Probiotics, prebiotics and postbiotics: the garden of microbes in the gut

An illustration of three flowers, with shapes inspired by various microbes.
(Illustrations by Chelsea Conrad/The Washington Post)

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 thrive or are displaced by unwanted guests largely depends on how well you take care of them.

Scientists estimate that a person’s typical gut microbiota contains between 300 and 500 species of bacteria. Your gut microbiome is a complex ecological community, and the food you feed it, the new species you invite, and the waste products they create can affect your physical and mental health.

Here’s a guide to the fast-paced world of biotic powers that populate your gut and how to take care of them.

The word biotic refers to life or living organisms. Prosbiotics are live microbes including bacteria and fungi that have beneficial effects on your health. Think of probiotics like the seeds you scatter on the ground—with the right care, they’ll grow into flowers that grace your garden, repelling pests and crowding out weeds.

Probiotics help metabolize food and produce vitamins, fatty acids and other nutrients. They regulate your immune system, reduce your risk of type 2 diabetes and other chronic diseases, and prevent bad guys from colonizing your gut.

Among the best known probiotics are bifidobacteria. These bacteria colonize our digestive system as soon as they are born. We get them from our mothers during childbirth 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 populate our intestinal gardens.

How do I increase the probiotics in my body?

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 some people, studies show they can also kill the wrong microbes. In general, a better way to grow your own gut garden is to eat lots of fermented foods and fiber-rich plants.

In a recent study, Stanford researchers found that assigning people to eat fermented foods every day for 2 months reduced their inflammation and increased the diversity of their gut microbiome. Higher levels of microbiome diversity are associated with better health and lower rates of disease.

Examples of fermented foods include the following:

  • Kimchi and sauerkraut.
  • Kombucha, a sweet and sour fizzy tea drink.
  • Fermented dairy products such as yogurt, kefir and cottage cheese.
  • Tempeh, natto, miso and other fermented soy products.
  • Some cheeses, such as gouda and gruyre. You can identify cheeses that contain probiotics by looking for phrases like live cultures or active cultures on their labels.

The best foods to feed your microbiome

Think of prebiotics as fertilizers for your microbiome. A prebiotic is typically a high-fiber food.

The trillions of microbes that live in your gut depend on you for sustenance: every time you eat, you feed 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 primarily of complex carbohydrates and fiber 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 the 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.

How can I eat more prebiotics?

  • Vegetables such as asparagus, onions, garlic, shallots, leeks, cabbage, peas, tomatoes, Jerusalem artichokes and chicory.
  • Chickpeas, lentils, beans and soy.
  • Whole grains such as oats, barley, rye, wheat and corn.
  • Fruits such as apples, berries, bananas, grapefruit and watermelon.
  • Almonds, pistachios, cashews and other nuts and seeds.

Prebiotic supplements are generally not recommended. A small study found that a prebiotic supplement called inulin in low doses was likely good for health, but that consuming more than 20 grams a day could be harmful. They also pointed out that the health effects vary from individual to individual.

Some vendors sell prebiotic drinks, but nutrition experts say there’s no clear evidence they work.

Prebiotic sodas claim to improve your health. Experts are sceptical.

Your gut microbes break down high-fiber foods. The waste products left over from this process 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 they are producing, Damman says.

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

One of the most studied short-chain fatty acids is butyrate. This compound helps maintain gut health because it serves as a fuel source for the cells lining the colon. Butyrate helps reduce inflammation and mediate the immune system. It affects brain health and may stimulate the production of GLP-1, a hormone that reduces appetite, Damman says. (Popular weight-loss and diabetes drugs Ozempic and Wegovy work by mimicking the action of GLP-1.)

Butyrate is perhaps the microbiome’s superpower, Damman says. It is one of the key things that it is producing which is fundamental in all aspects of our health.

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

It’s cyclical, says Damman. You have this network of many players, and in this community you both depend on each other and provide each other with sustenance.

What can I do to increase the postbiotics in my body?

Fermented foods contain postbiotics such as 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 make fun of all of this, Sonnenburg says. If it turns out that lactic acid, for example, is the most important part of all these probiotic pills people are taking, they may be missing the most active component of the fermented food. That’s why we tell people that it’s best to eat only fermented food.

We’ve talked a lot about friendly bacteria, but there are many pathogenic bacteria that cause deadly infections. The best line of defense against harmful bacteria is antibiotic medications, which kill bacteria or make it difficult for them to grow and multiply.

Antibiotics were one of the great discoveries of the last century. They have saved many lives and allowed doctors to pioneer medical procedures such as open heart surgery and organ transplants. Experts say the introduction of antibiotics a century ago helped extend the average human lifespan by 23 years.

But one drawback of antibiotics is that they kill both the bad and good bacteria in your gut. Think back to the lawn analogy. If you have a bunch of weeds growing all over your lawn, you may need to use a herbicide and destroy some of the grass and plants in the process so you can clear room for new grass to grow.

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

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

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

But research suggests it’s better to eat fermented foods or let your gut fend for itself than to take a supplement. In one study, the microbiomes of people who took a probiotic while using antibiotics took much longer to recover. While probiotic supplements are very helpful for specific conditions like irritable bowel syndrome, traveler’s diarrhea, and inflammatory bowel disease, there are more reliable ways to nourish the gut microbiome.

The way to promote lots of different friendly bacteria is to feed them lots of fiber and prebiotics, says Damman. It all comes back to diet, he added. Diet isn’t the only thing, but it’s a big thing and the problem for many people is that they don’t eat the right foods.

Have a question about healthy eating? E-mail and we may answer your question in a future column.

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