Surprise—some of the top offenders lurk in healthy foods.
Your gut microbiome consists of trillions of good and bad bacteria. Having a higher concentration of the good stuff is key: it facilitates healthy digestion and keeps you regular. It also impacts your overall health and helps you stave off chronic disease: Your gut microbiome plays a role in regulating the immune system, promoting a positive mood, and reducing inflammation. (1, 2, 3). And the foods you eat play a major role in maintaining microbial balance (4).
“Think of the microbes in your gut as translators between your food and your body,” says gastroenterologist and neuroscientist Emeran Mayer, M.D., Ph.D., the founding director of the Goodman Luksin Microbiome Center at UCLA. “They translate food into signals that communicate with the immune, nervous, and hormonal systems.”
When you eat gut-healthy foods, good gut bacteria feast on the fiber and polyphenols in them. This process creates anti-inflammatory molecules—like short-chain fatty acids, butyrate, and iterate—that protect the intestinal lining and support your immune system, Mayer notes (5, 6).
But when you eat foods devoid of fiber and polyphenols, the good bacteria don’t get enough fuel to thrive. “This essentially starves the good microbes in your gut’s ecosystem, which will decrease its diversity,” Mayer explains. “Consequently, other potentially harmful microbes begin to grow more aggressively in your gut.”
This bacterial imbalance is known as dysbiosis. In the short term, it can cause GI issues like bloating, diarrhea, acid reflux, and constipation. The stakes are even higher if your gut microbes stay out-of-whack: Prolonged imbalance can stoke inflammation in your intestinal lining, possibly making you susceptible to conditions like inflammatory bowel disease (IBD), a collection of autoimmune diseases including ulcerative colitis and Crohn’s disease (5, 7).
Emeran A. Mayer, M.D., Ph.D., is a gastroenterologist and neuroscientist specializing in microbiome health. He is the founding director of the Goodman Luskin Microbiome Center at UCLA.
Megan Hilbert, R.D.N., is a registered dietitian nutritionist with Top Nutrition Coaching. She specializes in the gut-brain axis and chronic gut health issues.
Some of the foods that do the most damage to your gut health are obvious: They’re not great for you on any front. But some healthy eats are discreetly hiding a few intestinal stressors, say experts.
Processed foods get a bad rap. But there’s a fine line between processed and ultra-processed—and the latter is what messes with your health.
“Almost all our food is processed unless you’re on a raw vegetable diet,” Mayer says. “Processed” just means a food has been altered from its original form to make it safer to eat or to extend its shelf life (8). Healthy foods like pasteurized milk, canned vegetables, and cheese fall into this camp.
Ultra-processed foods are Frankenfoods. “They have all sorts of additives like artificial sweeteners, salt, preservatives, and more,” Mayer says. The original food becomes almost unrecognizable from its original form.
“There has been a trend for a long time to take out all fiber from foods during ultra-processing,” he adds.
A whole potato, for example, is packed with fiber, polyphenols, and healthy carbs. But when the starchy vegetable is compressed into potato chips, it’s stripped of fiber and other core nutrients and pumped full of salt, hydrogenated oils, and preservatives.
“People have a preference for these fiber-devoid versions of originally healthy foods, thanks to the addictive properties that many additives have,” Mayer says. “And that’s a big problem for the microbes because fiber is their food.”
What happens when the good gut bugs can’t gobble up enough fiber? A 2024 review of human studies in the journal Nutrients revealed a link between ultra-processed foods and an overgrowth of Prevotella, a bacteria linked to increased inflammation and metabolic diseases such as insulin resistance (9, 10).
Common ultra-processed foods include:
While a fried chicken sandwich and a basket of fries is a classic combo, the high-in-sodium pairing can cause mayhem in your microbiome.
Research suggests that people who eat excessive amounts of sodium have more bad bacteria and less diversity in their microbiome (11, 12). (And by the way, that’s nearly all of us: The average American eats three times more sodium than recommended.)
This imbalance of gut bacteria can cause GI discomfort. It can also weaken your immune system—a whopping 70-80 percent of your immune cells reside in the gut (13, 4).
A gurgly, acidic stomach from a big night out is annoying, but short-lived. Chronic alcohol consumption has far bigger impacts.
Research suggests that alcohol destroys good gut bacteria, which allows bad bacteria to run rampant, creating a breeding ground for chronic inflammation. (14, 15). While the exact mechanisms of this inflammation are still being investigated, the authors of one 2017 review theorize it’s this inflammation that links alcohol consumption and GI cancers (16).
Ultra-processed foods contain a bunch of suspicious ingredients like artificial sweeteners that can impact your gut health.
A 2023 study by Cedars-Sinai researchers found that people who regularly eat non-sugar sweeteners like sucralose, aspartame, saccharin, and Stevia had less microbiome diversity in their small intestines. They also had more inflammatory markers than those who didn’t consume any synthetic sweeteners (17).
“Interestingly, when we looked at predicted metabolic pathways in these bacteria, we noted that the pathway of cylindrospermopsin, a toxin, was enriched specifically in small bowel bacteria of subjects who consumed aspartame,” said Ruchi Mathur, M.D., a professor of Medicine at Cedars-Sinai and the lead author of the study, in a press release (18). “This pathway is recognized for its harmful effects on the liver and the nervous system, and it is classed as a potential cancer-causing agent.”
