Gut-friendly Foods

FACT: What you eat has a bigger impact on your microbiome and its ability to protect you from viruses than anything else you do. The good news is microbial health is based on the sum total of what you eat, not on any one ingredient or food group. Gut bacteria need specific essential raw materials and nutrients to survive, and those requirements come from lots of different foods, which means you can eat a broad and bountiful diet while nourishing your microbes. The focus should be on adding the right stuff to your plate instead of worrying too much about what you need to eliminate, because it’s the absence of beneficial fiber rather than the presence of the not-so-good foods that leads to a depleted microbiome. For most of us, eating enough lentils and leeks can balance out a slice of cake here and there. By adding in more of the raw materials your microbes rely on, you’ll end up crowding out the less helpful foods, even if you don’t eliminate them altogether.

Eat More Plants

Plants, defined as vegetables, fruits, legumes, grains, nuts, and seeds (anything that comes out of the ground or off a shrub, vine, or tree), provide the raw material for bacterial fermentation, which produces short-chain fatty acids (SCFAs)—arguably the most important metabolites for gut and immune function, so eating more plants is the number one strategy for improving your gut shield. The diversity and number of plants you eat is reflected in the diversity and number of bacteria you grow in your gut, so you should try to eat lots of different types every day.

How do we know this? In 2018 researchers from the American Gut Project published the largest human microbiome study ever done, involving over ten thousand people from forty-five different countries. Their study confirmed that the number of plant types in your diet is the primary factor that determines the health and diversity of your gut microbiome. Regardless of what diet they ate (vegetarian, vegan, omnivore, etc.), participants who ate more than thirty different plant types per week had gut microbiomes that were much healthier than those who ate ten or fewer types of plants per week. This isn’t just a theoretical improvement—the diversity in your microbiome cultivated by eating a wide variety of fibrous plants is directly correlated with better outcomes from viral infections.

But here’s the problem: a report from the National Cancer Institute on the status of the American diet found that three out of four Americans don’t eat a single piece of fruit in a given day, and nine out of ten don’t reach the minimum recommended daily intake of vegetables. On a weekly basis, less than 5 percent of Americans achieve the minimum three servings a week for greens or beans, only 2 percent reach the minimum two servings a week for orange vegetables, and only 1 percent consume the recommended three to four ounces a day of whole grains. Almost the entire country is eating in a way that is virtually guaranteed to make them more susceptible to viruses and puts them at risk for poorer outcomes. Those habits are reflected in the tragically high rates at which the coronavirus has killed Americans.

But it doesn’t have to be this way. We can fight viruses effectively and efficiently by changing what we feed ourselves—and our army of microbes. Focusing on getting more plants on your plate is the best way to start. A helpful way to think about the relationship between eating plants and gut bacteria is that the plant fiber that can’t be broken down and absorbed by your body ends up feeding your bacteria instead. The tough fibrous part of plants, like the stems of broccoli or the base of asparagus, provide the most indigestible fiber, so make sure you’re eating those parts, too.

My 1-2-3 rule can help you get more plant foods onto your plate every day. Here’s how it works: eat one vegetable in the morning, two at lunch, and three at dinner. There are lots of ways to accomplish this. You could have a smoothie with kale or a spinach omelet for breakfast, salad with chopped raw veggies for lunch, and steamed asparagus plus a salad of lettuce and cucumbers with your dinner (or do what I do and make it 3-2-1 instead by starting off the morning with a green smoothie with at least three different vegetables in it). The 1-2-3 rule is a great way to make sure you’re getting enough dietary fiber without getting bogged down in too many details and focusing on building your meal around plants will help you think about meat as a side dish rather than the main event—a great microbe-boosting strategy. Here are some additional tips for increasing the amount of plant fiber you’re eating:


  1. zucchini “noodles” for wheat pasta
  2. roasted squash or sweet potato for french fries
  3. mashed green bananas for mashed potatoes
  4. mashed cauliflower for white rice
  5. spinach and kale to smoothies
  6. leeks and celery to soups and stews
  7. roasted pumpkin or squash instead of flour to thicken sauces
  8. onions, garlic, peppers, and spinach to scrambled eggs

Choose Your Carbs Carefully

Many of us have been conditioned to think of carbohydrates as “bad” foods that make us fat and cause diabetes. But all carbs are definitely not created equal, and it’s important to know which ones are actually good for your microbes and which ones you should avoid. Simple carbohydrates (“bad” carbs) found in soda, baked goods, and other processed foods are rapidly digested in your small intestine and absorbed as glucose. When you eat them, they cause a spike in your insulin levels and are associated with weight gain, diabetes, and inflammation. They also cause unhealthy shifts in the composition of your microbiome and can lead to overgrowth of undesirable yeast species.

