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When a Gluten Free Diet Isn’t Enough to Heal the Gut

I had a friend visiting last week who has celiac disease. Watching him carefully navigate restaurant menus made me realize how relaxed my “gluten free” diet truly was.

Why is he so careful at restaurants?

Celiac disease is an autoimmune condition marked by an inability to eat even trace amounts of wheat. In celiac sufferers tiny doses of gluten, regardless of how harmless they may seem, can actually damage the lining of the small intestine, leading to a whole host of symptoms, such as poor digestion, anxiety, fatigue, weight loss and more.

Needless to say, my friend must be vigilant in avoiding all wheat, even from foods that are believed to be “gluten free” such as corn tortillas. While it’s true that corn tortillas are naturally gluten free, they are often fried in the same oil that has been used to fry breaded foods or desserts, and as such those with celiac have to strictly avoid these sources of “cross-contamination.”

Hanging out with my friend made me realize how many times each week I was getting “glutened” even though I try to follow a gluten free diet. I decided to go gluten free originally because of lab tests that indicate I have sensitivity to gluten, even though I do not have full blown celiac (I have never had a biopsy of my small intestine done to confirm). I often notice joint pain in about a 2 week window after eating gluten, and also notice significant malaise and low energy immediately after.

But what about cases where someone’s blood work shows no gluten sensitivity and no signs of celiac disease?

Should we all be avoiding gluten even if we don’t have celiac disease?

Is a gluten free diet enough to heal those who have suffered damage to the gut as a result of reacting to wheat?

Should Everyone Avoid Gluten?

I don’t know.

I am sure there are some people who can eat wheat without any consequences. I also want to be clear that I do not think everyone needs to be vigilant against exposure to trace amounts of gluten. I have decided to take that step because of elevated tissue transglutaminase IgG antibodies in past labs I have had done while eating gluten. I understand that IgA is the gold standard in diagnosing celiac, and I am not IgA deficient, so the labs are presumably reliable, but nonetheless, my reaction to gluten is severe enough for me to have my doubts about even small amounts of wheat being healthy for me, so I take extra precautions to avoid the stuff. The net effect is I don’t eat fried food and low quality condiments, so I see it as a win win.

That and the damage caused by a wheat intolerance may be tough to spot. Celiac is a “delayed hypersensitivity reaction.” We do know that a reaction to gluten, when it occurs, is very often delayed for 48-72 hours after eating wheat, so it can be hard for people to pinpoint wheat as the culprit behind problems that pop up well after eating that delicious almond croissant (or maybe a couple of them).1

And even though my belief as a bio-individualist is that certain individuals can be healthy eating wheat, there are some in the medical community becoming more hard line arguing that gluten is a problem for everyone.

These doctors argue that everyone should avoid gluten, all the time.

Dr. Perlmutter, a neurologist and NY Times best selling author, is first man off the no gluten bus. In the updated 2.0 version of his book, he no longer recommends testing for gluten sensitivity, instead, he simply recommends that everyone avoid gluten like the plague.

To quote Dr. Perlmutter:

Multiple studies have emerged to further show the connection between gluten, and specifically the gliadin protein, and increased permeability of the gut, which we know is a fundamental mechanism for increasing inflammation. These studies confirm over and over again that non-celiac gluten sensitivity is real and much more widespread than we ever could have imagined.

Dr. Perlmutter is not alone in his assessment.

Indeed there is a science based movement of medical professionals pushing back against some who dismiss non-celiac gluten sensitivity as a fad, arguing that the damage caused by gluten is very real for millions and millions of people. Chris Kresser, who I find most convincing on issues related to gut health, has written at length about gluten sensitivity.

As far back as 2011, a panel that was convened in London tasked with the goal of classifying all the various conditions that are caused by the proteins found in wheat.2 Of course they list celiac, but they also included non-celiac gluten sensitivity.

I don’t intend to re-litigate the issue of gluten sensitivity in this post (in my view the evidence in favor is overwhelming).

Instead, I want to talk about the problems those of us avoiding wheat on a gluten free diet may encounter and why.

In my mind, restaurants present the biggest challenge because we can’t scan the ingredients list of the food we order, we trust that it comes out of the kitchen as the staff says it does. However, gluten free at restaurants often doesn’t really mean 100% gluten free. This is the problem of cross contamination.

Then, you have the foods with proteins so similar to gluten that the immune system reacts in much the same way as if you were eating wheat. This is the problem of cross reactivity.

But first up are the hidden sources of gluten in gluten free dishes.

Hidden Gluten in “Gluten Free” Dishes

Fried Foods

As a for example, I was at dinner last night at a local Mexican restaurant eating at the bar. I came to this same spot with my friend a week before, and he told the waiters he has celiac, so I knew there were many items on the menu that contained trace amounts of gluten due to cross contamination. However, the bartender assured me the entire menu was gluten free. Yikes, not true. Many of the corn and taco dishes have gluten, which leads me to my first source of hidden gluten: corn chips and fried foods. Corn chips are almost always fried. If the chip is fried in the same oil used for frying breaded food, it’s not gluten free.