Red meat gets a bad rap, but is chowing down on a hamburger actually bad for your gut?
“Red meat can contribute to excess inflammation in the digestive system which has been shown to contribute to colon cancer risk,” Megan Hilbert, R.D.N., explains. A 2024 study found that people who eat more processed or red meat may have a 30 to 40 percent increased risk for colorectal cancer (19).
Red meat has also been shown to raise levels of trimethylamine N-oxide (TMAO), a chemical produced in the digestive tract by gut bacteria after eating red meat. High levels of TMAO have been linked to a higher risk of heart attack and stroke (20).
While technically not a food, microplastics have been found in nearly everything we eat, especially seafood, poultry, pork, beef, and plant-based proteins like tofu (21).
Researchers have yet to prove microscopic plastic particles are as detrimental to your gut as they are to the rest of your body because it’s nearly impossible to find a control group or people who have never been exposed to microplastics. But emerging research suggests they tamper with the microbiome, Mayer notes.
“If you go to the supermarket and buy fruits and vegetables, many come in plastic bags or containers,” Mayer says. While the fiber and antioxidants from the produce fuel good gut bacteria, the microplastics that cling to them may cannibalize a small portion of healthy bacteria as they linger in the body. Your move: Consider ditching pre-wrapped produce.
Microplastics aren’t the only non-food offenders lurking on your plate. The pesticides and herbicides that prevent bugs and weeds from destroying fresh produce can negatively impact gut bacteria.
“It’s a misunderstanding that pesticides and herbicides are completely safe for human consumption,” Mayer says, adding that the body doesn’t have the right enzymes to break these chemicals down during digestion.
“For example, a common herbicide, glyphosate, by itself is not harmful to human cells. But it can disrupt your gut microbiome when you eat food that’s been treated with it,” he says. A 2022 study in Frontiers in Nutrition found that glyphosate can kill good bacteria in your microbiome (22).
Worse yet, constant exposure to the herbicide can alter some of your gut microbes, making them immune to the chemical. Without enough good bacteria in your gut, these glyphosate-resistant microbes can take over. They pump out excess pro-inflammatory proteins that damage the immune system and increase the risk of chronic inflammation and disease (22).
This doesn’t mean you should eat less fruits and veggies. Microplastics, herbicides, and pesticides don’t completely cancel out the gut health benefits of fiber and polyphenols from produce, Mayer says. Just try to limit your exposure by choosing organic and locally-grown produce over conventional varieties (23).
You’ve probably read that gluten and dairy cause mass destruction in your intestines. While they can cause flare-ups (aka, GI symptoms) in certain people, experts say they don’t deserve a spot on the list of foods that torpedo gut health.
“No two guts are created equal. Even identical twins have a significant difference in their gut microbiomes (24),” Hilbert explains. “Because of this, everyone reacts to foods differently and gut-healthy diets should be personalized.”
Let the fear-mongering around cow’s milk cease. Unless you have a lactose intolerance or an allergy, dairy doesn’t rev gut inflammation.
Many adults become lactose intolerant as they age since they lose the enzymes from infancy that break down breast milk, Mayer says. Still, there’s no evidence that suggests intolerance is linked to chronic gut conditions.
“You don’t need to eliminate dairy completely unless you have an allergy,” Mayer says. “Just cut back if you have sudden gastrointestinal symptoms.”
More good reasons to keep it in your diet: Dairy is packed with protein, vitamins A and D, and zinc—essential nutrients for a healthy gut (25). Plus, fermented foods like kefir and yogurt are rich in probiotics that can help restore microbial equilibrium in the gut (26).
Within the past few years, “people have blamed all their gut symptoms on gluten intake. And that has led to a multi-billion dollar industry of gluten-free products,” Mayer says. But gluten isn’t inherently bad for most people’s guts, he says.
He stresses that whole grain pastas and breads are great sources of fiber, which fuel the good gut bacteria (27).
Unless you have Celiac disease or a gluten allergy, there’s no need to eliminate gluten entirely. Instead, swap ultra-processed sources of gluten (think: white bread and baked goods) for fibrous, whole grain options.
Some people get particularly bloated or gassy when they eat foods high in FODMAPs. The FODMAP acronym stands for Fermentable, Oligosaccharide, Disaccharides, Monosaccharides, and Polyols (28)—what a mouthful.
In simple terms, FODMAPs are short-chain carbohydrates and sugar alcohols poorly absorbed by the small intestine. When these carbs are fermented by gut bacteria, bloating, gas, constipation, and other GI discomfort can arise in certain people, especially those with irritable bowel syndrome (IBS) (28).
But FODMAPs don’t disrupt the microbiome, says Hilbert. “FODMAPs are not problematic for all people, and in fact, they can be a wonderful way to increase microbial diversity,” she notes. And many strains of good gut bacteria thrive on the healthy fibers of FODMAP-rich foods.
Gut health is less about cutting out ‘bad’ foods and more about adding foods we know can help improve your microbiome, Hilbert says. Instead of lamenting the foods you should cut back on, focus on all of the ones you get to add to your grocery list.
Prebiotics are the indigestible fibers probiotics feast on, allowing them to populate and thrive in your gut (29). To get more prebiotics, eat:
Probiotics are the good gut bacteria, which you can ingest to improve your microbiome diversity (30). These fermented options can support a healthy gut:
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