Nearly every food Americans eat is processed in some way, from the apple that gets washed and sorted to the packaged snack rolling off a food factory assembly line. The fact that foods are processed is simply a reality of living in the modern world, but not all processing is created equal. Ultra-processed foods are notably different because they are typically formulated from refined or isolated ingredients along with additives that improve qualities like flavor, texture, convenience, and shelf life. In addition to their more familiar nutritional drawbacks, a diet heavy in ultra-processed foods may also have a negative impact on the gut microbiome.

What Are Ultra-Processed Foods?

The word “processed” covers a wide range of activities in food production, many of which developed simply to preserve food and make it available to more people. Basic processing can prepare raw ingredients for sale or extend how long they remain usable without fundamentally changing what they are. Ultra-processing goes further by breaking foods into constituent parts and then reformulating them into products designed around shelf life and consumer appeal. This continuum of less-processed to more-processed foods is commonly described using the NOVA classification:

  • Unprocessed or minimally processed foods: These remain close to their original form even after relatively simple preparation. Fruits, vegetables, oats, eggs, plain yogurt, and fish are common examples.
  • Processed culinary ingredients: Substances extracted from foods and used mainly in cooking, such as oils, sugar, salt, and butter.
  • Processed foods: Simple foods combined with culinary ingredients, often for preservation or convenience. Cheese, canned beans, and basic bread fall into this category.
  • Ultra-processed foods: Industrial formulations made largely from refined or isolated ingredients and often containing additives that are uncommon in home cooking. Sweetened drinks, packaged snacks, and processed meats are common examples, though the category is broad enough that a full list isn’t practical.

The refinement and reformulation involved in ultra-processed foods has long served practical goals related to creating a more stable and convenient food supply. These goals aren’t inherently related to nutrition, however, and the resulting foods often contain less fiber and are less nutritionally valuable than the foods they replace. When ultra-processed foods make up a large share of the diet, those tradeoffs may also affect the gut microbiome in ways researchers are still working to understand.1

How Do Ultra-Processed Foods Affect the Gut Microbiome?

Though the full picture of how the gut microbiome contributes to overall health continues to be studied, it is already well established that it plays an important role in digestive health. Located primarily in the large intestine, the trillions of microbes that make up the microbiome help the body process certain compounds and produce substances that support digestive and immune function. And because much of what reaches the large intestine comes from the foods a person regularly eats, dietary patterns can have a major influence on the environment in which these microbes live.

Fiber is especially relevant to gut health because many of the complex carbohydrates found naturally in plant foods can’t be completely digested while moving through the gastrointestinal tract. Yet the helpful bacteria of the microbiome thrive on many of the fibers that make it through to the colon. Through the process of fermentation, the microbes produce short-chain fatty acids (SCFAs) like butyrate that provide energy to cells in the colon and help support the intestinal barrier.

In whole or minimally processed plant foods, there tends to be more fermentable fiber available for the microbes to feed on. In a diet where ultra-processed foods are prominent, however, less of that material is available in the colon to actually be fermented. Over time, this different mix can make the intestinal environment less hospitable to beneficial bacteria; by extension, this is likely to reduce the production of short-chain fatty acids and the benefits that come with them.

Another aspect of ultra-processed foods that may affect the microbiome is the use of emulsifiers, which are additives designed to improve texture or to keep ingredients from separating. Research suggests that some emulsifiers can change the composition and activity of gut microbes while also reducing the production of SCFAs like butyrate. There is also evidence that certain emulsifiers may affect the protective mucus layer that normally helps keep those microbes separated from the intestinal lining.2

What Does This Mean for Digestive Health?

The effects of a diet heavy in ultra-processed foods become more concerning when they persist over time. There’s no known threshold at which the microbiome suddenly becomes unhealthy, and diet is only one of many influences on digestive health. But when lower fiber intake becomes part of a person’s normal dietary pattern, the resulting reduction in short-chain fatty acid production and other changes in the intestinal environment may contribute to conditions that develop gradually over many years.

For instance, people with diets high in ultra-processed foods are consistently at a higher risk level for developing Crohn’s disease. Genetics, immune system activity, and other environmental factors all play a role in the development of Crohn’s, but reduced microbial diversity and lower levels of SCFA-producing bacteria associated with ultra-processed foods are also commonly observed in Crohn’s patients. While it’s unclear how direct this connection is, it does suggest a potential mechanism for how long-term dietary patterns could contribute to an intestinal environment more prone to inflammation.

Another area of concern is the connection between ultra-processed foods and the development of colorectal cancer. Lower fiber intake, along with other diet-related factors, is already associated with higher risk of colorectal cancer, so problems in the gut microbiome are unlikely to be the lone explanation. But recent research has specifically linked greater intake of ultra-processed foods with certain precancerous adenomas in women under 50. When considered alongside the evolving understanding of how diet affects the microbiome, it reinforces the idea that heavy reliance on ultra-processed foods is a long-term digestive health concern.

Digestive Healthcare from Cary Gastro

Diet can have a significant influence on digestive health, but ongoing symptoms or concerns about conditions like Crohn’s disease and colorectal cancer deserve individualized medical attention. The gastroenterologists at Cary Gastro can evaluate digestive symptoms, discuss factors that may be affecting gut health, and recommend appropriate testing or treatment when needed. Contact our team today to request an appointment and learn more about protecting long-term digestive health.




1https://www.mdpi.com/2072-6643/17/5/859
2https://pubmed.ncbi.nlm.nih.gov/40816342/