different gut healing foods in bowls and cutting board on marble background

Six Foods to Heal Your Gut Microbiome, According to a Functional Medicine Doctor

Left unchecked, an unbalanced gut can lead to problems outside the bathroom.

30-Second Takeaway

  • Poor gut health is linked to an increased risk of Alzheimer’s, autoimmune conditions, and some cancers.
  • A diet high in fiber and prebiotic foods supports a balanced gut microbiome.


A lack of energy, bloating and gas, constipation, and acne are just a few ways an unbalanced gut microbiome can torpedo your everyday health. Worse, letting gut issues go unchecked can give way to more debilitating chronic health conditions like Alzheimer’s and autoimmune disease, says New York-based functional medicine doctor Neil Paulvin, M.D., who focuses on longevity and optimization.

Research shows one of the biggest factors in keeping gut bacteria in balance is diet  (1). Processed and sugary foods have been linked to an overgrowth in harmful proteobacteria (2), while  people who follow a diet rich in fiber and prebiotic foods have a lower risk of irritable bowel syndrome, leaky gut, and colon cancer (3, 4). 

Don’t know where to start? These are the five gut healing foods that Paulvin keeps on his weekly grocery list.

The Best Gut Healing Foods, According to a Longevity Doctor

Resistant starch

Resistant starch—a type of carb that can’t be digested in your small intestine—helps decrease gut inflammation and produce SCFA (small chain fatty acids), says Paulvin. Foods like oats, barley, cereals, and lentils are all resistant starches.

Research shows that resistant starch ferments in your large intestine, which boosts your levels of beneficial bacteria (5). This may lead to less constipation, lower cholesterol, and lower risk of colon cancer.


“Pomegranates contain indigestible fiber, which can help to calm an irritable bowel and trigger regular bowel movements, preventing or relieving constipation,” Paulvin says.

Indigestible fiber—also known as insoluble fiber—is the type that can’t  be broken down by your digestive system. It helps shuttle waste through your intestines, which relieve constipation and prevent diarrhea or loose stools. 

Pomegranate extracts increased levels of good bacteria in the digestive tract in a 2023 study, which also makes it an effective prebiotic (6).


Oily fish—like swordfish, salmon, and tuna—are a source of omega-3 fatty acids, which are thought to help regulate your gut microbiota, per Paulvin.

Omega-3 fatty acids lower inflammation by reducing oxidative stress (7). This lowers gut permeability, or the amount of water and nutrients that are able to leak through your intestinal lining. If you develop a leakage, you may be at risk for inflammation, digestive pain, diabetes, and irritable bowel syndrome (8). 


Berries contain phenolic compounds, which can help balance bacteria populations and serve as a type of prebiotic, Paulvin says. “They can also relieve gut inflammation and have a cancer-preventative effect on colon cancer.”

Cherries, blueberries, blackcurrants, cranberries, and grapes are particularly high in phenols. 

Green Leafy Vegetables

Like pomegranates, leafy greens are a great source of fiber. Collard greens, swiss chard, spinach, and beet greens contain the highest levels of fiber.

They also contain a specific type of gut-friendly sugar—called sulfoquinovose—per Paulvin.

While many sugars are associated with overgrowth of gut-harming yeast, sulfoquinovose feeds good bacteria in your gut. 

Olive oil

Olive oil is high in polyphenols, which have been linked to a boost in gut bifidobacteria, a good-guy bacteria that  has positive effects on cholesterol, obesity, and may help you feel full for longer (9). 

Olive oil is a healthier alternative to other cooking oils. “Olive oil is considered a monounsaturated fatty acid, which has a lower risk of disease than choices like butter or coconut oil, which are rich in saturated fats,” Paulvin explains.