These 4 Foods Could Be Harming Your Microbiome

What you eat may affect the tiny-yet-mighty microbes in your gut

Christine Richmond

Updated June 04, 2025

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You’re no doubt aware that committing to healthy habits can keep your body and mind strong as you age. But did you know that one of the reasons lifestyle changes are so beneficial is that they support your gut microbiome, the mix of microbes that live mainly in your large intestine?

Taking steps like eating more whole, unprocessed foods and getting regular exercise helps ensure you have a diverse community of gut microbes. This is important because a diverse microbiome has been linked to better cognitive function and a reduced risk of chronic diseases, such as heart disease.

On the other side of the coin, many of the behaviors you know you should avoid, like eating too much salt and drinking too much alcohol, can wreak havoc on your gut and potentially set you up for health problems. Below, we take a closer look at four types of food that can disrupt your microbiome.

Packaged foods loaded with salt

Despite a strong link between a high-sodium diet and high blood pressure (leading risk factors for stroke and dementia), Americans are still eating too much salt. According to the U.S. Food and Drug Administration, the average adult eats 3,400 mg of sodium per day, although the recommended limit is 2,300 mg per day — about one teaspoon of table salt. More than 70 percent of our daily sodium comes from packaged foods (e.g., deli meats, canned soups and potato chips) and prepared foods, including restaurant fare.

Your gut microbiome is not a fan of all that salt. Eating a high-sodium diet was linked to an unhealthy shift in the composition of the gut microbiome of six people ages 28 to 49 in a study published in Nutrients in 2024. A review of existing research on both animals and people, published in 2024 in Biology, echoed that result. The authors concluded that “a diet high in salt can exert a detrimental effect on the gut microflora (microbiome).”

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White bread, pastries and other refined carbs

You already know you shouldn’t load up on refined carbs, which have been stripped of fiber. Here’s one interesting reason: Your gut microbes will go hungry. “We process those foods very quickly in our stomachs, and they don’t travel to our intestinal tract where our gut microbiome is,” explains Stephen Perrine, author of The Full Body Fat Fix and a special projects editor at AARP. “We get all the calories, [but] the gut microbiome starves when we eat refined processed foods.”

A diet rich in whole grains, fruits, vegetables, nuts and seeds provides plenty of fiber. Most of that fiber reaches the colon undigested, and gut microbes feed on it. Our hunter-gatherer ancestors may have eaten upwards of 100 grams of fiber per day, research suggests. But today, the average American adult gets only 14 to 18 grams of fiber per day consuming a Western diet high in processed carbs and sweets. That is nowhere near our ancestors’ intake, and it also falls far short of the 28 to 34 grams recommended by the U.S. Department of Agriculture. “As a result, our microbiomes are not getting the nutrition they need to function at their best,” Perrine says.

Famished gut microbes will sometimes resort to eating the protective mucus layer of the colon, research suggests, which can trigger inflammation. In addition, the typical Western diet can negatively impact the composition of the microbiome, reducing the number of beneficial bacteria and allowing potentially "bad" bugs to thrive. This, in turn, can contribute to the development of chronic illnesses like Alzheimer’s disease, heart disease and type 2 diabetes, according to a review of research on diets and gut microbiota published in 2024 in Nutrients.

Sugar substitutes

Sugar substitutes negatively altered gut microbiome composition in a study of 120 adults with a median age of 30 published in Cell in 2022. During the trial, participants who didn’t normally use artificial sweeteners consumed six packets per day of either aspartame, saccharin, sucralose or stevia for two weeks. That may sound like a lot, but it’s well within the FDA’s safe levels for sugar substitutes.

Another study of 47 healthy adults ages 19 to 35, published in Microorganisms in 2022, found that ingesting 48 mg of sucralose (roughly equivalent to the amount in two no-sugar-added pudding cups) every day for 10 weeks resulted in an unhealthy shift in the microbiome. It also resulted in elevated blood sugar and insulin levels. More research is needed.

Alcohol

Heavy drinking can change the composition and function of the gut microbiome, potentially leading to nutrient deficiencies and inflammation, research suggests. Fewer studies have looked at moderate drinking, however, and the evidence thus far has been mixed.

One study actually found that occasional red wine drinkers had more diverse microbiomes. For the study, published in Gastroenterology in 2020, the researchers analyzed data from roughly 3,000 adults who reported consuming two or fewer drinks a day.

But this doesn’t necessarily mean you should raise a glass to your microbiome. The same results were not seen in people who drank beer, cider or spirits, leading the researchers to note that it may be the red wine’s polyphenols (antioxidants found in grape skin) that provided the benefits. And you can get polyphenols from a variety of plant foods, including grapes, walnuts, sweet potatoes, apples and blueberries. The advice from major medical associations has shifted lately, from recommendations to enjoy alcohol in moderation to — if you can — avoid it altogether, Damman says. “That’s based on tons of epidemiological research.”

Saying no to salt-laden foods, refined carbs, sugar substitutes and alcohol may benefit your gut. But one of the best — and easiest — ways to support your brain-gut connection is to simply say yes to more and different plants. A plant-based diet rich in whole grains, fruit, vegetables and nuts was "associated with microbiome features that have been linked to positive health" in a study of 705 adults ages 64 to 81 published in The American Journal of Clinical Nutrition in 2024.

“There are more than 50,000 edible plants on Earth, but about two-thirds of our diet is made of just three plants: wheat, corn and rice. And in most cases they’re refined,” Perrine says. His advice: Worry less about what’s in your food that might harm you, and focus more on eating a wider variety of whole foods.