Ultra Processed Food and Gut Health: What Research Says
An evidence-based review of how ultra-processed foods may affect the gut microbiome, digestive health, and what current research reveals about the connection between food processing and your gut.
Medical Disclaimer
This guide is for educational and informational purposes only. It is not medical advice. The research cited is observational and does not establish causation. Individual responses to dietary changes vary significantly. Always consult a qualified healthcare provider, registered dietitian, or gastroenterologist before making dietary changes for gut health concerns.
The Gut Microbiome: A Growing Area of Research
Over the past decade, the gut microbiome has emerged as one of the most active areas of nutritional science. Trillions of microorganisms residing in the human digestive tract play crucial roles in digestion, immune function, metabolism, and even mental health. Increasingly, researchers are turning their attention to how ultra-processed foods -- which account for approximately 57-60% of calorie intake in the average American diet -- may affect this complex microbial ecosystem.
The connection between ultra-processed foods and gut health is multifaceted. UPFs are typically characterized by long ingredient lists that include emulsifiers, artificial sweeteners, preservatives, and other additives that do not appear in home cooking. Several of these ingredients have been individually studied for their potential effects on gut bacteria, intestinal permeability, and inflammatory markers.
This guide reviews the published research on UPF consumption and gut health, presenting both findings and limitations. As with all emerging areas of nutrition science, the evidence ranges from well-established animal studies to preliminary human trials, and definitive conclusions remain elusive for many specific questions.
Important context: Much of the research on specific food additives and gut health has been conducted in animal models or small human trials. While these findings are informative, they should not be interpreted as definitive proof of harm in humans at typical dietary exposures. Larger, longer-term human studies are ongoing and will help clarify these relationships.
How Ultra-Processed Foods May Affect Your Gut
Researchers have identified several pathways through which ultra-processed food ingredients may influence gut health. Each of these mechanisms is supported by varying levels of evidence, and they are not mutually exclusive -- multiple pathways may operate simultaneously.
Emulsifiers and the Gut Lining
Emulsifiers are among the most widely used additives in ultra-processed foods, appearing in products from ice cream and salad dressings to baked goods and plant-based milks. They keep ingredients that would normally separate (such as oil and water) blended together, improving texture and shelf life.
Study: Dietary Emulsifiers Impact the Mouse Gut Microbiota (Chassaing et al., Nature, 2015)
Researchers at Georgia State University found that two common emulsifiers -- carboxymethylcellulose (CMC) and polysorbate 80 -- altered gut microbiota composition, promoted intestinal inflammation, and contributed to metabolic syndrome in mouse models. The emulsifiers appeared to thin the protective mucus layer separating gut bacteria from the intestinal wall, allowing bacteria to come into closer contact with epithelial cells.
A follow-up randomized controlled trial in humans (Chassaing et al., Gastroenterology, 2022) found that dietary CMC altered gut microbiota composition and reduced certain beneficial bacterial metabolites in a two-week feeding study of 16 healthy volunteers. While the clinical significance of these changes requires further investigation, the study provided the first direct human evidence supporting the animal model findings.
Artificial Sweeteners and Gut Bacteria
Non-nutritive sweeteners are found in a wide range of ultra-processed foods marketed as “sugar-free” or “diet” products. While they provide sweetness without calories, research suggests they may not be metabolically inert.
Study: Artificial Sweeteners Induce Glucose Intolerance by Altering the Gut Microbiota (Suez et al., Cell, 2014)
Researchers at the Weizmann Institute found that consumption of saccharin, sucralose, and aspartame altered gut microbiota composition in mice, leading to glucose intolerance. In a small human component of the study, saccharin consumption over one week altered gut bacteria in 4 of 7 participants, with corresponding changes in glycemic responses.
An expanded 2022 randomized controlled trial by the same research group (Suez et al., Cell, 2022) studied 120 healthy adults and confirmed that saccharin and sucralose significantly altered the human gut microbiome, while aspartame and stevia showed more modest effects. Importantly, individual responses varied substantially, suggesting that baseline microbiome composition may influence how a person responds to artificial sweeteners.
Low Fiber Content and Microbial Starvation
Dietary fiber is the primary fuel source for beneficial gut bacteria. When fiber-fermenting bacteria are deprived of their preferred substrate, they may turn to the gut's protective mucus layer as an alternative energy source, potentially compromising the intestinal barrier. Ultra-processed foods are typically low in fiber, and diets high in UPFs tend to displace fiber-rich whole foods.