Hash browns at MacDonald’s are not gluten free under this logic (it’s the best example of fried food I could come up with). But the handmade blue corn tortilla offered for the guacamole at my local spot wasn’t gluten free either since it was fried in the same oil as the churros, a breaded dessert.

The lesson here is to have a sharp eye for anything fried, it will usually contain gluten.


Staying gluten free at sushi restaurants takes more than just ordering Tamari, which is gluten free soy sauce. The soy, teriyaki and fish sauces used in many sushi dishes have wheat, as does wasabi. Ikura, or salmon roe, one of my favorite dishes is usually premixed in soy sauce and often cannot be made gluten free. Many sushi restaurants also use vinegar with trace amounts of gluten in their sushi rice, which means even the rice isn’t gluten free. This practice will vary by restaurant.

It’s also worth noting that soba noodles, made of buckwheat, often contain half wheat and half buckwheat and are therefore not gluten free. This brand of soba uses 100% buckwheat if you’re looking for a good clean soba option.

Hate to be the bearer of bad news, but many types of wasabi are not gluten free, they use wheat starch as a thickening agent. Thanks to my friends at Blue Ribbon Sushi on Sullivan Street for that tip.

If your mission is total avoidance of gluten, call ahead and ask about wasabi, whether vinegar in the rice has gluten, and whether there are “pure” gluten free options available.


This is a big one. In the grocery store, it’s relatively easy to read the label and determine whether a product is laced with gluten, but in restaurants it’s harder.

In addition to soy sauce and fish sauces, other condiments such as ketchup and certain salad dressings are sometimes thickened with gluten.

Bakeries and Pizzaries

On the last day of my friend’s visit, we decided on pizza. Being in New York City, it’s easy to find gluten free pizza. In fact, there is a good spot less than 3 blocks from my apartment. They proudly advertise “gluten free” dough on a chalkboard in front of the restaurant, However, dig a little further and you find this message on the footer of their website in very tiny print:

_____ pizza advises against gluten-free dough for extreme gluten intolerances; cross-contamination may occur.

Now, to be clear, these guys aren’t doing anything wrong. They make pizza dough and pizza dough is made with wheat flour. No surprise that there will be cross contamination between the gluten pizza and the gluten free dough pizza. Having said that, we took our business about a mile away to a spot that makes gluten free pizza in a dedicated gluten free facility. The restaurant is called Wild for those of you in NYC.

The same principle applies to any bakery that prepares food with wheat, cross contamination will be present.

Processed Foods

We saw a spike in traffic to the post I wrote on the Impossible Burger after Burger King announced they were going to give the Frankenstein concoction a try. As I wrote in my review of the burger, I first tried one assuming it was gluten free, but unfortunately, many Veggie Burgers, the Impossible Burger included, do contain wheat as a binding agent.

In fact, there is always the risk for gluten in any processed food, including hot dogs.

Cross Reactivity: Foods Your Body May Recognize as Gluten

Take a deep breath, because even though it’s been out there on the blogosphere for awhile, this one was shocking for me.

What we think of as gluten is actually two distinct proteins, gliadin and glutenin.3

We know that those with celiac disease show an immune response to the gliadin protein in wheat, with the body responding by generating gliadin antibodies. The downstream impact is the destruction of the villi of the small intestine and resulting poor absorption of nutrients.

The gluten free diet is the prescribed solution.

But here’s the problem: it has been estimated that in about 30% of individuals, going on a gluten free diet doesn’t heal the damage to the small intestine.4 A gluten free diet seems to place celiac patients in remission, but does not help to rebuild the “villous architecture” of the small intestine.5

Now, this could be because of how easy it is to be exposed unintentionally to gluten, but there is also evidence that the body reacts to plant proteins similar in structure to gliadin and that this drives continued damage, preventing the gut from healing even after wheat based foods are removed from the diet.6

This study looked at cross reactivity between gliadin antibodies and found that the following foods could be recognized by the body as “gluten like,” eliciting a significant immune system reaction:

  • cow’s milk
  • milk chocolate
  • whey protein
  • casein
  • yeast
  • oats
  • corn
  • millet
  • instant coffee
  • rice

These foods also caused a reaction, but it was barely above control, which presumably means they are a far safer bet and more likely to be tolerated by a greater number of people than the foods listed above:

  • sesame
  • buckwheat
  • sorghum
  • hemp
  • amaranth
  • quiona
  • tapioca
  • teff
  • soy
  • egg
  • potato

The study authors had this to say about the purpose of their experiments:

This study was conducted to identify cross-reactivity between gliadin and non-gluten containing foods that are commonly recommended for patients on a gluten free diet.

The bottom line here is that certain foods, in certain susceptible indivuduals, have an immmune system reaction to foods that are structurally similar to wheat, and in order to fully heal, additional foods beyond gluten should be excluded from the diet.

