Medically reviewed by Jonathan Purtell, RDN
For better gut heath, avoid red meat, alcohol, and processed or artificially sweetened foods.
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Your gut microbiome is home to trillions of microorganisms, including bacteria and viruses.
Some foods—especially ultra-processed ones—can encourage the growth of harmful microbes.
Foods rich in probiotics and prebiotics help support beneficial microbes.
Your gut is home to trillions of microorganisms—including fungi, bacteria, and viruses—that play a crucial role in digestion, immunity, and overall health. While beneficial microbes are ideal, some foods can encourage the growth of less helpful ones. Here are five foods that may harm your gut—and healthier options to try.
1. Red Meat
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Eating red meats like beef, lamb, and pork can increase certain toxins in your gut. Gut microbes turn L-carnitine, an amino acid found in red meat, into a harmful compound called trimethylamine-N-oxide (TMAO). TMAO may lead to artery hardening and increased risk of heart disease.
Eating processed red meat (bacon, sausage, pepperoni) may also increase levels of certain gut microbes that contribute to inflammation and raise the risk of colorectal cancer.
2. Ultra-Processed Foods
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Ultra-processed foods are industrially manufactured, ready-to-eat, or ready-to-heat. They contain little to no whole foods and are often high in saturated fat, added sugars, sodium (salt), and other additives that can harm the gut microbiome. Eating a lot of them may increase the risk of heart disease and obesity. Examples include:
Ultra-processed foods can reduce the amount and diversity of “good” gut microbes. This can lead to gut inflammation and increased gut permeability—meaning more harmful substances are absorbed into the bloodstream. It can increase the risk of diseases like obesity, dementia, and Alzheimer’s.
3. Alcohol
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Studies show that long-term alcohol use significantly changes the gut microbiome.
Alcohol decreases helpful gut microbes and increases harmful microbes. It may also lead to increased gut permeability, which can allow harmful substances to enter the bloodstream.
4. Artificial Sweeteners
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Sugar-free and calorie-free sugar substitutes can cause gut microbiome imbalance, increase inflammation, and reduce helpful short-chain fatty acids (SCFAs), which support digestive health.
Research suggests these effects on the gut may contribute to a higher risk of obesity and type 2 diabetes. In experiments, when gut microbes from hosts who consumed low-calorie sweeteners were transferred into healthy mice, the mice’s glucose (sugar) tolerance weakened.
5. Dairy
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People with certain conditions may have difficulty digesting dairy products:
Lactose intolerance: Lactose is a sugar found in dairy. Approximately 70% of adults worldwide don’t have enough intestinal lactase, the enzyme needed to digest lactose. For these individuals, high-lactose foods such as milk and cheese can trigger gastrointestinal (GI) symptoms like bloating, diarrhea, and abdominal pain.
Milk and dairy allergy: Milk is among the most common allergies. Those with milk allergies may experience gastrointestinal symptoms from dairy, such as abdominal pain, vomiting, and diarrhea.
Inflammatory bowel diseases (IBD): People with Crohn’s disease or ulcerative colitis (UC) may have trouble digesting lactose. These conditions cause inflammation in the GI tract. Avoiding trigger foods like dairy products can help prevent flare-ups and manage IBD symptoms like nausea, abdominal pain, and diarrhea.
What To Eat Instead
Certain foods promote gut health, such as:
Probiotic foods, including yogurt and fermented foods like kefir, kimchi, kombucha, tempeh, and sauerkraut. Probiotics are live microorganisms that change the makeup of your gut microbiota, reducing the growth of harmful bacteria and allowing helpful bacteria to thrive.
Prebiotic foods, such as bananas, onions, barley, garlic, leeks, and asparagus. Prebiotics help feed “good” probiotic bacteria in your gut and alter your intestinal pH, preventing harmful microbes from growing. These changes result in reduced gut inflammation and may increase the production of intestinal glucagon-like peptide 2 (GLP2), a hormone that helps strengthen the gut lining.
High-fiber foods, including whole grains, fruits, nuts, seeds, leafy greens, and other vegetables. Dietary fiber is a non-digestible carbohydrate that improves satiety (fullness) and supports intestinal health.
Foods rich in polyphenols, such as apples, berries, cocoa, artichokes, tea, citrus fruits, and pears. Polyphenols are antioxidants produced by certain plants. These natural compounds help balance the “good” and “bad” microbes in the gut, boosting immune support and helping to prevent diseases like colorectal cancer.
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