Study: Diet-Induced Extinctions in the Gut Microbiota Compound Over Generations (Sonnenburg et al., Cell Host & Microbe, 2016)
Research from Stanford University demonstrated that fiber-deprived diets led to progressive reductions in gut microbial diversity in mouse models, and that some of these reductions were not fully recoverable even when fiber was reintroduced. Over multiple generations, the microbial losses compounded, suggesting that chronic low-fiber diets may have lasting effects on the gut ecosystem.
Human observational data supports this finding. A 2021 analysis in the American Journal of Clinical Nutrition found that individuals consuming higher proportions of ultra-processed foods had significantly lower fiber intake and reduced gut microbial diversity compared to those consuming more whole foods. The displacement of fiber-rich foods by UPFs may be one of the most straightforward mechanisms linking ultra-processed diets to altered gut health.
Additives and Preservatives
Many preservatives are designed to inhibit microbial growth in food products -- an essential function for food safety and shelf life. However, some researchers have raised the question of whether these antimicrobial properties may also affect the beneficial bacteria in the human gut. Sodium benzoate, potassium sorbate, and sodium nitrite are among the preservatives that have been studied in this context.
A 2021 in vitro study published in the Journal of Agricultural and Food Chemistry found that several common food preservatives inhibited the growth of beneficial gut bacteria at concentrations relevant to dietary exposure. However, in vitro studies (conducted in laboratory settings) do not account for the complexity of the human digestive system, including dilution, metabolism, and interactions with other food components. More human studies are needed to determine whether preservative exposure through normal diets meaningfully affects gut microbiota composition.
For a deeper look at specific additives of concern, see our ingredients to avoid guide.
Key Research Studies
The following table summarizes major published studies examining ultra-processed foods and gut health or related outcomes. Both findings and limitations are included for balanced context.
| Study | Published | Key Finding | Limitation |
|---|---|---|---|
| Chassaing et al., Nature | 2015 | Common emulsifiers (CMC, polysorbate 80) altered gut microbiota and promoted intestinal inflammation in mouse models | Animal study; emulsifier doses may not reflect typical human exposure |
| Suez et al., Cell | 2014 | Artificial sweeteners altered gut bacteria and glucose metabolism in mice; saccharin affected gut bacteria in 4 of 7 human participants | Very small human component (n=7); primarily an animal study |
| Sonnenburg et al., Cell Host & Microbe | 2016 | Fiber-deprived diets caused progressive, partially irreversible losses in gut microbial diversity across generations | Mouse model; generational effects difficult to study in humans |
| Hall et al., Cell Metabolism (NIH Trial) | 2019 | Ultra-processed diets led to ~500 extra calories/day and weight gain vs. unprocessed diets matched for nutrients | Small sample (n=20); two-week duration; did not specifically measure gut microbiome |
| Suez et al., Cell (Follow-up RCT) | 2022 | Saccharin and sucralose significantly altered human gut microbiome in a randomized trial of 120 adults | Two-week intervention; long-term clinical consequences unknown |
| Lane et al., BMJ (Umbrella Review) | 2024 | Higher UPF exposure associated with 32 adverse health outcomes across ~10 million participants; gastrointestinal outcomes included | Review of observational data; cannot establish causation; gut-specific evidence graded lower than cardiovascular |
| NutriNet-Sante Cohort (Srour et al., BMJ) | 2019 | Each 10% increase in UPF calorie proportion associated with higher risk of irritable bowel symptoms and functional gastrointestinal disorders | Self-reported dietary data; observational design; potential recall bias |
Reading this table: The strongest evidence comes from randomized controlled trials (the Suez 2022 and Hall 2019 studies), followed by large cohort studies and meta-analyses. Animal studies provide mechanistic insights but require human confirmation. For a broader view of UPF health research beyond gut health, see our comprehensive health effects guide.
The Gut Microbiome: What It Is and Why It Matters
The human gut microbiome consists of approximately 38 trillion microorganisms -- including bacteria, viruses, fungi, and archaea -- that reside primarily in the large intestine. This microbial community collectively contains more genes than the human genome itself and plays essential roles in processes that extend far beyond digestion.
