the weight loss!!

      Just like you it had been so many decades i just thought of it as normal and was very careful about what i ate… all the time feeding it the real problems.

      Its so wierd for me NOT to have diarrehea that I’m having other problems with normal movements…. its like my track isnt used to regular stools… but i suppose time will heal these wounds.

      And on the cheating front – the best part – now when i decide this is a special enough moment – i want to cheat (like seeing my kids enjoy an ice cream) – now i will get an ice cream, cause the diary doesnt really bother me!!!

      And ice cream is better then pizza anyway 😉

      1. I definitely cheat too, but when I do it is with sugar & other carbs so long as it’s not wheat. Obviously, I’m not celiac but I just really don’t like it when my gut is on wheat. I’m ok with dairy and so ice cream is definitely on my cheat list!

        I’m the cook in my family, and let me tell you almond flour makes a dern good pizza crust, if not exactly the same as wheat. I use the recipe from Elana Amsterdam’s almond flour cookbook, but there are many others. The kids love it and we can all eat the same thing.

        I’m not sure what other problems you are referring to, but I will tell you something I went through: at first I was concerned that I could go a few days between movements. (That’s not really possible when you eat bran muffins, and yes, I used to do this because I thought it was healthy!) I thought I was constipated and this gave me a great deal of stress. Then, I did some reading and decided that it wasn’t constipation at all, I just needed to relax and not obsess. You know, listen to your body (like Mark says). So, when my body says I need a BM, I do and don’t worry about if I’m doing it often enough, or if I’m “regular” enough. I’m not straining, I don’t have diarrhea, so whatever is going on with me is way better than what I had before.

        1. Thanks for the followup.
          Yes now i sometimes go 2 days in between BM. Which is very wierd to me because I used to go multiple times a day. Whats been bothering me more lately though is that since they are finally formed, which my system is not used too… i’ve started having pain in trying to pass them. I went to a dr. and he said I had developed a fissure. (I’ve always tried eating alot of fiber + metamucil for the IBS issues – it never helped). Anyway, I still take the metamucil and eat a ton of fiber, figs, dates, apricots, etc… but I’m still having discomfort.

          I’m hoping after enough time, my body will be used to this working ‘correctly’ and kinda self adjust….


    2. Ditto!

      As was the clarity of thinking and the fact I could forget to eat meals.


  4. Regarding the IBS segment, I have been wondering the same thing since removing grains, legumes and dairy from my diet. I have found that I can drink coffee and wine (cup of coffee/glass of wine) with NO digestive symptoms, and have been wondering if adding dairy back might be an option. There definitely seems to be a relationship between gluten (or wheat or other grains) and other irritants and not just a cause-effect with wheat and symptoms. Thanks for sharing.

    1. Michele,

      I have started to add very very very little dairy back with no problems. Of course everyone is different… but right now i might add a bit of cream or half/hanlf to a cup of coffee — (which BLOWS my mind – those were two absolute no-nos for me before). I even had my first ice cream in years this past weekend with my kids — and it was a GREAT moment :).

      I haven’t yet been so brave as to actually eat any cheese or drink a cup of milk… but its been so long for me that i dont really crave either.

      I guess i should say i used to eat diary more actually because I would have yogurt every day thinking the probiotics were net benefit – but once i went primal i took all dairy and grains out so i replaced that with a probiotic pill.

      Now that i think about it, maybe ill try a yogurt again and see what that does.

      Anyway, i’m not a doctor, and recognize everyone is different, but if you want to try it… its going well for me….. Cheers and good luck.

    2. I do know when your gut is not well, you can be lactose intolerant and then tolerate it later after a few months of healing. So I would assume the answer could be the same for other irritants.

    3. Dairy caused Microscopic Colitis symptoms for me. After a couple of years of gluten free, I find I can now eat dairy products without symptoms. I have had high quality dairy more days than not over the past few months, and no problems at all. Hooray!

  5. Personally I’ve had trouble with the last few pounds, so to speak, and I intend to lengthen my IF intervals and do sprints once a week. However, right now I have a three month old baby, and sleep is at a premium. My inclination is to give up on any desire to lose the last few pounds until I have a consistent sleep schedule once again.

