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Think of your gut microbiome as an intestinal garden, teeming with trillions of bacteria, viruses and fungi that play a crucial role in your health.

Whether the beneficial microbes in your gut are flourishing or getting crowded out by unwelcome guests largely depends on how well you’re taking care of them.

<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3983973/#:~:text=Basic%20Definitions%20and%20Development%20of%20the%20Microbiota&text=Within%20the%20human%20gastrointestinal%20microbiota,million%20genes%20(the%20microbiome)." target=_blank>Scientists estimate</a> that a typical person’s gut microbiota contains between 300 and 500 species of bacteria. Your gut microbiome is a complex ecological community, and <a href="https://www.washingtonpost.com/wellness/2022/09/20/gut-health-microbiome-best-foods/" target=_blank>the food that you feed it</a>, the new species you invite, and the waste products they create all can affect your physical <a href="https://www.washingtonpost.com/wellness/2023/01/31/gut-microbiome-anxiety-depression/" target=_blank>and mental health.</a>

Here’s a guide to the busy world of “biotics” that inhabit your gut, and how to care for them.

An illustration of three seeds falling into soil from a package titled "good seeds"

The word “biotic” refers to “life” or living organisms. Probiotics are live microbes — including bacteria and fungi — that have beneficial effects on your health. Think of probiotics as the seeds that you sprinkle on soil: With proper care, they’ll turn into flowers that beautify your garden, repelling pests and crowding out weeds.

Probiotics help metabolize your food and produce vitamins, fatty acids, and other nutrients. They regulate your immune system, lower your risk for Type 2 diabetes and other chronic disease, and prevent the bad guys from colonizing your gut.

Among the most well-known probiotics are bifidobacteria. These bacteria colonize our digestive tracts as soon as we’re born. We get them from our mothers during delivery and through breast milk.

Another common probiotic, lactobacillus, is found in many fermented foods. Lactobacillus and bifidobacterium are just two of the many different types of bacteria that inhabit our intestinal gardens.

Probiotic supplements, which come in the form of capsules, gummies, powders, and pills, are immensely popular, but they shouldn’t be your first choice. While they may help certain people, studies show <a href="https://www.washingtonpost.com/wellness/2023/03/28/probiotics-supplements-gut-health-microbiome/" target=_blank>they can also crowd out the wrong microbes</a>. In general, a better way to cultivate your gut garden is to eat plenty of fermented foods and fiber-rich plants.

In one recent study, Stanford researchers found that assigning people to eat fermented foods every day for 2½ months reduced their inflammation and increased their gut microbiome diversity. Higher levels of microbiome diversity are associated with better health and lower rates of disease.

Examples of fermented foods include the following:

Kombucha, a fizzy sweet and sour drink made with tea.

Fermented dairy products like yogurt, kefir and cottage cheese.

Tempeh, natto, miso and other fermented soy products.

Some cheeses, like gouda and gruyère. You can identify cheeses that contain probiotics by looking for phrases like “live cultures” or “active cultures” on their labels.

An illustration of three small leaves growing and being sprinkled with fertilizer. The fertilizer bag has a picture of broccoli on it.

Think of prebiotics like fertilizer for your microbiome. A prebiotic is typically a high-fiber <a href="http://food.it/" target=_blank>food.</a>

The trillions of microbes that live in your gut depend on you for sustenance: Every time you eat, you’re feeding them too.

“If probiotics are the good guys, then prebiotics are the foods that promote the good guys,” says Erica Sonnenburg, a senior research scientist in microbiology and immunology at Stanford University.

Prebiotics consist mainly of complex carbs and fibers found in a variety of different plant foods. When you eat fruits, vegetables, whole grains, and other plants, much of the fiber they contain passes through your stomach and small intestine relatively intact because humans lack the enzymes to break it down. But the microbes in your large intestine can metabolize fiber and break it down into other compounds.

The way to promote lots of different friendly bacteria is to feed them lots of fiber and prebiotics, says Chris Damman, a gastroenterologist at the digestive health center at the University of Washington Medical Center.

Vegetables such as asparagus, onions, garlic, shallots, leeks, cabbage, peas, tomatoes, Jerusalem artichokes and chicory.

Chickpeas, lentils, kidney beans and soybeans.

Whole grains such as oats, barley, rye, wheat and corn.

Fruits like apples, berries, bananas, grapefruits and watermelon.

Almonds, pistachios, cashews, and other nuts and seeds.

Prebiotic supplements aren’t typically recommended. One <a href="https://www.cell.com/cell-host-microbe/fulltext/S1931-3128(22)00166-4#%20" target=_blank>small study found</a> suggested that a prebiotic supplement called inulin at low doses was likely good for health, but that consuming more than 20 grams of it daily could be harmful. They also pointed out that the “health effects vary among individuals.”

Some marketers are selling prebiotic beverages, but nutrition experts say there’s no strong evidence that they work.