What the Microbiome Does
- Fiber fermentation: Gut bacteria break down dietary fibers that human enzymes cannot digest, producing short-chain fatty acids (SCFAs) like butyrate that nourish colon cells and regulate inflammation
- Immune training: Approximately 70% of the body's immune tissue resides in or near the gut. The microbiome helps train immune cells to distinguish between harmful pathogens and harmless substances
- Vitamin synthesis: Certain gut bacteria produce essential vitamins including vitamin K, B12, folate, and biotin
- Barrier protection: A healthy microbiome helps maintain the intestinal barrier, preventing harmful substances from passing into the bloodstream
Why Diversity Matters
Microbial diversity -- the variety of different bacterial species in the gut -- is consistently associated with better health outcomes in research. A diverse microbiome is thought to be more resilient, adaptable, and functionally capable than a low-diversity one. Reduced microbial diversity has been observed in conditions including obesity, inflammatory bowel disease, type 2 diabetes, and allergies.
Diet is considered the single most important modifiable factor affecting gut microbial diversity. A 2018 study in Nature (Rothschild et al.) analyzing over 1,000 individuals found that dietary habits explained more variation in microbiome composition than genetics, confirming that what you eat has a profound and ongoing influence on your gut bacteria.
The Gut-Brain Axis
One of the most active areas of microbiome research is the gut-brain axis -- the bidirectional communication network between the gut microbiome and the central nervous system. The gut produces approximately 95% of the body's serotonin and communicates with the brain via the vagus nerve, immune signaling, and microbial metabolites.
Emerging research suggests that disruptions to the gut microbiome may influence mood, anxiety, and cognitive function through these pathways. A 2019 study in Nature Microbiology (Valles-Colomer et al.) analyzing data from over 1,000 participants in the Flemish Gut Flora Project found that certain gut bacteria (including Coprococcus and Dialister) were consistently depleted in individuals with depression, even after controlling for antidepressant use.
While this research is still in early stages and causality has not been established, it underscores the potentially far-reaching consequences of dietary patterns that alter gut microbial composition. For more on the mental health connections, see our UPF and health effects guide.
Specific UPF Ingredients and Gut Research
Individual ingredients commonly found in ultra-processed foods have been studied for their potential effects on the gut microbiome. The following table summarizes current research on specific additives, where they are commonly found, and the strength of available evidence.
| Ingredient | Found In | Research Concern | Evidence Level |
|---|---|---|---|
| Polysorbate 80 | Ice cream, sauces, baked goods | May thin gut mucus layer and promote bacterial translocation; linked to intestinal inflammation in animal models | Moderate |
| Carboxymethylcellulose (CMC) | Processed cheese, dressings, gluten-free products | Altered gut microbiota and reduced beneficial metabolites in both animal and human studies | Strong |
| Artificial Sweeteners (saccharin, sucralose) | Diet sodas, sugar-free snacks, flavored water | May alter gut microbiome composition and affect glucose metabolism; individual responses vary considerably | Strong |
| Titanium Dioxide (E171) | Candy, chewing gum, frosting, supplements | May alter gut microbiome composition and promote intestinal inflammation; banned as a food additive in the EU since 2022 | Moderate |
| Sodium Benzoate | Soft drinks, fruit juices, condiments | Antimicrobial properties may affect beneficial gut bacteria; in vitro studies show inhibition at dietary-relevant concentrations | Preliminary |
| Carrageenan | Plant-based milks, deli meats, ice cream | Associated with intestinal inflammation in animal studies; degraded forms (poligeenan) are more clearly harmful than food-grade carrageenan | Moderate |
| High-Fructose Corn Syrup | Sodas, candy, baked goods, cereals | Research suggests high fructose intake may reduce microbial diversity and increase intestinal permeability; may promote growth of less beneficial bacteria | Moderate |
Human RCTs or multiple consistent animal studies with human confirmation
Consistent animal studies or limited human data
In vitro or early-stage animal studies only
For more details on which ingredients to watch for on food labels, visit our ingredients to avoid guide or browse our ingredient database.
Important nuance: These ingredients are approved for use by food safety authorities including the FDA and EFSA (with the exception of titanium dioxide, which EFSA banned in 2022). Regulatory approval means the ingredients are considered safe at typical exposure levels based on available evidence at the time of assessment. The gut microbiome research summarized here is newer than many of these safety evaluations, and whether these findings will lead to revised regulatory assessments remains to be seen.
