Dr. Gianluca Ianiro has spent his career studying the gut microbiome at the Gemelli University Hospital in Rome, one of the leading gastroenterology centers in Europe. In February 2025, he and a team of researchers at the Università Cattolica del Sacro Cuore published a comprehensive review in the journal Nutrients that mapped what ultra-processed foods do to the human gut in precise biological detail. The findings were not speculative. They were a synthesis of controlled trials, observational studies, and mechanistic research that had accumulated over the previous decade. The picture they assembled was specific enough to be alarming and broad enough to apply to virtually everyone eating a modern Western diet.
Ultra-processed foods now account for more than half of total caloric intake in the United States and a growing share of diets across every high-income country. The gut microbiome, the roughly 100 trillion microorganisms that live in the human digestive tract and perform functions ranging from immune regulation to neurotransmitter production, is being reshaped by that diet. The reshaping is not random. It follows a pattern. The bacteria that decline under a UPF-heavy diet are consistently the ones associated with health protection. The bacteria that increase are consistently associated with inflammation.
Two Bacteria and What Happens to Them
The research consistently identifies two species as the clearest indicators of a healthy gut microbiome. One is Akkermansia muciniphila, which lives in the mucus layer of the intestinal wall, strengthens the gut barrier, regulates immune responses, and is associated with lower rates of metabolic disease, obesity, and type 2 diabetes. The other is Faecalibacterium prausnitzii, one of the most abundant bacteria in a healthy human gut, which produces butyrate, a short-chain fatty acid that feeds the cells lining the colon, reduces intestinal inflammation, and has been linked to protection against colorectal cancer.
Ianiro and his colleagues documented that ultra-processed foods, characterized by high content of synthetic additives and emulsifiers combined with low fiber content, are consistently associated with decreased levels of both Akkermansia muciniphila and Faecalibacterium prausnitzii across multiple studies. The mechanism is not mysterious once you understand what these bacteria need to survive. Akkermansia muciniphila feeds on the mucin layer of the intestine, which it helps maintain. Faecalibacterium prausnitzii requires dietary fiber, the prebiotic substrate that ferments in the colon and fuels the bacteria that produce butyrate. Ultra-processed foods are almost devoid of dietary fiber and loaded with emulsifiers, artificial sweeteners, and additives that alter the intestinal environment these bacteria depend on.
What replaces them matters as much as what disappears. The Nature Reviews Gastroenterology and Hepatology review by Benoit Chassaing and colleagues, published in 2024, documented that certain emulsifiers widely used in ultra-processed food production directly disrupt the mucus layer that Akkermansia muciniphila inhabits and trigger the proliferation of pro-inflammatory bacteria. The emulsifiers do not just fail to feed the right bacteria. They actively damage the environment, and the right bacteria need to survive and create conditions that favor their competitors.
The Emulsifier That Moved the Barrier
The most specific human evidence of what UPF additives do inside the gut came from a randomized controlled trial published in the journal Gastroenterology in 2022. Participants consumed food containing carboxymethylcellulose, one of the most widely used emulsifiers in processed food manufacturing, added to breads, ice cream, sauces, and hundreds of other products to improve texture and extend shelf life.
The results were precise and unsettling. Participants who consumed carboxymethylcellulose experienced measurable alterations in their intestinal microbiota, depletion of health-promoting metabolites in the fecal metabolome, and increased gastrointestinal discomfort. In two of the participants, bacteria invaded the normally sterile inner mucus layer of the large intestine, an event that does not normally occur and that researchers at Stanford Medicine described as a central feature of gut inflammation. The mucus layer is the physical barrier between the contents of the intestine and the intestinal wall itself. When bacteria breach it, the immune system responds. When the breach is chronic, the immune response becomes chronic inflammation.
Carboxymethylcellulose appears on ingredient labels as E466. It is in the bread aisle. It is in the ice cream section. It is in the sauces, the frozen meals, the packaged desserts. Its function in the food is to prevent ingredients from separating and to improve the texture of products that would otherwise be less palatable. Its function in the gut is different.
What 60 Percent of the Diet Does
Ultra-processed foods now account for approximately 60 percent of total caloric intake in the United States, according to research published in the journal BMJ Open. In the United Kingdom, the figure is approximately 57 percent. In Canada, roughly 48 percent. In Brazil, which has among the most rigorous UPF tracking data globally, the proportion has risen continuously for two decades. The trend is not reversing. It is accelerating.
The NOVA food classification system, developed by Carlos Monteiro and colleagues at the University of São Paulo, defines ultra-processed foods as industrial formulations made mostly from substances extracted from oils, fats, sugars, starch, proteins, plus additives used to imitate or enhance the qualities of foods or disguise undesirable qualities of the final product. The definition is not about sugar or fat content alone. A product can be low in sugar and still be ultra-processed. The defining characteristic is industrial reformulation with additives that do not appear in home cooking.