Prebiotic sodas claim to boost your health. Experts are skeptical.

An illustration of three flowers, with shapes inspired by various microbes.

Your gut microbes break down high-fiber foods. The waste products this process leaves behind are called postbiotics. These compounds include a wide range of new compounds including vitamins, enzymes and amino acids.

“There are thousands and thousands of compounds that they’re making,” says Damman.

When you feed your gut microbes prebiotics, they transform them into a group of postbiotic compounds called short-chain fatty acids, which are exceptionally good for your health.

One of the most well-studied short-chain fatty acids is butyrate. This compound helps to maintain gut health because it serves as a source of fuel for the cells that line your colon. Butyrate helps to <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7192831/" target=_blank>reduce inflammation</a> and <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8608412/" target=_blank>mediate the immune system</a>. It influences brain health and can stimulate the production of GLP-1, a hormone that reduces appetite, says Damman. (Ozempic and Wegovy, the popular weight loss and diabetes drugs, work by mimicking the action of GLP-1.)

“Butyrate is maybe the superpower of the microbiome,” Damman says. “It’s one of the key things that it’s producing that is critical in all aspects of our health.”

Postbiotics are created during the digestive process as your gut microbes break down fiber. One of the fascinating things about postbiotics is that the compounds that one species of bacteria produces can be the food — or prebiotic — that another species of bacteria depends on.

“It’s cyclical,” Damman says. “You have this web of many players, and in this community they’re both depending on one another and providing sustenance for each other.”

What can I do to increase postbiotics in my body?

Fermented foods contain postbiotics like lactic acid (yogurt) and acetic acid (kombucha), and these compounds have been shown to confer health benefits.

Coffee, chocolate and some teas don’t contain live bacteria, but they do contain postbiotics, which may be part of their healthful effects, Damman says.

“We’re still trying to tease this all apart,” Sonnenburg says. “If it turns out that lactic acid, for example, is the part that’s most important than all these probiotic pills that people are taking may be missing the most active component of fermented food. That’s why we tell people it’s better to just eat the fermented food.”

An illustration of three flowers being sprayed with pesticide and dying.

We’ve talked a lot about friendly bacteria, but there are plenty of pathogenic bacteria that cause deadly infections. The best line of defense against harmful bacteria are <a href="https://www.cdc.gov/antibiotic-use/q-a.html#:~:text=Antibiotics%20are%20medicines%20that%20fight,Bacteria%20are%20germs." target=_blank>antibiotic medications</a>, which kill off bacteria or make it difficult for them to grow and multiply.

Antibiotics were one of the great discoveries of the last century. They’ve saved many lives and <a href="https://www.sciencedirect.com/science/article/pii/S1369527419300190#:~:text=In%20just%20over%20100%20years,human%20lifespan%20by%2023%20years." target=_blank>made it possible</a> for doctors to pioneer medical procedures like open-heart surgery and organ transplants. <a href="https://www.sciencedirect.com/science/article/pii/S1369527419300190#:~:text=In%20just%20over%20100%20years,human%20lifespan%20by%2023%20years." target=_blank>Experts say</a> the introduction of antibiotics a century ago helped to extend the average human life span by 23 years.

But one downside of antibiotics is that they kill both the harmful and friendly bacteria in your gut. Think back to the lawn analogy. If you’ve got a bunch of weeds growing all over your lawn, you may have to use an herbicide and destroy some of your grass and plants in the process — so you can clear space for new grass to grow.

If you have a bacterial infection, taking an antibiotic will kill off the bad microbes and perhaps sacrifice some good ones in the process.

Should I use a probiotic to counter the effects of antibiotics on gut health?

Many people who take a course of antibiotics combine it with a probiotic supplement, hoping that the supplement will protect or restore their communities of good gut microbes.

But research suggests that it’s better to eat fermented foods instead or let your gut recover on its own rather than taking a supplement. <a href="https://www.washingtonpost.com/wellness/2023/03/28/probiotics-supplements-gut-health-microbiome/" target=_blank>In one study,</a> the microbiomes of people who took a probiotic while using antibiotics took far longer to recover. While probiotic supplements are very useful for specific conditions — like irritable bowel syndrome, traveler’s diarrhea and inflammatory bowel disease — there are <a href="https://www.washingtonpost.com/wellness/2023/03/28/probiotics-supplements-gut-health-microbiome/" target=_blank>more reliable ways</a> to nourish your gut microbiome.

The way to promote lots of different friendly bacteria is to feed them lots of fiber and prebiotics, Damman says. “It all comes back to diet,” he added. “Diet is not the only thing, but it’s a big thing — and the problem for a lot of people is that they’re not eating the right foods.”

Do you have a question about healthy eating? Email <a href="mailto:EatingLab@washpost.com">EatingLab@washpost.com</a> and we may answer your question in a future column.

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Anahad O'Connor is a columnist on The Washington Post's Well+Being desk, where he writes about food and nutrition. 

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