Foods That Research Suggests May Support Gut Health
While much of the research on UPFs and gut health focuses on potential harms, a complementary body of evidence examines which dietary patterns and foods are associated with a healthy, diverse gut microbiome. The following categories have the most research support, though it is important to note that the science of “gut-friendly” eating is still evolving.
Fermented Foods
Fermented foods contain live microorganisms that may contribute to gut microbial diversity. A 2021 randomized controlled trial at Stanford University (Wastyk et al., Cell) found that participants assigned to a high-fermented-food diet -- including yogurt, kefir, sauerkraut, kimchi, and kombucha -- significantly increased their gut microbial diversity and showed decreases in 19 inflammatory markers over 10 weeks, compared to a high-fiber diet group.
Examples: plain yogurt, kefir, sauerkraut, kimchi, miso, tempeh. When shopping for fermented foods, look for products that contain live, active cultures and have short ingredient lists. Learn about yogurt processing levels.
High-Fiber Foods
Dietary fiber serves as the primary substrate for beneficial gut bacteria through fermentation. Different types of fiber feed different bacterial species, so fiber diversity -- consuming a variety of plant foods -- is associated with greater microbial diversity. Research published in Nature (Sonnenburg & Sonnenburg, 2014) has consistently linked higher fiber intake to increased production of beneficial short-chain fatty acids, particularly butyrate, which nourishes colon cells and has anti-inflammatory properties.
Examples: whole grains (oats, barley, brown rice), legumes (lentils, chickpeas, black beans), vegetables (broccoli, Brussels sprouts, artichokes), and fruits (berries, apples, pears).
Prebiotic Foods
Prebiotics are specific types of fiber and compounds that selectively promote the growth of beneficial bacteria. Foods rich in prebiotics include garlic, onions, leeks, asparagus, bananas (especially slightly green ones), Jerusalem artichokes, and chicory root. Research published in the British Journal of Nutrition has shown that prebiotic supplementation can increase populations of Bifidobacteria and Lactobacilli, both associated with beneficial health effects.
Minimally Processed Whole Foods
Beyond specific food categories, the overall pattern of eating more whole, minimally processed foods is consistently associated with greater microbial diversity. The American Gut Project -- one of the largest citizen-science microbiome studies -- found that the single strongest predictor of gut microbial diversity was the number of different plant foods consumed per week, with individuals eating 30 or more different plants per week showing the most diverse microbiomes.
For ideas on minimally processed alternatives, see our food swaps guide and non-UPF snack ideas.
A note of caution: The “gut health” category has attracted significant marketing interest, and many products are marketed with gut health claims that exceed the supporting evidence. Probiotic supplements, for example, have shown mixed results in research -- some strains show benefits for specific conditions, while others show no effect. The most consistent evidence supports whole-food dietary patterns rather than individual supplements or products. Consult a registered dietitian before investing in specialized gut health products.
Practical Takeaways
Based on the current body of research -- while acknowledging its limitations -- the following practical steps are supported by evidence for those interested in supporting their gut health through dietary choices. These are general guidelines, not medical prescriptions.
Increase Fiber Gradually
If your current diet is low in fiber (as most UPF-heavy diets tend to be), increase fiber intake slowly over several weeks. A sudden large increase in dietary fiber can cause bloating, gas, and digestive discomfort as gut bacteria adjust. Aim for the recommended 25-38 grams per day by adding one additional serving of vegetables, legumes, or whole grains every few days. Adequate water intake helps fiber move through the digestive system smoothly.
Include Fermented Foods Regularly
Based on the Stanford trial results, incorporating fermented foods such as plain yogurt, kefir, sauerkraut, or kimchi into your regular diet may support microbial diversity. Start with small portions (a few tablespoons) and increase gradually. Look for products containing live, active cultures rather than pasteurized versions where beneficial bacteria have been killed during processing.
Read Ingredient Lists for Emulsifiers and Artificial Additives
Given the research on emulsifiers and artificial sweeteners, reading ingredient lists can help you make more informed choices. Look for names like polysorbate 80, carboxymethylcellulose, carrageenan, sucralose, and saccharin. This does not mean these ingredients need to be completely avoided, but being aware of your exposure allows you to make deliberate choices. Our food label reading guide can help you navigate ingredient lists more effectively.