The gut’s response to this category of food is now well enough documented to describe mechanistically. The Nutrients 2025 review from the Gemelli team identified the sequence: UPFs reduce microbial diversity, lower the abundance of protective species like Akkermansia muciniphila and Faecalibacterium prausnitzii, increase the abundance of pro-inflammatory microorganisms, contribute to gut dysbiosis and increased intestinal permeability, the condition sometimes called leaky gut, and through these changes drive persistent low-grade systemic inflammation. That inflammation is the mechanism linking UPF consumption to the chronic conditions that keep appearing in the epidemiological data: metabolic syndrome, irritable bowel syndrome, type 2 diabetes, colorectal cancer, and inflammatory bowel disease.
The gut-brain axis adds another dimension that is still being mapped. The microbiome produces neurotransmitters, including serotonin, dopamine precursors, and gamma-aminobutyric acid. It communicates with the central nervous system via the vagus nerve. When the microbial community changes, the chemical signals it sends change with it. The Nutrients 2025 review noted that UPFs may alter the gut-brain axis in ways that affect cognitive function and mental health, a connection that researchers are now actively investigating but have not yet fully characterized.
The Evolution Researchers Were Not Expecting
In December 2025, evolutionary biologists at UCLA published a finding that reframed the UPF-microbiome story in a way that had not previously been considered. Analyzing gut microbiome data from thousands of people in industrialized and non-industrialized populations globally, they found that gut bacteria in industrialized populations had undergone rapid genetic adaptation to digest industrial food additives, including maltodextrin, a starch derivative ubiquitous in ultra-processed food manufacturing.
The bacteria were not passively declining. They were evolving to survive in the new environment. The species that thrived were the ones that could metabolize maltodextrin and synthetic additives. The species that could not were declining. This evolutionary shift had not occurred in non-industrialized populations eating traditional diets. It was specific to the industrial food environment and had happened within decades, an extraordinarily rapid timescale for microbial evolution.
The finding does not contradict the evidence of harm. It deepens it. A gut microbiome that has been reshaped by industrial food is not simply a depleted version of the original. It is a different ecosystem with different functional outputs. The bacteria that evolved to digest maltodextrin are not the bacteria that produce butyrate, regulate immunity, or maintain the intestinal mucus layer. The ecosystem that forms around ultra-processed food is one adapted to ultra-processed food, not one optimized for human health.
What the Evidence Does Not Prove
The UK Scientific Advisory Committee on Nutrition published an evidence update in 2025 that is worth taking seriously. SACN’s review concluded that associations between higher UPF consumption and adverse health outcomes are concerning, but that it remains unclear how much of the observed risk is attributable to food processing itself versus the fact that many UPFs are high in calories, saturated fat, salt, and free sugars while being low in fiber.
That distinction matters. If the harm from UPFs is primarily driven by poor nutritional composition, too much sugar, too much saturated fat, too little fiber, then the solution is nutritional improvement, not necessarily a categorical rejection of processed food. A low-sugar, high-fiber ultra-processed product would, by this logic, carry less risk than a high-sugar, low-fiber ultra-processed product of equivalent processing level.
The emulsifier research complicates that argument. Carboxymethylcellulose is not a nutrient. It contributes no calories, no sugar, no saturated fat. Its effect on the gut microbiome and the mucus barrier appears to be independent of the nutritional profile of the food it is added to. If emulsifiers, thickeners, and other additives common to UPFs damage the microbiome through mechanisms unrelated to macronutrient composition, then improving the nutritional profile of ultra-processed foods addresses only part of the problem.
SACN’s caveat is scientifically honest. It is also not a reason for complacency. The totality of evidence connecting ultra-processed food consumption to gut dysbiosis, intestinal permeability, and chronic inflammation is substantial, consistent across multiple research groups and methodologies, and mechanistically grounded in ways that simple correlations are not.
The Food System the Microbiome Was Not Built For
The human gut microbiome evolved over hundreds of thousands of years in relationship with whole foods, fermented foods, and the fiber-rich plant matter that fed the bacteria that regulated immunity and protected the intestinal wall. The industrial food system that replaced that diet in high-income countries over the past century did not consult the microbiome.
The same corporate food system that shrinks products without changing the price and expands into neighborhoods until the only food available is packaged and shelf-stable is also the system that designed carboxymethylcellulose into bread to improve its texture and maltodextrin into hundreds of products to extend their shelf life. The additives serve the food manufacturer’s operational needs. Their effects on the intestinal mucus layer and the microbial ecosystem were not the primary design consideration.
Ianiro and his colleagues concluded their 2025 review by noting that dietary modifications incorporating fiber, fermented foods, and probiotics can help mitigate the effects of UPFs. That is accurate as far as it goes. It is also individual-level advice for a population-level problem. The same systemic structures that drive up healthcare costs through facility fees and consolidation are also the structures that have made ultra-processed food the most accessible and affordable dietary option for the majority of the population. The bacteria that protect the gut barrier do not care about market economics. They need fiber, and they need an intestinal environment free of the additives that breach the walls they are built to maintain.
The research Ianiro and his colleagues assembled in Rome describes what is happening inside hundreds of millions of bodies, with specificity that was not possible a decade ago. Akkermansia muciniphila is declining. Faecalibacterium prausnitzii is declining. The bacteria that evolved to digest maltodextrin are spreading. The mucus layer is thinning. The immune system is responding. The inflammation is building. The food that caused it is in the bread aisle.
