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Doctors Warn Juice Cleanses Can Wreck Your Microbiome in Just 3 Days

“I can’t, I’m on a juice cleanse.”

Despite their negative press, juice cleanses are still an extremely popular method for people looking to detox their digestive systems, reset their diets, or lose weight quickly. Influencers push the cleanses on TikTok, and several brands claim their products deliver an array of holistic benefits. This is fueling the juice cleanse market, which was valued at $18 billion in 2023 and is expected to grow to $37 billion by 2031.

However, doctors are urging caution as new research suggests juice cleanses might be doing harm to your body’s “good” bacteria. Specifically, a fresh study from Northwestern University found that short-term vegetable and fruit juicing can rapidly alter your microbiome, particularly in the mouth, in ways that could lead to inflammation and gut health issues. Let’s unpack the findings.

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Study Findings: Major Bacterial Shifts in Just Three Days

The new research, published January 27, 2025 in the journal Nutrients, collected saliva, cheek swab, and stool samples from three groups of 14 healthy adults over the course of three days:
  • a juicing group
  • a juicing group on a whole foods diet
  • a group on a whole foods, plant-based diet

Samples were taken at 4 different times over the three days to analyze bacterial changes in the body. The researchers found that the biggest microbiome disruption wasn’t in the gut—but in the mouth—for those on the juicing-only diet.

According to the results, following a juice-based cleanse for only three days led to:

  • Increased Proteobacteria, a group of microbes in the mouth linked to inflammation and disease when present in high numbers
  • A drop in beneficial Firmicutes bacteria, which help maintain oral health and prevent infections
  • An increase of bacteria in the gut associated with leaky gut and inflammation, as well as microbes that have been linked to cognitive decline

These effects were seen most dramatically in the juicing-only group, whereas the group on a whole foods, plant-based diet actually experienced positive microbial shifts. The group that was juicing while on a whole foods diet had less severe bacterial changes than the strictly juicers, suggesting that fiber plays a key part in drinking fruits and vegetables to enjoy their benefits.

Why fiber? Juicing removes most of the insoluble fiber found in whole fruits and vegetables while concentrating natural sugars. The delicate balance of bacteria in the gut and mouth rely on fiber to thrive. With a lack of fiber, these new findings suggest juice cleanses can wreak havoc on the microbiome in a short period of time.

What Experts Are Warning About Juice Cleanses

“Most people think of juicing as a healthy cleanse, but this study offers a reality check,” said the study’s senior author, Dr. Melinda Ring, a director of the Osher Center for Integrative Health at Northwestern University Feinberg School of Medicine and a Northwestern Medicine physician.

“Consuming large amounts of juice with little fiber may lead to microbiome imbalances that could have negative consequences, such as inflammation and reduced gut health.” Dr. Ring also pointed out that the results suggest the oral microbiome is “a rapid barometer of dietary impact.”

Interestingly, when the researchers asked the 14 study participants to follow a pre-study “elimination diet” focused on whole plant foods that cut out alcohol, processed foods, and caffeine, their gut bacteria experienced positive changes.

This suggests that trying a juice cleanse isn’t all it’s cracked up to be—especially if it can have such negative impacts in as little as three days.

However, by simply shifting your diet to more whole, plant-based foods, like fruits, vegetables, nuts, grains, fish, and lean meats can be even better for your overall health.

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What’s the Best Way to Cleanse?

Juice cleanses may not be the gut-friendly detox they claim to be—and skipping fiber could be doing you more harm than good.
“If you love juicing, consider blending instead to keep the fiber intact, or pair juices with whole foods to balance the impact on your microbiome,” Dr. Ring suggests.
If you’re looking to detoxify your body, lose weight, and reset your diet, try focusing on science-backed, sustainable habits that support your liver, gut, and metabolism.
For instance, you can drink lemon water in the morning or herbal teas at night.
Load up on fiber-rich foods like leafy greens, flaxseeds, chia seeds, and whole grains. And, put protein-rich picks, like chicken, fish, or tofu, at the center of your diet, to keep you full, boost your metabolism, and aid in weight loss.

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