    1. Definitely don’t fast when sleep disrupted with a new baby. Adds so much extra stress and cortisol is the prime hormone for fat storing. Just love that little baby and worry about a few pounds when life is a little less stressful!

  6. I’m another IBS sufferer, particularly after getting a very bad case of food poisoning April 2013.

    For much of the past 12 months I’ve been sick or at best, unwell. I’ve also been miserable, but I just tried to keep pushing on hoping things would improve. They didn’t until I started eating differently.

    I’ve been off wheat for 6 weeks plus, focusing on Primal for past month.

    I told my husband today, that I feel better than I’ve felt in years. It’s nothing short of amazing.

    I’m your age Mark, and I thought the way I’ve been feeling was just how it was going to be. I’m thrilled I have a choice! I will continue to exercise that choice and stay grain free.

    Thanks for everything you do, and to everyone posting on the forums and via comments – thank you. You’ve all helped me turn my life around.

  7. For me, it took tracking my Carbs, Protein, and Fat to see that I had way too much carbs (+200g/day) in my diet. Once I lowered the carb intake the weight fell but!, that’s a big but not butt, I plateaued. This is my new challenge now to lose the last 5-10 pounds of BF to be where I want to be. I have bulletproof coffee every morning with protein and collagen. Lunch is extremely sensible followed by an even more sensible meal (usually the Big Ass Salad).

  8. “I think the worst way for most people to lose the last few bits of body fat is to lower calories drastically and keep them that low for days, weeks, months on end.”

    It seems that for the two first weeks whenever I up the intensity of my training, I have a hard time eating enough calories to stay at the maintenance level. (Provided I’m avoiding bread, pasta, peanuts and potatoes, of course.) That is, my stomach revolts if I try to shove more than 1600 kcal in per day. (If I’m eating a lot of starches, the problem swings the other way – where I’m routinely eating 3000 kcal per day.)

    After some time, my appetite re-normalizes. Are the two-ish weeks at low calories likely to be a problem? If so, what do I do – besides eating unhealthy things and accepting the over-swing?

    Thanks, amc

  9. Re gluten, etc.
    I was off gluten for 2 years. Great move, but I was neither celiac nor visibly sensitive to it as far as I can say. I did have some brain fog and gained bad weight (visceral fat), had chronic vitamin D deficiency, bad dental health, etc. The change of diet that I underwent is so full of confounders that I cannot say gluten removal improved everything for me.

    BUT! A few weeks after I started a clean diet of whole foods (not particularly low carb because I do love to eat starches but to drop some bad weight, I also restricted starches for a while), I got glutenized by mistake and I paid for it … (weird body pain, sore joints, etc, for 2-3 days). That confirmed me that gluten was a nogo.

    Fast forward: I eat tons of prebiotic (inulin, RS) and some probiotics once in a while. The other day at work, a colleague celebrated his 50th birthday. There were a few big cakes full of wheat, sugar, cream, etc. I thought that after 2 years being rather strict, I would experiment. So I took a big portion of every cake and ate them (it was about 3pm, that was my first “food” of the day). It was disgustingly sweet and not particularly tasty (I am about 99% on real foods most of the time). So I expected to experience weirdish consequences after eating these cakes. I actually experienced nothing AT ALL. No bloat, no pain, no screwed up sleep, no sudden weird cravings, no mood swings.

    Conclusion: if you treat your gut correctly and boost its ability to work optimally, the occasional crap is not an issue. The funny thing is really this: once I ate the stuff, I did not feel like some more and it did not change my whole food routine at all. That’s to me a sign that my gut health is very good 🙂 It took 2 years …

  10. We get many dogs/cats at our clinic having been already diagnosed with food allergies (chicken is a particularly common one).

    We treat these animals with a protocol designed to ‘seal up’ the permeability of a dysbiotic gut (which includes feeding them solely a species-appropriate, grain-free, carnivorous diet).

    At the end of the protocol, they can invariably fully digest the proteins they have reacted to in the past. Partially digested proteins are no longer escaping through an inflamed and leaky gut wall, causing immune reactions throughout the body.

