Bloating & Digestion

The No-Hype Truth About What Gluten Does to Your Gut

The No-Hype Truth About What Gluten Does to Your Gut

It seems like there’s always some new health craze bouncing around the news. One month, it’s all about the fermented foods, the next it’s about skipping carbs, the next it’s all about the kale, açai, kombucha, butter coffee, spirulina…the list goes on.

With so much information about health being attached to a fad, it’s easy to think that going gluten-free may not be a trend to stick around for long.

The truth is, gluten can have some serious effects on your gut microbiome—and that can affect your body in ways you’d never imagine.

Here’s the thing: your digestive tract is home to millions of microbes. That might sound scary, but actually, these microbes are what keep everything working the way it should. And, the healthier your microbiome—that’s the collective name for all those microbes—the healthier you’ll tend to be overall.

As it turns out, the whole “You are what you eat” thing is more true than you’d think.

The foods you eat have a big impact on your microbiome, for better or worse. Gluten specifically can cause demonstrable, long-term changes in your gut bacteria, including reducing the amount of certain types of important bacteria in your gut.

Gluten can also affect part of the immune system, 80% of which resides in your gut, called the gut-associated lymphoid tissue (GALT). If you are gluten-intolerant or sensitive, the components that gluten is broken down into register with your GALT as a problem, so it signals to your body to create antibodies to fight it.

So, what does that actually mean for you?

If you have a sensitivity to gluten, you might just feel bloated, have an upset stomach, or find yourself in the bathroom more often than normal. If you’re fully gluten-intolerant, then things get more serious. The antibodies that attack the substances that gluten is broken down into as it’s digested also attack the enzyme that breaks them down, which is called tissue transglutaminase (tTG).

The problem is, tTG doesn’t only break down gluten—it also keeps your microvilli healthy. (These are tiny, finger-like protrusions from the walls of your intestines. Picture the threads on the surface of a towel and you’ll get the idea). These are responsible for absorbing nutrients from food as it passes through your intestines, so if your tTG is under attack, they’re not going to be able to function the way they should. If this goes on, the microvilli start to break down, which means that you can’t absorb nutrients properly, and you may have symptoms like malnutrition, temporary constipation or diarrhea, and unexplained weight loss.

But that’s just a gut problem, right? What does that have to do with the rest of the body?

It starts as a gut problem, but it can quickly spread to the rest of the body. Besides triggering your GALT, gluten can also cause the cells of your intestines to produce a protein called zonulin, which can break down the connections between the cells that make up the walls of your intestines, which means that anything that’s going through your intestines—microbes, food particles, toxins, and those antibodies— can leak into your bloodstream, and from there, go anywhere in your body.

Once they’re in other parts of your body, they can get a little overzealous and start attacking whatever’s around them, which is why people who have a problem with gluten may see health problems showing up in seemingly unrelated places, like the thyroid gland, the skin, or even the brain.

Your gut on gluten, according to science:

Many studies have been done on the effects of gluten on gut health, including one that found that mice who were fed a gluten-free diet had significantly more of several types of important gut bacteria than those who were fed a diet containing gluten.¹ There was also a strong correlation between the presence of gluten in the mice’s diet and how likely it was for them to struggle with blood sugar.

In another study, which was done on humans, researchers found that people who went on a gluten-free diet for four weeks had significant changes in the types of bacteria in their guts.2 Finally, another study found that even people without sensitivities to gluten may have gastrointestinal symptoms after eating foods containing it.3

So what can you actually do to keep your gut healthy?

We’re not going to tell you that you instantly have to give up all gluten forever and ever, or that you need to go on a particular cleanse (although if that’s your thing, go for it!). We know that you have your life to live, and that means that you need tips that you can actually follow without having to spend your whole day worrying about what you’re eating.

The great news is, even small changes can make a huge difference in the health of your gut flora, and it’s never too late to start!

Our bodies are amazingly resilient, and with a little help, they can come back from all kinds of things. So that’s why we’d recommend that you:

1. Learn to love your microbes.

We’ve been surrounded by the idea that bacteria are bad for decades. And while it’s true that there are some bacteria that are harmful to us, there are way more that keep us healthy. Give them the chance to do their thing by avoiding toxins when you can, eating organic whole foods (especially prebiotics like asparagus, garlic, bananas, and onions), and don’t take antibiotics or other medications unless you really need them.

