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!

Primal Kitchen Ranch

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 more than three decades 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 flavorful and delicious kitchen staples crafted with premium ingredients like avocado oil. With over 70 condiments, sauces, oils, and dressings in their lineup, Primal Kitchen makes it easy to prep mouthwatering meals that fit into your lifestyle.

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