    I expect it works like this in all mammals – gut conditions are the key to good health, and gut conditions rely on biologically-appropriate diets (something that only a minority of us vets, or human nutritionists/doctors seem to have cottoned on to!).

  11. If you have gluten sensitivity there are several common foods which cross react with gluten (coffe, dairy etc). This basically means your immune system believes its still getting exposed to gluten prolamines and therefore your immune system is effectively in high alert despite gluten being removed from your diet. Of all the foods which cross react with gluten dairy cross reacts most commonly in around 50% of those with gluten sensitivity. Probably the reason why so many people feel hugh improvements when going paleo/primal.

    Your immune system can basically mediate most of the syptoms you are getting from brain fog, aches and pains to persistant colds and infections.

  12. I´m also one of those people, who lived a pretty normal and painless (gut) life, until I decided that maybe all this occational GI problems, in the shape of “loose” stomach could be linked to gluten/wheat. I was puzzeled by the fact that after drinking beer, I would get mild diarrea symptoms the next day, but bought into the general saying that “it happens to a lot of people after drinking alcohol”. Finally i stopped drinking beer (I was drinking too many anyway, so I decided to cut back drastically). Soon there after the symptoms diminished. I then took the step to cut out all gluten containing products (wheat, rye and barley). Guess what happened? I got a gut that I haven´t had before 😉 No bloating after meals, no more occational abdominal craps followed by diarrea.
    I then lived a couple of months, on a pretty low carb regimen, with veggies only. The logic behind this, was perhaps : all (non veg) carbs was bad news… But after a while I found out, that I was maybe not made for this extreme low carbing e.i below 50-60 grams/day. (muscle spasms, brain fog, loss of sex drive ect.), so I gradually introduced some potatoes, the occasional rice or corn serving. This did the trick. I now have my diet more or less dialed in, the way I want it. The only thing I am trying to reintroduce is greek yoghurt, as I cut that out as well when all this started. Maybe there is connection between dairy and gluten, where gluten is the reason for lactose intolerance. I eat hard cheeses, but the GY, is a thing I sometimes miss for my breakfast.

  13. I’ve had similarly puzzling IBS reactions to egg yolks before I tried eliminating gluten, and now that I’ve eliminated it, I appear to have no digestive issues with yolks and I can eat them all the time. Conversely, going paleo introduced stomach pains for me when drinking my daily latte, but eliminating the milk and keeping the coffee is just fine for me. Those two things are what really opened my eyes to how my body behaves complexly to the inputs I give it.

  14. IBS is a syndrome, not an actual disease. It basically means you have symptoms similar to a lot of other people, but no one knows what’s causing them.

    I was “diagnosed” with IBS for about 5 years until bloodwork done during a routine physical showed some abnormal results.
    One colonoscopy and upper GI later, and I walked out with a celiac diagnosis. The doctor took a biopsy, but apparently came out of the procedure and told my SO that it looked like a textbook case of celiac disease. A few weeks later the lab confirmed.

    Sure enough, eliminating gluten cleared up all IBS symptoms… And my indigestion as well.

    My suspicion is that a lot of the IBS is actually celiac disease.

  15. Manat, gluten sensitivity (GS) outnumbers Coeliac Disease by possibly 10 to 1, maybe more. This is hard to diagnose and isn’t picked up by standard screens for Coeliac Disease. So don’t assume if you get a negative CD screen that your don’t have a gluten related disorder, as many do.

    GS can cause all the symptoms you are describing. It doesn’t always manifest in the gut however and most commonly presents as neurological symptoms (headaches, migraines, brain fog, memory problems etc).

  16. I have had so-called IBS-C for over 10 years. I still struggle with it even though I’ve given up refined sugar and wheat/gluten. IBS-C is a whole different monster and the only thing that has kept me semi-regular for my 10+ years of this .. is my morning coffee. Sometimes I think it’s physiological, sometimes I think it’s the actual properties of the coffee, sometimes I think it’s the warm liquid .. but whatever it is, it works.

    Another thing that works is eating all your veggies and fruits cooked, and eating easy to digest foods like eggs, chicken, etc. until the constipation resolves. Eating like this totally keeps the bloating away as well.