2. Move in ways that make you feel good.

Regular exercise is great for your gut. In fact, researchers have found that moving regularly can increase the amount of good bacteria in your gut by 40%!4 To make it even better, do your workout outside. Exposure to soil, animals, and all the other things we tend to wash off as soon as we step in the door can also expose you to lots of great bacteria.

3. Experiment with your eating.

Again, this doesn’t mean that you immediately have to adhere to some kind of extreme diet—remember, you’re going for health, which is a long-term thing. So just be mindful of what you’re eating, and see how you feel before and after you eat certain things.

We’d encourage you to experiment with eliminating gluten from your diet for two weeks, then reintroduce it and see how you feel. The thing is, if you’re constantly exposed to a food trigger, you might not be noticing how it makes you feel until you get rid of it for a while. So try removing all gluten from your diet––and we really mean all of it, so check the ingredients in everything, from your spice cabinet to your sauces and everything in between––and see if you notice a difference once you add it back in.

If you’re on the fence about this because you’re pretty sure you don’t have a problem with gluten, we’d say give it a try anyway. Even if you’re not specifically gluten-sensitive, many of the most respected holistic physicians (including Dr. Mark Hyman and Dr. David Perlmutter) are adamant that gluten is just not good for your gut.

4. Get your doctor in the game.

This is actually a good idea whether you think you have a gluten sensitivity or not; an integrative or functional doctor can help you figure out how healthy your gut microbiome is and give you personalized suggestions for making it even healthier.

But you should definitely get in touch if you think you might have a problem with gluten. Ask them if you can get tested for those antibodies that are produced in people with gluten sensitivity: anti-gliadin antibodies, anti-endomysial antibodies, and tTG antibodies, to start with.

5. Give your gut a boost with a probiotic.

If you haven’t really been paying attention to your gut before, you know you have a sensitivity to gluten, or you’re getting some unexplained gastrointestinal issues, consider giving your gut some extra help with a probiotic that will help you replenish all those good gut bacteria. It’s one of the easiest ways to take care of your health, and as you now know, improving the health of your gut can affect every single other part of your body.

Not sure where to start? We’d recommend trying PRO-15, our foundational Hyperbiotics formula. It’s packed with 15 different health-supporting probiotic strains and features a time-released delivery for 15x more survivability than other probiotic capsules, and is a great way to get your gut back on track. And our organic, food-based Prebiotic Powder will give your new probiotic colonies all the nourishment they need to really thrive!

All pretty doable, right? We promised it was easy.


1. Marietta, E. V., Gomez, A. M., Yeoman, C., Tilahun, A. Y., Clark, C. R., Luckey, D. H., . . . Rajagopalan, G. (2013). Low Incidence of Spontaneous Type 1 Diabetes in Non-Obese Diabetic Mice Raised on Gluten-Free Diets Is Associated with Changes in the Intestinal Microbiome. PLoS ONE,8(11). doi:10.1371/journal.pone.0078687

2. Bonder M.J., Tigchelaar E.F., Cai X., Trynka G., Cenit M.C., Hrdlickova B., Zhong H., . . . Vatanen T., Gevers D., Wijmenga C., Wang Y. and Zhernakova A. (2016). The Influence of a Short-Term Gluten-Free Diet on the Human Gut Microbiome. Genome Medicine, 8(45). doi: 10.1186/s13073-016-0295-y

3. Biesiekierski, J. R., Newnham, E. D., Irving, P. M., Barrett, J. S., Haines, M., Doecke, J. D., . . . Gibson, P. R. (2011). Gluten Causes Gastrointestinal Symptoms in Subjects Without Celiac Disease: A Double-Blind Randomized Placebo-Controlled Trial. The American Journal of Gastroenterology,106(3), 508-514. doi:10.1038/ajg.2010.487

4. Campbell SC, Wisniewski PJ, Noji M, McGuinness LR, Häggblom MM, Lightfoot SA, et al. (2016). The Effect of Diet and Exercise on Intestinal Integrity and Microbial Diversity in Mice. PLoS ONE 11(3). doi:10.1371/journal.pone.0150502


Rachel Allen is a writer at Hyperbiotics who's absolutely obsessed with learning about how our bodies work. She's fascinated by the latest research on bacteria and the role they play in health, and loves to help others learn about how probiotics can help the body get back in balance. For more ideas on how you can benefit from the power of probiotics and live healthier days, be sure to subscribe to our newsletter. To learn more about how a healthy microbiome can enrich your life, subscribe to our newsletter.