Focus on Reducing Exposure, Not Perfection
The research does not suggest that every additive at every exposure level causes harm. Rather, the evidence indicates that cumulative, chronic exposure to multiple additives through a heavily ultra-processed diet may have effects over time. The practical goal is to shift the overall balance of your diet toward more whole foods and fewer heavily processed products -- not to eliminate every trace of every additive, which is neither practical nor supported by the evidence. For step-by-step strategies, see our guide to reducing UPFs.
Consult a Healthcare Provider for Gut Concerns
If you are experiencing persistent digestive symptoms such as bloating, abdominal pain, changes in bowel habits, or suspected food intolerances, consult a gastroenterologist or registered dietitian. These symptoms can have many causes beyond diet, and a healthcare professional can provide appropriate evaluation and personalized guidance. Self-diagnosing and self-treating based on general dietary information is not a substitute for professional medical care.
Final reminder: This guide summarizes published research on ultra-processed food and gut health. It is not a substitute for professional medical or nutritional advice. The gut microbiome field is evolving rapidly, and recommendations may change as new evidence emerges. Please consult qualified healthcare professionals for guidance specific to your health situation.
Frequently Asked Questions
Can ultra-processed foods damage your gut lining?
Animal studies have found that certain emulsifiers commonly used in ultra-processed foods -- such as carboxymethylcellulose and polysorbate 80 -- may thin the protective mucus layer of the gut lining and promote intestinal inflammation. A 2015 study published in Nature by Chassaing et al. at Georgia State University demonstrated these effects in mouse models. However, translating animal model findings directly to humans requires caution. A small 2022 randomized trial in humans (published in Gastroenterology) found that carboxymethylcellulose altered gut microbiota composition and reduced certain beneficial metabolites, though clinical significance remains under investigation. Consult a gastroenterologist if you have concerns about your gut health.
Do artificial sweeteners harm gut bacteria?
Research suggests some artificial sweeteners may alter the gut microbiome. A landmark 2014 study published in Cell by Suez et al. at the Weizmann Institute found that saccharin, sucralose, and aspartame altered gut bacteria composition in mouse models, and a small human trial within the same study showed that saccharin consumption changed gut microbiota in a subset of participants. A follow-up 2022 study (also in Cell, by Suez et al.) confirmed that saccharin and sucralose affected human gut microbiomes in a randomized controlled trial of 120 participants. However, the health consequences of these microbiome shifts are not yet fully established. Individual responses vary considerably, and more long-term human research is needed.
How quickly does diet affect the gut microbiome?
Research indicates that dietary changes can begin shifting gut microbiome composition within 24 to 48 hours, though stable, lasting changes typically require sustained dietary modification over weeks to months. A 2014 study in Nature by David et al. showed that switching between plant-based and animal-based diets altered microbial communities within days. However, the degree of change depends on the individual baseline microbiome, the magnitude of the dietary shift, and other factors. Gradual dietary transitions are generally recommended to minimize digestive discomfort and allow the microbiome to adapt.
What foods are best for rebuilding gut health?
Research consistently points to dietary fiber and fermented foods as beneficial for gut microbiome diversity. A 2021 randomized trial published in Cell by Wastyk et al. at Stanford University found that a high-fermented-food diet (including yogurt, kefir, kimchi, and sauerkraut) increased microbial diversity and decreased inflammatory markers over 10 weeks. Prebiotic fibers found in foods such as garlic, onions, leeks, and asparagus serve as fuel for beneficial gut bacteria. Whole grains, legumes, fruits, and vegetables provide diverse fibers that support microbial diversity. Always introduce high-fiber and fermented foods gradually, and consult a dietitian for personalized guidance.
Is the research on UPFs and gut health conclusive?
The research is growing and suggestive but not yet conclusive for most outcomes. Many of the strongest findings come from animal studies or small human trials. Large, long-term randomized controlled trials specifically examining how ultra-processed food consumption affects gut microbiome composition and clinical health outcomes in humans are still needed. The 2024 BMJ umbrella review noted that while gastrointestinal outcomes were among the adverse effects associated with UPF consumption, the evidence grade for gut-specific outcomes was lower than for cardiovascular disease or type 2 diabetes. The field is evolving rapidly, and recommendations may change as new evidence emerges.
Disclaimer: All tools and data visualizations are provided for educational and informational purposes only. They are not intended as health, medical, or dietary advice. Product formulations change frequently — always check the actual label for current ingredients and nutrition facts before making purchasing decisions. Consult healthcare professionals for personalized dietary guidance.