Skip to content

The Best & Worst Foods For Healing Your Gut & Better Gut Health

Vincent M. Pedre, M.D.
Author: Medical reviewer:
Updated on October 21, 2019
Vincent M. Pedre, M.D.
Board-Certified Internist
By Vincent M. Pedre, M.D.
Board-Certified Internist
Dr. Vincent M. Pedre is a board-certified internist in private practice in New York City since 2004. He serves as medical director of Pedre Integrative Health, president of Dr. Pedre Wellness, and is the author of Happy Gut.
Wendie Trubow, M.D., MBA
Medical review by
Wendie Trubow, M.D., MBA
Functional Medicine Gynecologist
Wendie Trubow is a functional medicine gynecologist with almost 10 years of training in the field. She received her M.D. from Tufts University.

In my practice, I get patients who want to understand why gut disorders such as small intestinal bacterial overgrowth (SIBO) develop. They want to discuss the biochemical pathways underlying nutrient and other treatment options. They ask a lot of questions and become very, very invested in every step of their gut-healing journey.

And then I get the occasional impatient patient who says, "Just tell me what to do to heal my gut." They aren't interested in the mechanics behind it; they just want the problem fixed.

This ad is displayed using third party content and we do not control its accessibility features.

As a medical doctor specializing in gut health, I implement nutrient and lifestyle interventions to alleviate leaky gut and lifelong gut distress. At the same time, I realize the real gut-healing prescription lies at the end of your fork. After all, food is the most powerful medicine.

In functional medicine, we take a systematic approach to issues like gut health, which can be summarized as follows: Remove the offenders and add in the good stuff. It starts with what you eat.

From that perspective, here's how I instruct the "just tell me how" patients to heal their gut.

The worst foods for your gut.

The first step to healing your gut is to remove foods making you sick, leaving you toxic, overweight1, and feeling zapped of energy.

Be forewarned: Many of these foods sometimes hide in the ingredients used in prepackaged products. One patient was using a stevia powder with lactose (milk sugar) as a bulking agent. Another used a well-known mustard that contained gluten. Always read ingredients and stick with whole, unprocessed foods whenever possible.

This ad is displayed using third party content and we do not control its accessibility features.

1. Dairy

Despite what the dairy industry promises, milk doesn't necessarily do a body good. For many people, the two proteins in milk (casein and whey) are hard to digest and can lead to food sensitivities. Many people also lack sufficient quantity of the enzyme lactase2 to break down the lactose in milk, creating symptoms like gas, bloating, and diarrhea as gut bacteria ferment this sugar instead.

2. Gluten.

Gluten gives food a pleasing texture—like the light, fluffy, porousness of "risen" bread. Unfortunately, for many people it poses a real problem. Researchers find up to 30% of Americans have a gluten sensitivity3 and approximately one in 100 people have celiac4 disease. Most have no idea they are sensitive. Studies confirm what I've found in my own practice: Going gluten-free lowers inflammation and insulin resistance5 while helping people lose weight. However, subbing in gluten-free alternatives alone won't lead to weight loss. This is because most substitutes are higher in sugar and carbs to make up for the lack of gluten. Be sure to choose whole, unprocessed foods instead.

This ad is displayed using third party content and we do not control its accessibility features.

3. Soy

Soy and soy derivatives are everywhere, from tofu to edamame to protein bars and powders and even nutritional supplements. Over 90% of the soy mass-produced in the United States is genetically modified (GMO). Much of this soy is "Roundup® ready," meaning it gets doused with more pesticide than you care to find out. Studies show6 Glyphosate (the active ingredient in Roundup®) leads to dysbiosis and then leaky gut.

4. Corn

Like soy, over 90% of the corn grown in the United States is genetically modified. This GMO corn is often adapted to be Roundup®-tolerant and contains residues of this formulation. A corn sensitivity can result in all sorts of reactions, similar to those from gluten and other food allergens. In my practice, the most common reactions I see are rashes like eczema and hives.

This ad is displayed using third party content and we do not control its accessibility features.

5. Lectins and phytates.

These "anti-nutrients" are found in all gluten-containing grains. Lectins are also found in beans and the nightshade vegetables like tomatoes, eggplant, peppers, and potatoes. Corn is also high in lectins. Lectins bind to the cells lining your intestines, disrupting the tight junctions between the intestinal cells and creating tiny holes that allow larger partially digested food particles to get through. This disrupts your gut flora, leads to inflammation, eventually causes insulin and leptin resistance, and potentially leads to an autoimmune response. Phytates7, another anti-nutrient, interfere with the absorption of important minerals like calcium, iron, magnesium, copper, and zinc.

