Is juicing good for your gut? Research shows surprising microbiome changes

By Vijay Kumar MalesuReviewed by Susha Cheriyedath, M.Sc.Jan 29 2025

While juicing is often seen as a healthy shortcut, new research reveals that it temporarily disrupts the microbiome—so is your juice cleanse really helping your gut?

Study: Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition. Image Credit: YesPhotographers / Shutterstock

In a recent study published in the journal Nutrients, researchers from Northwestern University in the United States and San Raffaele University in Italy investigated how short-term fruit and vegetable juicing influences the composition of gut and oral microbiota.

Background

Many people replace meals with juices, believing they detoxify the body. But could this trend be harming your gut and oral health instead? The modern diet, high in sugars and processed foods and low in fiber, has been linked to chronic diseases such as obesity, diabetes, and cardiovascular disorders.

The gut and oral microbiome play a vital role in metabolism, immunity, and overall health, and dietary choices significantly influence microbial composition.

Juicing, promoted for its detoxifying effects, is a popular dietary trend. While it provides vitamins and antioxidants, it lacks insoluble fiber, which is crucial for gut microbiota health.

Studies suggest fiber reduction alters gut bacteria, leading to metabolic and immune imbalances. Additionally, high sugar intake from juices may encourage the growth of pro-inflammatory bacteria.

Although previous research has explored the impact of whole fruits and vegetables on the microbiome, the specific effects of juicing remain unclear. Understanding these effects is essential, as many people consider juice an alternative to whole fruits.

Further research is needed to assess the implications of juicing on microbial balance and long-term health outcomes.

About the Study

The present study recruited 14 participants aged 18–35 with a body mass index (BMI) between 18.5 and 30 kg/m². They were randomly assigned to one of three dietary interventions for three days: (1) exclusive juice diet, (2) juice plus regular food diet, and (3) plant-based whole food diet. The study spanned three weeks, including a three-day elimination diet, a three-day intervention period, and a 14-day post-intervention follow-up.

Prior to the intervention, all participants followed a three-day elimination diet consisting of organic fruits, vegetables, gluten-free grains, and eggs while avoiding processed foods, dairy, caffeine, and alcohol.

Microbiota samples (saliva, stool, and inner cheek swabs) were collected at baseline, post-elimination diet, immediately after the intervention, and 14 days later.

Deoxyribonucleic acid (DNA) was extracted from microbiota samples using a commercial kit, and 16S ribosomal ribonucleic acid (rRNA) gene sequencing was conducted to analyze taxonomic composition.

Bacterial diversity and abundance were assessed through computational tools, and statistical analyses were performed using R software.

Differences in microbial composition across time points and diet groups were evaluated using permutational multivariate analysis of variance (PERMANOVA) and regression models.

Alpha and beta diversity metrics were calculated, and differential abundance was analyzed at the phylum and family levels.

Study Results

The elimination diet significantly altered the saliva microbiome, reducing Firmicutes and increasing Proteobacteria, suggesting early microbial shifts in response to dietary changes. However, the cheek microbiome did not show significant changes in response to the elimination diet. No significant changes were observed in the gut microbiota during this phase, though there was a trend toward increased Firmicutes, which are associated with beneficial effects on gut health.

Following the three-day intervention, the oral microbiome showed pronounced changes, particularly in participants on the juice-exclusive diet. A significant increase in Proteobacteria and a reduction in Firmicutes were observed, indicating a shift towards a microbial composition associated with inflammation. These changes were driven by specific bacterial families such as Comamonadaceae, Aerococcaceae, and Flavobacteriaceae. The juice plus food group exhibited similar, albeit less pronounced, trends. The plant-based whole-food diet decreased Bacteroidetes and Firmicutes but increased Fusobacteria and Proteobacteria, likely due to its higher carbohydrate and sugar content despite its higher fiber content.

Microbial families associated with inflammation, including Comamonadaceae, Aerococcaceae, Burkholderiaceae, and Flavobacteriaceae, showed increased relative abundance in the juice diet groups. In contrast, Veillonellaceae, which plays a role in nitrite production and oral health, decreased in abundance. These patterns suggest that a juice-heavy diet may promote bacterial shifts linked to gum disease and systemic inflammation.

In the gut microbiota, overall composition remained relatively stable across the dietary interventions, though trends were observed. The juice-exclusive diet led to an increase in Porphyromonadaceae, Rikenellaceae, and Alcaligenaceae, taxa associated with gut permeability and inflammation. While some studies have suggested potential links between these bacterial families and inflammatory conditions, cognitive health effects remain speculative and were not a focus of this study. The juice-plus-food diet also raised the levels of Porphyromonadaceae and Erysipelotrichaceae, which have been associated with inflammatory conditions in some research, though the clinical significance of these shifts remains unclear.

Notably, these microbial changes did not persist beyond 14 days post-intervention, as microbial composition returned toward baseline levels. This suggests that while short-term dietary shifts may cause transient microbial changes, long-term impacts remain uncertain and require further research.

The plant-based whole food diet had a lesser impact on gut microbiota, though it increased beneficial fiber-fermenting bacteria. Faecalibacterium prausnitzii, a butyrate-producing bacterium associated with gut health, increased in relative abundance after the elimination diet but remained stable following the intervention diets. Bacteroides uniformis, which promotes fiber digestion and immune balance, also showed an increase. These findings suggest that the elimination diet had potential benefits by increasing fiber-degrading bacteria linked to gut health.

Overall, the juice-exclusive diet caused the most pronounced changes, particularly in the oral microbiome. The juice plus food diet had moderate effects, while the plant-based whole food diet showed the least disruption, suggesting that fiber presence mitigates negative microbial shifts.

Conclusions

To summarize, short-term fruit and vegetable juicing alters the oral microbiome, favoring pro-inflammatory bacterial taxa and reducing beneficial species. In the gut microbiome, the juice-exclusive diet led to microbial shifts associated with increased gut permeability and inflammation, though these changes were less pronounced than in the oral cavity. The juice-plus food diet resulted in moderate alterations, while the plant-based whole-food diet showed the least impact. The elimination diet had potential benefits by increasing fiber-degrading bacteria linked to gut health.

These findings suggest that while juicing provides nutrients, its low fiber and high sugar content may negatively impact microbial balance. If you frequently start your mornings with juice, consider pairing it with whole foods to reduce the risk of microbial imbalances. A juice-heavy diet, especially without fiber, may contribute to microbial shifts associated with inflammation. However, given that the study’s microbial changes were largely reversible after 14 days, the long-term effects of repeated or extended juicing require further investigation.