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One Surprising Side Effect of Eating Apples, According to Science

An apple a day can keep the bad bacteria that live in your gut microbiome away! 

There are countless reasons why an apple a day can keep the doctor away. Some of the benefits of eating apples include weight loss, immune support, reduced risk of heart disease, and lower cholesterol. But there is one lesser-known, but equally as important, influence, and health-supporting as these: apples have been shown to support the growth of "good" bacteria that live in your gut, improving your microbiome health.

But first, what is the microbiome?

The microbiome is a community of bacteria, fungi, archaea, and viruses that live in and on your body. The greatest concentration of these microorganisms is in your gut, where they are responsible for an incredible number of health functions. Your gut microbiome has been linked to everything from supporting your immune system to regulating your mood to even controlling your appetite and weight.

But the only way the microbiome can do its job of supporting your overall health is by keeping the "good" bacteria in balance with the "bad" bacteria. Unfortunately, the bad bacteria have taken over most of our microbiome. Studies show that our Westernized diets, high in saturated fat and sugar while being low in plants and fiber, support the growth of bad bacteria and kill off the good bacteria. The result is an array of health issues, from obesity to poor mental health.

One of the ways to support your gut health is by eating foods that nourish the good bacteria—and apples just happen to be one of them.

How apples support your gut health.

Apples contain two compounds that may contribute to their microbiome-supporting benefits: polyphenols and pectin, a type of prebiotic fiber found in apple skin.

Prebiotics are compounds that promote the growth of good bacteria. Most prebiotics are plant fibers, but emerging research has found that some polyphenol antioxidants may also have prebiotic properties.

Pectin, a fiber found in apple skins, has been shown to promote the presence of anti-inflammatory beneficial bacterial species in the Firmicutes family, which are known for their health-supporting functions.

Procyanidins, a class of antioxidant flavonoids, from apples can prevent obesity in mice by improving the ratio of good to bad bacteria in the microbiome, according to a Scientific Reports study.

Studies have also shown that eating whole apples can have an effect on your microbiota. An Anaerobe study found that when women consumed two apples a day for two weeks, they increased an abundance of good bacteria.

How can you eat apples to promote your health?

To reap the microbiome-supporting health benefits of apples, make sure to eat the whole fruit when you grab one—that includes the skin. The skin is the part of the apple that includes the highest levels of prebiotic fiber pectin.

You should also opt for organic apples whenever possible. (And it's not just because the Environmental Working Group has consistently found that apples are more likely to be tainted with pesticides than other fresh fruit and vegetables.) A Frontiers in Microbiology study published in 2019 found that organic apples contain a more diverse and balanced bacterial community compared to conventional apples, which support a more diverse and healthier microbiome.

Do not rely on apple cider vinegar for prebiotics. Despite what you may have read or seen, there is not enough scientific evidence to support that apple cider vinegar contains enough pectin to act as a prebiotic. As you'll see on the nutrition label, ACV contains zero grams of fiber.

"Apple cider vinegar cannot be considered a true probiotic or prebiotic," Melissa Mitri, MS, RDN, Owner of Melissa Mitri Nutrition LLC tells us.

"There are several proposed benefits of apple cider vinegar such as improving digestive issues, increasing healthy gut bacteria, weight loss, and blood sugar control. However, so far the research done is from small studies and so more research is needed to prove these benefits are directly from the ACV itself or if there are other diet habits playing a role. The health benefits in the research are stronger for other prebiotic foods that have a significant amount of non-digestible fiber – such as onion, garlic, leeks, asparagus, and whole apples with the skin."

In addition to apples, you can try these 15 Prebiotic Foods for Your Probiotic Efforts.


Right now, evidence supports that apples may have a positive influence on microbiome health, but there is still research to be done. At the end of the day, it's important to know that there is no one food that will support gut health.

The best thing you can do to support the growth of beneficial microbes is to eat a diverse diet with different proportions of macronutrients and micronutrients and one that includes the recommended 28 grams of fiber per day, as recommended by a Frontiers in Immunology review.

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Olivia Tarantino
Olivia Tarantino is the Managing Editor of Eat This, Not That!, specializing in nutrition, health, and food product coverage. Read more about Olivia
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