6. Eggs

Many people develop a sensitivity to egg yolk, egg white, or both. Egg yolks are high in arachidonic acid8 (AA), an inflammatory omega-6 fatty acid. Most commercial eggs come from hens fed an unnatural diet of soy and corn. When you eat these eggs, you are consuming these food allergens indirectly. Instead, if you do opt for eggs, look for organic ones from cage-free hens fed their natural, omnivorous, free-range diet rich in anti-inflammatory omega-3 fatty acids.

This ad is displayed using third party content and we do not control its accessibility features.

7. Nightshades

The nightshade family includes tomatoes, tomatillos, eggplant, potatoes, bell peppers, sweet and hot peppers, pepinos, and pimentos. They produce alkaloids, a natural insect repellent that can be toxic to humans in large amounts9. Common nightshades don't have enough of these alkaloids to be deadly, yet some people with inflammatory conditions are particularly sensitive to even tiny amounts. For these people, even cooking the nightshades, which lowers the alkaloid content by 40 to 50%, can still create problems. Like gluten-containing grains, nightshades also harbor lectins or sugar-binding proteins, which can activate your immune system and increase inflammation10. Nightshades can be a particular source of agony for many people who suffer from arthritic conditions or autoimmune disorders.

8. Sugar

I've saved the biggest offender for last. I'm not just talking about refined cane sugar but also high-fructose corn syrup (HFC) or any other sweetening derivatives, including "healthy" sweeteners like monk fruit and coconut sugar. Any form of sugar in excess, including refined carbohydrates, poses a risk to your gut health. Sugar wreaks havoc in your gut11, and research shows it feeds the bad bugs, creates dysbiosis, and leads to yeast overgrowth (like Candida). And don't forget liquid sugar in the form of sweetened and alcoholic beverages—probably the most common unsuspected offender in people who consume too much sugar.

The best foods for your gut.

When you give the body the right nutrition, you won't need to fill it with endless calories from low-nutrient, calorie-dense foods that leave it wanting more and more but never sate its true needs. You'll feel energized by the richness of a power-packed, phytonutrient-dense way of eating.

The eating plan I give patients to heal their gut is simple but powerful. It can help you feel better, lose weight, and provide steady sustained energy. In a nutshell, here's the plan:

  • Healthy fats
  • Nuts and seeds
  • High-fiber, low-glycemic carbs like leafy greens and cruciferous vegetables
  • Slow carbs, like sweet potatoes and butternut squash
  • Hypoallergenic proteins (pea, rice, hemp, chia)
  • Clean and lean proteins like free-range poultry, wild-caught fish, and grass-fed meats

I also include fermented foods like kimchi and unpasteurized sauerkraut. These probiotic-rich foods help crowd out nasty pathogens like unfavorable bacteria, yeast, or parasites.*

Besides eating these and other fermented foods, many patients take a professional-quality probiotic supplement that contains billions (not millions) of colony-forming units (CFUs, which measure a probiotic's potency).

While they get less attention, prebiotics—these are the food that probiotics feed on—are equally important for gut health because they feed your friendly flora.*

These prebiotic foods aren't easily digested or absorbed. Instead, they bypass your small intestine and beeline into your colon, where, among their many benefits, they feed the good gut bacteria to create healthy, energy-producing short-chain fatty acids12.

Prebiotics fall under several categories, including fructans (also called fructooligosaccharides, or FOS13) and resistant starch. Each feed different types of gut flora. Excellent choices include:

  • Raw chicory root
  • Raw Jerusalem artichoke
  • Raw dandelion greens
  • Chickpeas
  • Raw garlic, onions, and scallions

To optimize gut health, I also recommend that you incorporate soluble fiber-rich foods like apples, gluten-free oatmeal, ground flaxseeds, and nuts because they slow digestion, keeping you full longer, and stabilize your blood sugar response14 while providing a steady source of energy.

Overall, I focus on clean ingredients with easy-to-digest foods that are low in fructose and sugar and devoid of any substances, including sugar alcohols and pesticides, that are hard on the gut. These foods are organic, non-GMO, full of healthy fats, and ideally locally grown and sustainably farmed.

Vincent M. Pedre, M.D.
Vincent M. Pedre, M.D.
Board-Certified Internist

Vincent M. Pedre, M.D., medical director of Pedre Integrative Health and president of Dr. Pedre Wellness, is a board-certified internist in private practice in New York City since 2004. He completed his bachelor’s degree in Biology at Cornell University before attending the University of Miami School of Medicine and completed his residency in Internal Medicine at the Mount Sinai School of Medicine. He has appeared on the Martha Stewart Show and ABC and is the author of Happy Gut: The Cleansing Program to Help You Lose Weight, Gain Energy, and Eliminate Pain. Dr. Pedre is a clinical instructor in medicine at the Mount Sinai School of Medicine and is certified in yoga and medical acupuncture.