What Refined Sugars Are Doing to Your Gut (And Why It Matters)

Annalisa
May 26
3 min read

You’ve probably heard that ultra-processed foods (UPFs) aren’t great for your health—but did you know they might be disrupting your gut microbiome in ways that affect everything from your digestion to your mood?

Let’s explore what the latest research reveals about how refined sugars from UPFs are linked to gut dysbiosis—an imbalance in your gut’s microbial ecosystem that can trigger inflammation and chronic disease.

Meet Your Gut Microbiota: The Tiny Powerhouse Within

Your gut is home to trillions of microbes—bacteria, viruses, fungi, and more—that play a vital role in digestion, immunity, metabolism, and even brain function. A healthy gut microbiota is diverse and balanced, dominated by beneficial bacteria like Bifidobacterium and Lactobacillus. But this delicate harmony can be disrupted by diet, especially one high in ultra-processed foods and refined sugars (Afzaal et al., 2022).

What Is Gut Dysbiosis?

Dysbiosis refers to an imbalance in the gut microbiota—when harmful bacteria overtake beneficial ones. It can lead to inflammation, “leaky gut” (increased intestinal permeability), and the development of conditions like inflammatory bowel disease, obesity, type 2 diabetes, and even mental health disorders (Afzaal et al., 2022).

Ultra-Processed Foods: More Than Empty Calories

UPFs are highly modified, shelf-stable foods that often contain ingredients not used in home kitchens—such as preservatives, emulsifiers, and refined sugars. Studies show that these ingredients not only lack nutritional value but also feed pro-inflammatory gut bacteria while reducing diversity in beneficial species (Cuevas-Sierra et al., 2021; Atzeni et al., 2022).

The Sugar-Gut Connection: What the Research Shows

A 2023 animal study found that early-life sugar consumption led to sharp decreases in beneficial bacteria like Lactobacillus, Bifidobacterium, and Prevotella in juvenile mice. Although some recovery occurred after switching to a healthier diet, Prevotella levels never fully rebounded (Alasmar et al., 2023).

Another study showed that just two days on a high-sugar diet significantly decreased short-chain fatty acids (SCFAs), increased gut permeability, and heightened inflammatory responses (Laffin et al., 2019). SCFAs are crucial metabolites that help maintain the gut barrier, modulate immunity, and prevent inflammation.

The Domino Effect: Inflammation and Beyond

Disrupted gut barriers allow endotoxins like lipopolysaccharides (LPS) to enter the bloodstream, triggering systemic inflammation. This creates a vicious cycle: inflammation worsens gut permeability, and dysbiosis continues to grow (Afzaal et al., 2022).

This inflammatory state is now being linked to conditions well beyond the gut. For instance, low levels of SCFA-producing bacteria like Faecalibacterium prausnitzii are associated with metabolic and neurodegenerative diseases (Bolte et al., 2021).

Can a Better Diet Heal the Gut?

Yes! Research suggests that dietary changes—especially switching to whole, plant-based foods—can help rebalance the microbiota. The Mediterranean diet, rich in fruits, vegetables, legumes, and healthy fats, promotes the growth of anti-inflammatory bacteria and SCFA production (Bolte et al., 2021).

Even more encouraging, the gut microbiome is dynamic. With consistent dietary changes, you can shift the microbial balance in your favor.

Takeaway: Your Gut Deserves Better Than Sugar and UPFs!

This growing body of evidence makes a strong case: cutting down on refined sugars and ultra-processed foods is not just about weight or blood sugar—it’s about protecting your microbiome, reducing inflammation, and supporting whole-body health.

References

Afzaal, M., Saeed, F., Shah, Y. A., et al. (2022). Human gut microbiota in health and disease: Unveiling the relationship. Frontiers in Microbiology, 13, 999001. https://doi.org/10.3389/fmicb.2022.999001

Alasmar, R. M., Varadharajan, K., Shanmugakonar, M., & Al-Naemi, H. A. (2023). Early-Life Sugar Consumption Affects the Microbiome in Juvenile Mice. Molecular Nutrition & Food Research, 67(24), e2200322. https://doi.org/10.1002/mnfr.202200322

Atzeni, A., Martínez, M. Á., Babio, N., et al. (2022). Association between ultra-processed food consumption and gut microbiota in senior subjects. Frontiers in Nutrition, 9, 976547. https://doi.org/10.3389/fnut.2022.976547

Bolte, L. A., Vich Vila, A., Imhann, F., et al. (2021). Long-term dietary patterns are associated with features of the gut microbiome. Gut, 70(7), 1287–1298. https://doi.org/10.1136/gutjnl-2020-322670

Cuevas-Sierra, A., Milagro, F. I., Aranaz, P., Martínez, J. A., & Riezu-Boj, J. I. (2021). Gut Microbiota Differences According to Ultra-Processed Food Consumption in a Spanish Population. Nutrients, 13(8), 2710. https://doi.org/10.3390/nu13082710

Laffin, M., Fedorak, R., Zalasky, A., et al. (2019). A high-sugar diet enhances susceptibility to colitis via depletion of SCFAs. Scientific Reports, 9, 12294. https://doi.org/10.1038/s41598-019-48749-2