Gluten sensitive and therefore grain free?

In the high reactivity list, 3 gluten free staple grains appear: oats, rice, and corn. These foods are often the first a gluten intolerant patient turns to once wheat has been ruled out. The less reactive list contain pseudo grains like quinoa and buckwheat.

In light of the fact that it is highly unlikely they will want to undergo a second biopsy to check on the health of their small intestine, what is the celiac or gluten sensitive patient to do with regard to grains?

I think this quote regarding oats is instructive:

There is considerable clinical evidence that some patients with celiac disease have mucosal T cells that react to the [proteins in oats] which can lead to mucosal inflammation.

So, does everyone with sensitivity to gluten need to avoid oats?

No, certainly not.

But does everyone with gluten sensitivity need to watch their body’s response to grain?

Yes, I think so.

For what it’s worth, I eat buckwheat as a staple, and less often quinoa.

A Note on Coffee

I think many of us will be shocked to see instant coffee appear as a cross reactive food with gliadin.

The cross reactivity study authors explain the large reaction with instant coffee as due to the fact that instant coffees appear to commonly be contaminated with small amounts of gluten.

Higher quality whole bean coffee is thought to be safe as long as the individual is not allergic to coffee, which apparently is somewhat common.

Bottom line: drink good coffee and use a milk alternative if you’re sensitive.

Key Takeaways

Am I convinced that everyone has to take such extreme measures to avoid gluten that they keep cross contamination and cross reactivity on their radar?


However, I think the blog posts suggesting that everyone without celiac should “eat all the bread they want because non celiac gluten sensitivity is a myth” are dangerous to a large and growing segment of the population that is sensitive to wheat.

If you have celiac or gluten sensitivity, it may pay dividends to explore a lifestyle where you are careful to avoid foods with trace amounts of gluten as well as some of the foods that are cross reactive when you notice issues.

For example, I eat buckwheat porridge rather than oats because I feel sluggish after a big breakfast of oats and find it harder to concentrate on my work. On the other hand, potatoes, listed as mildly cross reactive are find for me.

But, that’s just me.

Everyone will have to experiment for themselves.

Bottom line is for some people, going well beyond just gluten free will be a necessary step to feel their best.

John O'Connor

John O'Connor is the founder of Gene Food, a nutrigenomic startup helping people all over the world personalize nutrition. John is the host of the Gene Food Podcast and a health coach trained at Duke's Integrative Medicine Program. Read his full bio here.

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  1. Lynn says:

    First, PLEASE use something other than pale green for links…it’s virtually impossible to read. And white type on pale green IS impossible to read.

    Over the past 6 years I’ve devoted endless hours to figure out the cause/causes of miscellaneous health issues. I do not have celiac disease but, regarding gluten sensitivity, I found that not eating ANY gluten-containing grains resulted in improved health. I lost my addiction to carbohydrates as well as the extra 20-25 pounds I’d been carrying around for the last 50 years (that’s not a typo – I’ll be 75 in a few months). However, simply stopping eating grains didn’t solve all my health problems. I then tried a low-carb/high-fat diet and my health continued to improve. Among many other issues, I have had continuous tinnitus since about 1986. The LCHF and then the Paleo diet resulted in short periods – a day or several days -when the tinnitus went away. Then I discovered I’m histamine intolerant and thought I’d found the cause of the tinnitus. But, no, something I was eating still caused the tinnitus even though I’d controlled the histamine reactions. Then I discovered what I believe to be the cause of the tinnitus : salicylate intolerance. And that is a BIG deal, as salicylates are present in virtually all plants. Salicylates decrease oxidative phosphorylation, i.e., they uncouple and inhibit mitochondrial electron transport. So I’ve been avoiding plants and trialing a carnivore diet for many months now, eating nothing but fatty meat and eggs. My tinnitus is more gone than not, but yesterday, when my ears were quiet, I ate some fennel seeds (a plant, it contains salicylates) and woke up this morning with my ears hissing once again. Salicylates (think aspirin) are in virtually all plants and sensitivity to them is apparently due to a reduced activity of the SULT1A1 gene that controls production of the phenol sulfotransferase enzyme. I’m currently examining ways to increase activity of that gene, mainly through increasing the amount of sulfate in my diet to encourage my SULT1A1 to work better.

    Why am I bringing this up when your article specifically addresses the effects of gluten? Because If someone finds eliminating all gluten from their diet doesn’t eliminate all their health issues, they may need to explore what else may be causing the issues. In my rather extreme case, plants are the problem. Effectively by eating a carnivore diet I’m trialing an extreme form of an elimination diet. It may be permanent or I may eventually be able to add back some plant food, but I doubt it. My hypersensitivity to carbohydrates will never go away. My sensitivity to histamines and salicylates may or may not. I’m slowing figuring out the epigenetic puzzle, and my motto has become “stay calm, keep testing,” so I’ll continue this attempt to improve my health. I hope this encourages anyone struggling with health issues to “keep testing.”

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