Complex carbohydrates (“good” carbs) are typically high in fiber and include foods like fruits, vegetables, some whole grains, beans, and brown rice. Because of their high fiber content, these foods don’t cause a surge in insulin levels and, from a microbial point of view, they’re some of the most important foods for nurturing essential microbes. Resistant starches and inulin are two types of good carbs that you need to know about, because they’re great for your microbiome.

Resistant starches are a specific type of complex carbohydrate that don’t get digested in your small intestine. They travel through your gastrointestinal (GI) tract relatively intact until they reach your colon, where they’re fermented by gut bacteria to produce SCFAs. Resistant starches function more like dietary fiber than starch, encouraging the growth of healthy microbes in your colon and acting as a prebiotic food: one that actually feeds your gut bacteria and reduces production of potentially harmful compounds.


  • Green bananas
  • Green peas
  • Lentils
  • Uncooked rolled oats
  • White beans

Inulin is another type of complex carbohydrate known as a fructan. Like resistant starches, inulin also has prebiotic qualities: it feeds your microbes to promote healthy gut flora. Adding inulin- containing foods such as leeks to soups or stews, bananas to your green smoothies, and garlic and onion for sautéing whatever you’re cooking can help to increase the amount of inulin in your diet.


  • Artichokes
  • Asparagus
  • Bananas
  • Chicory root
  • Dandelion root
  • Garlic
  • Leeks Onions

Ferment Your Food

Fermented vegetables such as sauerkraut, kimchi, and pickles are microbiome rock stars because they contain live bacteria (probiotics) and prebiotic fiber to nourish your gut bacteria. During the fermentation process the microorganisms in fermented foods produce lots of different nutrients, so a jar of sauerkraut is really a living food with vitamins and other helpful substances that are actively being produced. When you eat those foods, you’re consuming all of those microbially produced substances that are good for you. A study by researchers at Stanford University published in the journal Cell found that eating fermented foods every day resulted in marked reductions in over a dozen different inflammatory compounds in the body, plus more diversity of gut bacteria. The more fermented foods people ate, the greater the number of microbial species that bloomed in their guts. These foods also activate antioxidants in humans, and they’ve been clinically proven to help reduce severity of viral illnesses like COVID.

You should try to include some fermented vegetables in your diet every day. They’re super easy to make—mostly involving just adding a little sea salt and some water to veggies—and after fermenting, they can keep in your refrigerator for weeks.

Eat Dirty Food

The main difference between the produce you buy at the supermarket and what you find at most farm stands is dirt and distance. These days, our produce travels long distances—sometimes thousands of miles from other continents—before it gets to us. The enzymatic activity and nutrient value of these foods starts to decline right after harvesting, and so does its microbial value. Buying locally grown food from small farmers means that the food has traveled a shorter distance to get to you, so more of the nutrients and bacteria are intact. You’ll probably find that it stays fresh longer, too.

Chances are also higher that it’s been grown in small batches in soil, rather than in the aseptic factory environment of mass- produced food. Look for produce that has evidence of dirt on it (although you still need to wash it before you eat it) and isn’t perfectly uniform in color or size, reflecting the normal variation of food grown in nature, rather than engineered to look a certain way. And of course, organically produced food, grown with dirt rather than chemicals, is always best.

Farm Yes, Factory No

If you’re ever in a bind about whether something is good for you or your microbes, this is my absolute favorite and simplest way to figure it out: If it came straight from the farm, go ahead. If it made a stop in a factory, don’t bother. That means yes to apples but no to applesauce; yes to lentils but no to lentil chips; yes to brown rice but no to brown rice cereal. You get the gist.

By Dr. Robynne Chutkan, excerpted from her book THE ANTI-VIRAL GUT.  (By arrangement with Avery Books, a member of Penguin Group (USA) LLC, A Penguin Random House Company. Copyright © 2022, Robynne Chutkan).

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